Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease

Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR), a model of cardiovascular disease, and the Brown Norway (BN) control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI) strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB), a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will stimulate further investigation of the molecular basis of locally regulated variation in CpG methylation and provide a starting point for understanding the relationship between the genetic control of CpG methylation and disease phenotypes.
Frustrated quantum antiferromagnetism with ultracold bosons in a triangular lattice

We propose to realize the anisotropic triangular-lattice Bose-Hubbard model with positive tunneling matrix elements by using ultracold atoms in an optical lattice dressed by a fast lattice oscillation. This model exhibits frustrated antiferromagnetism at experimentally feasible temperatures; it interpolates between a classical rotor model for weak interaction, and a quantum spin-(1/2) XY-model in the limit of hard-core bosons. This allows to explore experimentally gapped spin-liquid phases predicted recently (Schmied R. et al., New J. Phys., 10 (2008) 045017).
Osteogenic Differentiation of Mesenchymal Stem Cells in their Native Niche Like Environment

Niche is an important microenvironment regulating stem cell's natural behavior and its fate. Mesenchymal Stem Cells (MSCs) are the most common cells used in bone tissue engineering. However, common culture procedures do not retain MSCs in their niche and apply in vitro expansion which can cause abnormal behavior. In this study, we propose that, by Keeping MSCs in their native niche, natural behavior of these cells and their interactions are maintained and the quality of differentiation will enhance. In our previous studies, we isolated MSCs kept in their native niche-like environment (nativeMSCs) in the form of aggregates. Herein, in order to explore the osteogenic differentiation of these cells, they were isolated from bone marrow, and in vitro osteogenesis was assessed via alizarin red and real time PCR. It was observed that they differentiated after 6 days, which is remarkably faster than the conventional 21-day period. Higher expression of Runx2, Spp1 and alkaline phosphatase in native-MSCs also confirmed in vitro results. We also examine their attachment on poly (L-lactic acid) (PLLA) scaffold. In sum, native-MSCs exhibited faster differentiation than expanded MSCs which proves the importance of keeping stem cells in their niche.
The effect of macro-synthetic fibres on the drying shrinkage cracking behaviour of concrete slabs on grade

ENGLISH ABSTRACT: Slabs on grade are the most commonly used floors for the ground floor of structures without basements. These slabs are made from the generally used construction material called concrete. Concrete is known for its relatively high compressive strength, but because of its comparatively low tensile capacity the concrete cracks easily under tensile forces. Cracks in the concrete slabs on grade reduce the serviceability and durability of the floor. The use of synthetic fibre reinforced concrete (SynFRC) in slabs on grade has shown major advantages particularly in controlling the extent and size of cracks that are formed due to drying shrinkage. An investigation is done to determine the effect of locally produced macro-synthetic fibres on the drying shrinkage cracks in slabs on grade. This is done thought a large scale test that compared the drying shrinkage cracking of polypropylene fibre reinforced concrete (PPFRC) with that of conventional concrete. The results of the large scale tests are then compared with that of a mathematical finite element method (FEM) model created in a finite element program called Diana. The different material properties of the PPFRC that are needed for the FEM analyses are obtained through flexural three point beam tests, wedge splitting tests, compression tests and shrinkage tests. The effect of the fibres are tested in terms of the different spacings between saw cut joint, the different fibre dosages, the slab thickness and the degree of friction between the concrete and the sub-base under the concrete. It is found that the use of macro-synthetic fibres results in an increase in the number of cracks between the saw cut joints, especially if the joint spacing is increased. Although there is an increase in the number of cracks, the use of fibres does consequently lead to a decrease in the crack widths. The use of macro polypropylene fibres in slabs on grade will thus result in an increase in the number of cracks, but with smaller crack widths, especially with an increase in spacings between the joints. %%%%AFRIKAANSE OPSOMMING: Grond ondersteunde vloere is die mees gewilde tipe vloer vir die grondvloer van strukture sonder kelders. Hierdie vloere word van beton gemaak wat 'n bekende konstruksie materiaal is. Beton het die kapasiteit om ‘n relatiewe hoe drukspanning te kan weerstaan, maar as gevolg van beton se relatiewe lae trekspanning, kraak die beton maklik onder as dit bloodgestel word aan trek kragte. Krake in die beton vloere wat deur laagwerk en direk deur die grond ondersteun word, verminder die diensbaarheid en duursaamheid van die vloer. Die gebruik van sintetiese vesel gewapende beton in grond ondersteunde vloere, het bewys dat dit groot voordele het veral in die beheer oor die aantal en die grootte van krake wat vorm as gevolg van droog krimping. 'n Ondersoek is gedoen om die effek van plaaslik vervaardigde makro-sintetiese vesels op die droog krimping krake in grond ondersteunde vloere te bepaal. Dit word gedoen deur gebruik te…
Periodically switched nonlinear structures for frequency conversion: theory and experimental demonstration

