Miracle-dz/UniFAR-FTUs huggingface dataset:
Alcohol and Coronary Artery Calcification: An Investigation Utilizing Alcohol Flushing as an Instrumental Variable.

Background: We examined whether alcohol flushing could be used as an instrumental variable (IV) and investigated the effect of alcohol consumption on coronary calcification using alcohol flushing status as an IV. Methods: We analyzed cross-sectional data from 24,681 Korean adults (20,696 men and 3,985 women) who had been administered a questionnaire assessing alcohol consumption and alcohol flushing, as well as a coronary artery calcium (CAC) measurement. The associations of alcohol flushing status with potential confounders and alcohol consumption were examined. We employed the two-stage predictor substitution methodology for the IV analysis. Results: The prevalence of alcohol flushing did not differ depending on gender, education, household income, cigarette smoking, or physical activity. Balanced levels of confounders were observed between alcohol flushers and non-flushers. Alcohol flushing was closely related to alcohol consumption and levels of liver enzymes. In men, a doubling in alcohol consumption was associated with increased odds of coronary calcification in both the IV analysis (odds ratio [OR] of CAC scores of 1 or over=1.11; 95% confidence interval [CI]=1.03–1.20) and the multivariable regression analysis (OR=1.04; 95% CI=1.01–1.07). For cardiovascular risk factors, the IV analysis showed a positive association between alcohol consumption and blood pressure and high-density lipoprotein-cholesterol. Conclusions: Alcohol flushing can be used as an IV in studies evaluating the health impact of alcohol consumption, especially in East Asian countries. Through such an analysis, we found that increased alcohol consumption was associated with an increased risk of subclinical coronary atherosclerosis.
NDE of Low-Velocity Impact Damage in GFRP Using Infrared Thermography Techniques

In this study, low-velocity impact damage (LVID) in glass fiber reinforced plastic (GFRP) was investigated using pulse thermography (PT) and lock-in thermography (LIT) techniques. The main objective of this study was to evaluate the detection performance of each technique for LVID in GFRP. Unidirectional and cross-ply GFRPs were prepared with four energy levels using a drop weight impact machine and they were inspected from the impact side, which may be common in actual service conditions. When the impacted side was used for both inspection and thermal loading, results showed that the suggested techniques were able to identify the LVID which is barely visible to the naked eye. However, they also include limitations that depend on the GFRP thickness at the location of the delamination produced by the lowest impact energy of five joule.
Porcine MKRN1 Modulates the Replication and Pathogenesis of Porcine Circovirus Type 2 by Inducing Capsid Protein Ubiquitination and Degradation

ABSTRACT Porcine circovirus type 2 (PCV2) capsid protein (Cap) is a unique structure protein that plays pivotal roles in the process of viral replication and pathogenesis. Herein, we characterized a putative porcine Makorin RING finger protein 1 (pMKRN1) variant, an N-terminal-truncated variant of putative full-size porcine MKRN1 which has a unique expression pattern resulting from the porcine mkrn1 gene and which interacts with PCV2 Cap. A domain mapping assay showed that the C terminus of pMKRN1 and fragments (amino acids 108 to 198) of Cap are required for this interaction. PCV2 transiently upregulated pMKRN1 in PK-15 cells, but persistent viral infection downregulated pMKRN1 in major pathological tissues of PCV2-infected piglets. Overexpression of pMKRN1 significantly inhibited the generation of progeny PCV2 via ubiquitination and degradation of Cap, whereas knockout of pMKRN1 blocked Cap degradation and promoted progeny virus replication. pMKRN1 specifically targeted PCV2 Cap lysine residues 164, 179, and 191 to induce polyubiquitination and subsequent degradation. Mutation of either of the three lysine residues in the Cap protein or mutation of the histidine at residue 243 within the RING finger domain of pMKRN1 abrogated the E3 ligase activity of pMKRN1, rendering cells incapable of inducing Cap ubiquitination and degradation. Consistent with this finding, a Cap ubiquitination-deficient PCV2 strain showed enhanced virus replication and produced severe histological lesions in the lung and lymph node tissues compared with wild-type PCV2. Taken together, the results presented here suggest that PCV2 downregulates the pMKRN1 variant to avoid pMKRN1-mediated Cap ubiquitination and degradation, thus promoting viral replication and pathogenesis in its targeted tissues. IMPORTANCE Porcine circovirus type 2 is the pathogen to which pigs are the most susceptible, causing immense economic losses in the global swine industry, but whether host cells have developed some strategies to prevent viral replication is still unclear. Here, we found that porcine MKRN1 (pMKRN1) was upregulated in the early stage of PCV2 infection and mediated the polyubiquitination and degradation of Cap protein to block PCV2 replication, yet persistent PCV2 infection downregulated pMKRN1 levels to avoid degradation, promoting viral replication and pathogenesis in its targeted tissues. These data present new insight into the molecular mechanisms underlying the antiviral effects of pMKRN1 E3 ligase during PCV2 infection and also suggest potential new control measures for PCV2 outbreaks.
Impact of veA on the development, aggressiveness, dissemination and secondary metabolism of Penicillium expansum.

