Miracle-dz/UniFAR-FTUs huggingface dataset:
Arabidopsis DRB4 protein in antiviral defense against Turnip yellow mosaic virus infection.

RNA silencing is an important antiviral mechanism in diverse eukaryotic organisms. In Arabidopsis DICER-LIKE 4 (DCL4) is the primary antiviral Dicer, required for the production of viral small RNAs from positive-strand RNA viruses. Here, we showed that DCL4 and its interacting partner dsRNA-binding protein 4 (DRB4) participate in the antiviral response to Turnip yellow mosaic virus (TYMV), and that both proteins are required for TYMV-derived small RNA production. In addition, our results indicate that DRB4 has a negative effect on viral coat protein accumulation. Upon infection DRB4 expression was induced and DRB4 protein was recruited from the nucleus to the cytoplasm, where replication and translation of viral RNA occur. DRB4 was associated with viral RNA in vivo and directly interacted in vitro with a TYMV RNA translational enhancer, raising the possibility that DRB4 might repress viral RNA translation. In plants the role of RNA silencing in viral RNA degradation is well established, but its potential function in the regulation of viral protein levels has not yet been explored. We observed that severe infection symptoms are not necessarily correlated with enhanced viral RNA levels, but might be caused by elevated accumulation of viral proteins. Our findings suggest that the control of viral protein as well as RNA levels might be important for mounting an efficient antiviral response.
Atrial Fibrillation Atrial Fibrillation Pathophysiology Implications for Management

— Atrial fibrillation (AF), the most common sustained cardiac arrhythmia, is an important contributor to population morbidity and mortality. An arrhythmia that is particularly common in the elderly, AF is growing in prevalence with the aging of the population. Our understanding of the basic mechanisms that govern AF occurrence and persistence has been increasing rapidly. This article reviews the basic pathophysiology of AF over a broad range of levels, touching on the tissue mechanisms that maintain the arrhythmia, the relationship between clinical presentation and basic mechanisms, ion channel and transporter abnormalities that lead to ectopic impulse formation, basic models and tissue determinants of reentry, ion channel determinants of reentry, the nature and roles of electric and structural remodeling, autonomic neural components, anatomic factors, interactions between atrial and ventricular functional consequences of AF, and the basic determinants of atrial thromboembolism. We then review the potential implications of the basic pathophysiology of the arrhythmia for its management. We first discuss consequences for improved rhythm control pharmacotherapy: targeting underlying conditions, new atrium-selective drug targets, new targets for focal ectopic source suppression, and upstream therapy aiming to prevent remodeling. We then review the implications of basic mechanistic considerations for rate control therapy, AF ablation, and the prevention of thromboembolic events. We conclude with some thoughts about the future of translational research related to AF mechanisms. ( Circulation . 2011; 124:2264-2274.) Words:
A zebrafish unc‐45–related gene expressed during muscle development

We report the isolation and expression pattern of zebrafish unc45r, a gene related to Caenorhabditis elegans unc‐45. UNC‐45 is a muscle‐specific protein thought to interact with myosin and promote the assembly of muscle thick filaments during C. elegans development. Zebrafish Unc45r shares sequence features with C. elegans UNC‐45, including three tetratricopeptide repeats and a CRO1/She4p homology domain. unc45r is expressed in mesoderm adjacent to the dorsal midline during late gastrula stages and is coexpressed with muscle specific genes in somitic mesoderm during development of trunk skeletal muscle. unc45r is also expressed in cranial skeletal muscle as well as in cardiac and smooth muscle. The isolation of a muscle‐specific unc‐45 related gene from zebrafish suggests a common mechanism for muscle filament assembly between vertebrates and invertebrates. © 2002 Wiley‐Liss, Inc.
Quantifying glenoid bone loss arthroscopically in shoulder instability.

PURPOSE Our goal was to establish a consistent methodology for quantifying glenoid bone loss by arthroscopic means. TYPE OF STUDY This study was an anatomic investigation of glenoid structure and its consistent anatomic landmarks as determined by arthroscopic means in live subjects and by direct measurement in fresh-frozen cadaver specimens. METHODS We arthroscopically evaluated and measured the location of the bare spot of the glenoid in 56 subjects that had no evidence of instability (average age, 40 years). We also measured the exact location of the glenoid bare spot in 10 cadaver shoulders (average age, 76 years). RESULTS The bare spot of the glenoid was a consistent reference point from which to determine glenoid bone loss because it was located almost exactly at the center of the circle that was defined by the articular margin of the inferior glenoid below the level of the midglenoid notch. The tightly clustered standard deviations of the bare spot measurements in both the live subjects and the cadaver specimens confirmed its consistent location. CONCLUSIONS The glenoid bare spot can be used as a central reference point to quantify the percentage bone loss of the inferior glenoid. Such objective measurement of glenoid bone loss can be clinically useful to the surgeon in deciding whether bone grafting is necessary to restore stability to the shoulder with a bone-deficient glenoid.
Short-Term Effect of Zidovudine on Plasma and Genital Human Immunodeficiency Virus Type 1 and Viral Turnover in These Compartments

ABSTRACT The effect of zidovudine on plasma and genital human immunodeficiency virus type 1 (HIV-1) was determined in 42 antiretroviral-naive HIV-1-seropositive women in Nairobi. After 7 days of zidovudine treatment, HIV-1 RNA levels decreased by 0.5 to 1.1 log10 in plasma and genital secretions. HIV-1 RNA half-life following zidovudine treatment was 4.7, 1.3, and 0.9 days in plasma, cervix, and vagina, respectively, and significantly shorter in genital secretions than in plasma (P < 0.001). Defining the short-term effect of zidovudine on plasma and genital HIV-1 is important for improving perinatal HIV-1 interventions.
Capture and analysis of quantitative proteomic data