In this paper, we report on the analytical study of a first-order quasi-phase-matched structure based on a periodically switched nonlinearity. The general average equations describing parametric wave interaction for this structure are obtained. The theoretical results are then used to analyze the special case of a device based on a semiconductor Al/sub x/Ga/sub 1-x/As waveguide for efficient frequency doubling in the mid-infrared to the far-infrared range. The necessary conditions to obtain an optimal configuration are discussed in both continuous wave and femtosecond-pulse regimes. Our analysis indicates that the conversion efficiency obtained should significantly exceed the efficiency obtained with a periodically poled lithium niobate crystal at long wavelengths. Finally, we include the preliminary results of the experimental demonstration of a waveguide device based on alternating domains of GaAs and Al/sub 0.4/Ga/sub 0.6/As.
In Vivo Visualizations of Drought-Induced Embolism Spread in Vitis vinifera1[W][OA]

Time-lapse x-ray tomography uncovers the importance of intervessel connections in the xylem network in drought-induced embolism. Long-distance water transport through plant xylem is vulnerable to hydraulic dysfunction during periods of increased tension on the xylem sap, often coinciding with drought. While the effects of local and systemic embolism on plant water transport and physiology are well documented, the spatial patterns of embolism formation and spread are not well understood. Using a recently developed nondestructive diagnostic imaging tool, high-resolution x-ray computed tomography, we documented the dynamics of drought-induced embolism in grapevine (Vitis vinifera) plants in vivo, producing the first three-dimensional, high-resolution, time-lapse observations of embolism spread. Embolisms formed first in the vessels surrounding the pith at stem water potentials of approximately –1.2 megapascals in drought experiments. As stem water potential decreased, embolisms spread radially toward the epidermis within sectored vessel groupings via intervessel connections and conductive xylem relays, and infrequently (16 of 629 total connections) through lateral connections into adjacent vessel sectors. Theoretical loss of conductivity calculated from the high-resolution x-ray computed tomography images showed good agreement with previously published nuclear magnetic resonance imaging and hydraulic conductivity experiments also using grapevine. Overall, these data support a growing body of evidence that xylem organization is critically important to the isolation of drought-induced embolism spread and confirm that air seeding through the pit membranes is the principle mechanism of embolism spread.
Patient knowledge on reporting adverse drug reactions in Poland

Aim The aim of the study was to assess patient knowledge on reporting of adverse drug reactions. Materials and methods A prospective study was conducted among 200 patients. The study was based on an original survey composed of 15 single- and multiple-choice questions. The study involved individuals who have experienced adverse reactions as well as individuals who have never experienced any adverse reactions; people over the age of 18; literate; residing in Mazowieckie Voivodeship, who have not been diagnosed with any disease that could compromise their logical thinking skills. Results The respondents who lived in the city had a greater knowledge compared to the respondents who lived in the countryside (Pearson’s χ2=47.70, P=0.0013). The respondents who lived in the city were also more statistically likely to provide a correct answer to the question about the type of adverse reactions to be reported (Pearson’s χ2=50.66, P=0.012). Statistically significant associations were found between the place of residence of the respondents and the correct answer to the question about the data that must be included in the report on adverse reactions (Pearson’s χ2=11.7, P<0.0001).
Intercomparison of air ion spectrometers: an evaluation of results in varying conditions

Abstract. We evaluated 11 air ion spectrometers from Airel Ltd. after they had spent one year in field measurements as a part of the EUCAARI project: 5 Air Ion Spectrometers (AIS), 5 Neutral cluster and Air Ion Spectrometers (NAIS) and one Airborne NAIS (ANAIS). This is the first time that an ANAIS is evaluated and compared so extensively. The ion spectrometers' mobility and concentration accuracy was evaluated. Their measurements of ambient air were compared between themselves and to reference instruments: a Differential Mobility Particle Sizer (DMPS), a Balanced Scanning Mobility Analyzer (BSMA), and an Ion-DMPS. We report on the simultaneous measurement of a new particle formation (NPF) event by all 11 instruments and the 3 reference instruments. To our knowledge, it is the first time that the size distribution of ions and particles is measured by so many ion spectrometers during a NPF event. The new particle formation rates (~0.2 cm−3 s−1 for ions and ~2 cm−3 s−1 for particles) and growth rates (~25 nm h−1 in the 3–7 nm size range) were calculated for all the instruments. The NAISs and the ANAIS gave higher concentrations and formation rates than the AISs. For example, the AISs agreed with the BSMA within 11 % and 28 % for negative and positive ion concentration respectively, whereas the NAISs agreed within 23 % and 29 %. Finally, based on the results presented here, we give guidelines for data evaluation, when data from different individual ion spectrometers are compared.
Debiasing Decisions