Penicillium expansum, the causal agent of blue mould disease, produces the mycotoxins patulin and citrinin amongst other secondary metabolites. Secondary metabolism is associated with fungal development, which responds to numerous biotic and abiotic external triggers. The global transcription factor VeA plays a key role in the coordination of secondary metabolism and differentiation processes in many fungal species. The specific role of VeA in P. expansum remains unknown. A null mutant PeΔveA strain and a complemented PeΔveA:veA strain were generated in P. expansum and their pathogenicity on apples was studied. Like the wild-type and the complemented strains, the null mutant PeΔveA strain was still able to sporulate and to colonize apples, but at a lower rate. However, it could not form coremia either in vitro or in vivo, thus limiting its dissemination from natural substrates. The impact of veA on the expression of genes encoding proteins involved in the production of patulin, citrinin and other secondary metabolites was evaluated. The disruption of veA drastically reduced the production of patulin and citrinin on synthetic media, associated with a marked down-regulation of all genes involved in the biosynthesis of the two mycotoxins. Moreover, the null mutant PeΔveA strain was unable to produce patulin on apples. The analysis of gene expression revealed a global impact on secondary metabolism, as 15 of 35 backbone genes showed differential regulation on two different media. These findings support the hypothesis that VeA contributes to the pathogenicity of P. expansum and modulates its secondary metabolism.
Trimester-Specific Urinary Bisphenol A Concentrations and Blood Glucose Levels Among Pregnant Women From a Fertility Clinic

Context Women with a history of infertility are at increased risk of impaired glucose tolerance during pregnancy. Studies suggest higher urinary bisphenol A (BPA) concentrations are associated with diabetes in nonpregnant populations, but the association between BPA and glucose levels among pregnant women is unclear. Objective To assess trimester-specific urinary BPA concentrations in relation to blood glucose levels among subfertile women. Design Environment and Reproductive Health Study, an ongoing prospective cohort study. Setting A fertility center in a teaching hospital. Patients A total of 245 women contributed at least one urine sample during first and/or second trimesters, delivered a singleton or twin pregnancy, and had available blood glucose data (2005 to 2015). Main Outcome Measure Blood glucose levels after a nonfasting 50-g glucose challenge test at 24 to 28 weeks of gestation. Results The specific gravity-adjusted geometric mean urinary BPA concentrations during first and second trimesters were 1.39 and 1.27 µg/L, respectively. Second-trimester BPA concentrations were positively associated with blood glucose (P, trend = 0.01). Specifically, the adjusted mean glucose levels (95% confidence interval) for women in the highest quartile of second-trimester BPA concentrations was 119 (112, 126) mg/dL compared with 106 (100, 112) mg/dL for women in the lowest quartile. No associations were observed between first-trimester BPA concentrations and glucose levels. Conclusions BPA exposure during the second trimester may have adverse effect on blood glucose levels among subfertile women. As the findings represent the first report suggesting a potential etiologically relevant window for BPA and glucose in humans, further studies are needed.
Miniaturization of the Clonogenic Assay Using Confluence Measurement

The clonogenic assay is a widely used method to study the ability of cells to ‘infinitely’ produce progeny and is, therefore, used as a tool in tumor biology to measure tumor-initiating capacity and stem cell status. However, the standard protocol of using 6-well plates has several disadvantages. By miniaturizing the assay to a 96-well microplate format, as well as by utilizing the confluence detection function of a multimode reader, we here describe a new and modified protocol that allows comprehensive experimental setups and a non-endpoint, label-free semi-automatic analysis. Comparison of bright field images with confluence images demonstrated robust and reproducible detection of clones by the confluence detection function. Moreover, time-resolved non-endpoint confluence measurement of the same well showed that semi-automatic analysis was suitable for determining the mean size and colony number. By treating cells with an inhibitor of clonogenic growth (PTC-209), we show that our modified protocol is suitable for comprehensive (broad concentration range, addition of technical replicates) concentration- and time-resolved analysis of the effect of substances or treatments on clonogenic growth. In summary, this protocol represents a time- and cost-effective alternative to the commonly used 6-well protocol (with endpoint staining) and also provides additional information about the kinetics of clonogenic growth.
A Process of Seamlessly Replacing CG Elements into Live-Action Footage