From failures of intelligence analysis to misguided beliefs about vaccinations, biased judgment and decision making contributes to problems in policy, business, medicine, law, education, and private life. Early attempts to reduce decision biases with training met with little success, leading scientists and policy makers to focus on debiasing by using incentives and changes in the presentation and elicitation of decisions. We report the results of two longitudinal experiments that found medium to large effects of one-shot debiasing training interventions. Participants received a single training intervention, played a computer game or watched an instructional video, which addressed biases critical to intelligence analysis (in Experiment 1: bias blind spot, confirmation bias, and fundamental attribution error; in Experiment 2: anchoring, representativeness, and social projection). Both kinds of interventions produced medium to large debiasing effects immediately (games ≥ −31.94% and videos ≥ −18.60%) that persisted at least 2 months later (games ≥ −23.57% and videos ≥ −19.20%). Games that provided personalized feedback and practice produced larger effects than did videos. Debiasing effects were domain general: bias reduction occurred across problems in different contexts, and problem formats that were taught and not taught in the interventions. The results suggest that a single training intervention can improve decision making. We suggest its use alongside improved incentives, information presentation, and nudges to reduce costly errors associated with biased judgments and decisions.
A Novel LiDAR-Based Instrument for High-Throughput, 3D Measurement of Morphological Traits in Maize and Sorghum

Recently, imaged-based approaches have developed rapidly for high-throughput plant phenotyping (HTPP). Imaging reduces a 3D plant into 2D images, which makes the retrieval of plant morphological traits challenging. We developed a novel LiDAR-based phenotyping instrument to generate 3D point clouds of single plants. The instrument combined a LiDAR scanner with a precision rotation stage on which an individual plant was placed. A LabVIEW program was developed to control the scanning and rotation motion, synchronize the measurements from both devices, and capture a 360° view point cloud. A data processing pipeline was developed for noise removal, voxelization, triangulation, and plant leaf surface reconstruction. Once the leaf digital surfaces were reconstructed, plant morphological traits, including individual and total leaf area, leaf inclination angle, and leaf angular distribution, were derived. The system was tested with maize and sorghum plants. The results showed that leaf area measurements by the instrument were highly correlated with the reference methods (R2 > 0.91 for individual leaf area; R2 > 0.95 for total leaf area of each plant). Leaf angular distributions of the two species were also derived. This instrument could fill a critical technological gap for indoor HTPP of plant morphological traits in 3D.
The quest for a non-vector psyllid: Natural variation in acquisition and transmission of the huanglongbing pathogen ‘Candidatus Liberibacter asiaticus’ by Asian citrus psyllid isofemale lines

Genetic variability in insect vectors is valuable to study vector competence determinants and to select non-vector populations that may help reduce the spread of vector-borne pathogens. We collected and tested vector competency of 15 isofemale lines of Asian citrus psyllid, Diaphorina citri, vector of ‘Candidatus Liberibacter asiaticus’ (CLas). CLas is associated with huanglongbing (citrus greening), the most serious citrus disease worldwide. D. citri adults were collected from orange jasmine (Murraya paniculata) hedges in Florida, and individual pairs (females and males) were caged on healthy Murraya plants for egg laying. The progeny from each pair that tested CLas-negative by qPCR were maintained on Murraya plants and considered an isofemale line. Six acquisition tests on D. citri adults that were reared as nymphs on CLas-infected citrus, from various generations of each line, were conducted to assess their acquisition rates (percentage of qPCR-positive adults). Three lines with mean acquisition rates of 28 to 32%, were classified as ‘good’ acquirers and three other lines were classified as ‘poor’ acquirers, with only 5 to 8% acquisition rates. All lines were further tested for their ability to inoculate CLas by confining CLas-exposed psyllids for one week onto healthy citrus leaves (6–10 adults/leaf/week), and testing the leaves for CLas by qPCR. Mean inoculation rates were 19 to 28% for the three good acquirer lines and 0 to 3% for the three poor acquirer lines. Statistical analyses indicated positive correlations between CLas acquisition and inoculation rates, as well as between CLas titer in the psyllids and CLas acquisition or inoculation rates. Phenotypic and molecular characterization of one of the good and one of the poor acquirer lines revealed differences between them in color morphs and hemocyanin expression, but not the composition of bacterial endosymbionts. Understanding the genetic architecture of CLas transmission will enable the development of new tools for combating this devastating citrus disease.
The absorption of iron from whole diets: a systematic review.