This research focused on inserting a computer-generated element into live-action footage, and seamlessly replacing unwanted objects in the footage in order to creating a realistic and seamless visual representation in the field of digital compositing. The purpose of this paper is to cover a detailed working process of digital compositing in order to clarify the production process and provide a clear idea for those entry-level artists to improve an overall understanding of the digital compositing and visual effects and hopefully inspire further collaboration and participants particularly between academia and industry.
Genetic Dissection and Simultaneous Improvement of Drought and Low Nitrogen Tolerances by Designed QTL Pyramiding in Rice

Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (ILs) in a Xian (indica) variety Huanghuazhan (HHZ) background, we identified nine DT-QTL and seven LNT-QTL by a segregation distortion approach and a genome-wide association study, respectively. Based on performances of DT and LNT and genotypes at the detected QTL, two ILs M79 and M387 with DT and LNT were selected for cross-making to validate the identified QTL and to develop DT and LNT rice lines by pyramiding two DT-QTL (qDT3.9 and qDT6.3) and two LNT-QTL (qGY1 and qSF8). Using four pairs of kompetitive allele specific PCR (KASP) SNP markers, we selected 66 F2 individuals with different combinations of the target DT- and LNT-QTL favorable alleles and they showed expected improvement in DT and/or LNT, which were further validated by the significant improvement in DT and/or LNT of their F3 progeny testing. Based on evaluation of pyramiding lines in F3 lines under drought, low nitrogen (LN) and normal conditions, four promising pyramiding lines having different QTL favorable alleles were selected, which showed significantly improved tolerances to drought and/or LN than HHZ and their IL parents. Our results demonstrated that trait-specific ILs could effectively connect QTL mapping and QTL pyramiding breeding, and designed QTL pyramiding (DQP) using ILs could be more effective in molecular rice breeding for complex quantitative traits.
Chest imaging for the diagnosis of complicated parapneumonic effusions

Purpose of review To provide an overview of the contribution of thoracic ultrasound (TUS) and computed tomography (CT) in the identification of complicated parapneumonic effusions (CPPE), defined as those which need chest tube drainage for resolution. Recent findings A recent retrospective study found that visualization of complex (nonanechoic) effusions on TUS (likelihood ratio positive = 6.92) outperformed the recognition of loculated/septated effusions on CT (likelihood ratio = 2.20) or chest radiographs (likelihood ratio = 1.54) for predicting a CPPE. In another retrospective study, a weighted CT scoring system consisting of pleural contrast enhancement (three points), pleural microbubbles, increased extrapleural fat attenuation, and fluid volume at least 400 ml (one point each) had relatively good accuracy for labeling CPPE (likelihood ratio positive = 3.4; likelihood ratio negative = 0.22) when four or more points were achieved. Summary Although a gold standard for CPPE diagnosis is lacking, bedside TUS primarily, and CT scan in certain circumstances, may help to drive clinical decisions regarding chest tube placement in parapneumonic effusions (PPE). However, recommendations are limited by the absence of prospective trials.
Arkema Graphistrength Multi-Walled Carbon Nanotubes

Arkema Inc. produces multi-walled carbon nanotubes (CNT’s) under the trade name Graphistrength ® . Typical dimensions are 10-15 nm in diameter (5-15 walls) and 1-10 microns in length. Commercial and developmental products comprise plain CNT’s (Graphistrength ® C100), high-purity CNT’s (Graphistrength ® U100), thermoplastic masterbatches, water dispersions and epoxy pre-mix. Masterbatches, which comprise CNT’s blended in a resin (up to 50%) have advantages – CNT’s in a resin are easier to handle and dispersed already. Shown is the value of the masterbatch approach. Electrical conductivity data are presented for a variety of polymers containing CNT’s – polyamides, polycarbonate, polyesters, and fluoropolymers. Mechanical properties data are presented as well. For epoxy, use of a masterbatch enables properties above that possible with plain CNT’s – and simultaneous increase in both strength and toughness – an excellent combination.
Linking structure and activity in nonlinear spiking networks

Recent experimental advances are producing an avalanche of data on both neural connectivity and neural activity. To take full advantage of these two emerging datasets we need a framework that links them, revealing how collective neural activity arises from the structure of neural connectivity and intrinsic neural dynamics. This problem of structure-driven activity has drawn major interest in computational neuroscience. Existing methods for relating activity and architecture in spiking networks rely on linearizing activity around a central operating point and thus fail to capture the nonlinear responses of individual neurons that are the hallmark of neural information processing. Here, we overcome this limitation and present a new relationship between connectivity and activity in networks of nonlinear spiking neurons by developing a diagrammatic fluctuation expansion based on statistical field theory. We explicitly show how recurrent network structure produces pairwise and higher-order correlated activity, and how nonlinearities impact the networks' spiking activity. Our findings open new avenues to investigating how single-neuron nonlinearities—including those of different cell types—combine with connectivity to shape population activity and function.
Unveiling turbo codes: some results on parallel concatenated coding schemes

A parallel concatenated coding scheme consists of two simple constituent systematic encoders linked by an interleaver. The input bits to the first encoder are scrambled by the interleaver before entering the second encoder. The codeword of the parallel concatenated code consists of the input bits to the first encoder followed by the parity check bits of both encoders. This construction can be generalized to any number of constituent codes. Parallel concatenated schemes employing two convolutional codes as constituent codes, in connection with an iterative decoding algorithm of complexity comparable to that of the constituent codes, have been previously shown to yield remarkable coding gains close to theoretical limits. They have been named, and are known as, "turbo codes". We propose a method to evaluate an upper bound to the bit error probability of a parallel concatenated coding scheme averaged over all interleavers of a given length. The analytical bounding technique is then used to shed some light on some crucial questions, which have been floating around in the communications community since the proposal of turbo codes.
A Metropolitan Area Infrastructure for Data Intensive Science

The increasing amount of data being collected from simulations, instruments and sensors creates challenges for existing e-Science infrastructure. In particular, it requires new ways of storing, distributing and processing data in order to cope with both the volume and velocity of the data. The University of Queensland has recently designed and deployed MeDiCI, a data fabric that spans the metropolitan area and provides seamless access to data regardless of where it is created, manipulated and archived. MeDiCI is novel in that it exploits temporal and spatial locality to move data on demand in an automated manner. This means that data only needs to reside locally in high speed storage whilst being manipulated, and it can be archived transparently in high capacity, but slower, technologies at other times. MeDiCI is built on commercially available technologies. In this paper, we describe these innovations and present some early results.
High Mutation Frequency of the PIGA Gene in T Cells Results in Reconstitution of GPI Anchor−/CD52− T Cells That Can Give Early Immune Protection after Alemtuzumab-Based T Cell–Depleted Allogeneic Stem Cell Transplantation

Alemtuzumab (ALM) is used for T cell depletion in the context of allogeneic hematopoietic stem cell transplantation (alloSCT) to prevent acute graft-versus-host disease and graft rejection. Following ALM-based T cell–depleted alloSCT, relatively rapid recovery of circulating T cells has been described, including T cells that lack membrane expression of the GPI-anchored ALM target Ag CD52. We show, in a cohort of 89 human recipients of an ALM-based T cell–depleted alloSCT graft, that early lymphocyte reconstitution always coincided with the presence of large populations of T cells lacking CD52 membrane expression. In contrast, loss of CD52 expression was not overt within B cells or NK cells. We show that loss of CD52 expression from the T cell membrane resulted from loss of GPI anchor expression caused by a highly polyclonal mutational landscape in the PIGA gene. This polyclonal mutational landscape in the PIGA gene was also found in CD52− T cells present at a low frequency in peripheral blood of healthy donors. Finally, we demonstrate that the GPI−/CD52− T cell populations that arise after ALM-based T cell–depleted alloSCT contain functional T cells directed against multiple viral targets that can play an important role in immune protection early after ALM-based T cell–depleted transplantation.
Recombineering in Streptococcus mutans Using Direct Repeat-Mediated Cloning-Independent Markerless Mutagenesis (DR-CIMM)

Studies of the dental caries pathogen Streptococcus mutans have benefitted tremendously from its sophisticated genetic system. As part of our own efforts to further improve upon the S. mutans genetic toolbox, we previously reported the development of the first cloning-independent markerless mutagenesis (CIMM) system for S. mutans and illustrated how this approach could be adapted for use in many other organisms. The CIMM approach only requires overlap extension PCR (OE-PCR) protocols to assemble counterselectable allelic replacement mutagenesis constructs, and thus greatly increased the speed and efficiency with which markerless mutations could be introduced into S. mutans. Despite its utility, the system is still subject to a couple limitations. Firstly, CIMM requires negative selection with the conditionally toxic phenylalanine analog p-chlorophenylalanine (4-CP), which is efficient, but never perfect. Typically, 4-CP negative selection results in a small percentage of naturally resistant background colonies. Secondly, CIMM requires two transformation steps to create markerless mutants. This can be inherently problematic if the transformability of the strain is negatively impacted after the first transformation step, which is used to insert the counterselection cassette at the mutation site on the chromosome. In the current study, we develop a next-generation counterselection cassette that eliminates 4-CP background resistance and combine this with a new direct repeat-mediated cloning-independent markerless mutagenesis (DR-CIMM) system to specifically address the limitations of the prior approach. DR-CIMM is even faster and more efficient than CIMM for the creation of all types of deletions, insertions, and point mutations and is similarly adaptable for use in a wide range of genetically tractable bacteria.