BACKGROUND Absorption factors are required to convert physiologic requirements for iron into Dietary Reference Values, but the absorption from single meals cannot be used to estimate dietary iron absorption. OBJECTIVE The objective was to conduct a systematic review of iron absorption from whole diets. DESIGN A structured search was completed by using the Medline, EMBASE, and Cochrane CENTRAL databases from inception to November 2011. Formal inclusion and exclusion criteria were applied, and data extraction, validity assessment, and meta-analyses were undertaken. RESULTS Nineteen studies from the United States, Europe, and Mexico were included. Absorption from diets was higher with an enhancer (standard mean difference: 0.53; 95% CI: 0.21, 0.85; P = 0.001) and was also higher when compared with low-bioavailability diets (standard mean difference: 0.96; 95% CI: 0.51, 1.41; P < 0.0001); however, single inhibitors did not reduce absorption (possibly because of the limited number of studies and participants and their heterogeneity). A regression equation to calculate iron absorption was derived by pooling data for iron status (serum and plasma ferritin) and dietary enhancers and inhibitors from 58 individuals (all from US studies): log[nonheme-iron absorption, %] = -0.73 log[ferritin, μg/L] + 0.11 [modifier] + 1.82. In individuals with serum ferritin concentrations from 6 to 80 μg/L, predicted absorption ranged from 2.1% to 23.0%. CONCLUSIONS Large variations were observed in mean nonheme-iron absorption (0.7-22.9%) between studies, which depended on iron status (diet had a greater effect at low serum and plasma ferritin concentrations) and dietary enhancers and inhibitors. Iron absorption was predicted from serum ferritin concentrations and dietary modifiers by using a regression equation. Extrapolation of these findings to developing countries and to men and women of different ages will require additional high-quality controlled trials.
Perceptual Evaluation of Color‐to‐Grayscale Image Conversions

Color images often have to be converted to grayscale for reproduction, artistic purposes, or for subsequent processing. Methods performing the conversion of color images to grayscale aim to retain as much information about the original color image as possible, while simultaneously producing perceptually plausible grayscale results. Recently, many methods of conversion have been proposed, but their performance has not yet been assessed. Therefore, the strengths and weaknesses of color‐to‐grayscale conversions are not known. In this paper, we present the results of two subjective experiments in which a total of 24 color images were converted to grayscale using seven state‐of‐the‐art conversions and evaluated by 119 human subjects using a paired comparison paradigm. We surveyed nearly 20000 human responses and used them to evaluate the accuracy and preference of the color‐to‐grayscale conversions. To the best of our knowledge, the study presented in this paper is the first perceptual evaluation of color‐to‐grayscale conversions. Besides exposing the strengths and weaknesses of the researched methods, the aim of the study is to attain a deeper understanding of the examined field, which can accelerate the progress of color‐to‐grayscale conversion.
Decrease in the activities of lysosomal enzymes may contribute to the urotoxicity of cyclophosphamide in the rat

One of the most common adverse side effects of cyclophosphamide, a potent anticancer drug which limits its clinical utility is its urotoxicity. The mechanism of cyclophosphamide induced urotoxicity (cystitis) is poorly understood. In the present study the possible role of lysosomal enzymes in cyclophosphamide induced hemorrhagic cystitis was investigated using rat model. Adult female Wistar rats weighing 200-250 gm were used for the study. The rats were administered single intraperitoneal injection of cyclophosphamide at the dose of 150 mg/ kg body wt and sacrificed at various time intervals 6 hr, 16 hr or 24 hr after the dose of cyclophosphamide. The control rats were administered saline alone. The urinary bladder was removed, weighed and used for histological examination and assay of lysosomal enzymes namely acid phosphatase, β glucuronidase and N acetyl glucosaminidase. The weight of the urinary bladder (g/ 100 g body wt) of the drug treated rats was significantly higher compared to that of the untreated rat (0.12± 0.01 Vs 0.064 ± 0.005, P≤ 0.004). Histologically, all the characteristic features of hemorrhagic cystitis and hematuria were observed in the drug treated rats. The extent of damage to the bladder increased with time after treatment. A highly significant increase in protein content (mg/ g wt) was observed in the bladders of the cyclophosphamide treated rats as compared with the control (16.4± 3.0 Vs 6.5 ± 1.7, P ≤0.009). A significant drastic decrease in the activities of the entire lysosomal enzyme studied was observed in the bladders of drug treated rats at 16 hrs and 24 hrs. Acid phosphatase activity was decreased by 437% (P≤0.004); N acetyl glucosaminidase activity was decreased by 403% (P≤ 0.05) and glucuronidase activity by 392% (P≤ 0.009) as compared with the control.Decrease in the activities of lysosomal enzymes in the urinary bladder of cyclophosphamide treated rat may contribute to the urotoxicity of cyclophosphamide.