Whilst the array of techniques available for quantitative proteomics continues to grow, the attendant bioinformatic software tools are similarly expanding in number. The data capture and analysis of such quantitative data is obviously crucial to the experiment and the methods used to process it will critically affect the quality of the data obtained. These tools must deal with a variety of issues, including identification of labelled and unlabelled peptide species, location of the corresponding MS scans in the experiment, construction of representative ion chromatograms, location of the true peptide ion chromatogram start and end, elimination of background signal in the mass spectrum and chromatogram and calculation of both peptide and protein ratios/abundances. A variety of tools and approaches are available, in part restricted by the nature of the experiment to be performed and available instrumentation. Currently, although there is no single consensus on precisely how to calculate protein and peptide abundances, many common themes have emerged which identify and reduce many of the key sources of error. These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge.
The Nck-interacting Kinase (NIK) Phosphorylates the Na+-H+ Exchanger NHE1 and Regulates NHE1 Activation by Platelet-derived Growth Factor*

NIK, a recently identified Nck-interacting kinase, acts upstream of the MEK kinase MEKK1 to activate the c-Jun N-terminal kinase JNK. We now show that NIK binds to and divergently activates the plasma membrane Na+-H+exchanger NHE1. In a genetic screen, NHE1 interacted with NIK at a site N-terminal (amino acids 407–502) to the Nck-binding domain, and this site is critical for its association with NHE1 in vivo. NIK also phosphorylates NHE1; however, the phosphorylation sites, which are distal to amino acid 638, are distinct from the NIK-binding site on NHE1 (amino acids 538–638). Expression of wild-type, but not a kinase-inactive, NIK in fibroblasts increased NHE1 phosphorylation and activity. The kinase domain of NIK, however, was not sufficient for this response in vivo. Full phosphorylation and activation of NHE1 required both the kinase and the NHE1-binding domains of NIK, suggesting that the NHE1-binding site functions as a targeting signal. The functional significance of an interaction between NIK and NHE1 was confirmed by the ability of a kinase-inactive NIK to selectively inhibit activation of NHE1 by platelet-derived growth factor but not by thrombin. Moreover, although NIK activates JNK through a mechanism dependent on MEKK1, it phosphorylated and activated NHE1 independently of MEKK1. These findings indicate that NIK acts downstream of platelet-derived growth factor receptors to phosphorylate and activate NHE1 divergently of its activation of JNK.
Ethical Climate and Employee Turnover Intention in the Ready-Made Garment Industry of Bangladesh

A study based on an extensive literature review and a survey of operators in the labor-intensive ready-made garment industry in Bangladesh examined the impact of an organization's ethical climate on employees’ intention to leave. It showed that as the ethical climate of an organization improves, the intention to leave declines and the more likely employees are to develop a sense of commitment to the organization. It also found an increase in the likelihood that the ethical climate of the workplace would reduce turnover when employees had a higher level of support from their line managers or supervisors. © 2016 Wiley Periodicals, Inc.
The Impact of Atopic Dermatitis on Quality of Life

Approximately 5-20% of children worldwide suffer from atopic dermatitis (AD), a kind of dermatitis characterized as an inflammatory, relapsing, noncontagious and itchy skin disorder. Children often develop AD during their first year of life. An increased rate of sensitization to both food and aeroallergens has been shown to coexist in patients with AD. Sensitization to well-known allergens such as cow's milk protein can occur on average in 50% of children with AD. In general, quality of life (QoL) is perceived as the quality of an individual's daily life, that is, an assessment of their well-being or lack thereof. QoL is a broad concept that includes such things as standard of living, community, and family life. Patients with skin diseases experience a wide range of symptoms ranging from trivial problems to major handicaps which affect their lives. The misery of living with AD cannot be overstated for it may have a profoundly negative effect on the health-related QoL of children and their families in many cases. Physicians taking care of children with AD should consult parents on how their child's illness has impacted their lifestyle and recommend professional intervention if deemed necessary.
Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach

Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation involves germline transmitted epimutations. The primary epimutations identified involve altered differential DNA methylation regions (DMRs). Different environmental toxicants have been shown to promote exposure (i.e., toxicant) specific signatures of germline epimutations. Analysis of genomic features associated with these epimutations identified low-density CpG regions (<3 CpG / 100bp) termed CpG deserts and a number of unique DNA sequence motifs. The rat genome was annotated for these and additional relevant features. The objective of the current study was to use a machine learning computational approach to predict all potential epimutations in the genome. A number of previously identified sperm epimutations were used as training sets. A novel machine learning approach using a sequential combination of Active Learning and Imbalance Class Learner analysis was developed. The transgenerational sperm epimutation analysis identified approximately 50K individual sites with a 1 kb mean size and 3,233 regions that had a minimum of three adjacent sites with a mean size of 3.5 kb. A select number of the most relevant genomic features were identified with the low density CpG deserts being a critical genomic feature of the features selected. A similar independent analysis with transgenerational somatic cell epimutation training sets identified a smaller number of 1,503 regions of genome-wide predicted sites and differences in genomic feature contributions. The predicted genome-wide germline (sperm) epimutations were found to be distinct from the predicted somatic cell epimutations. Validation of the genome-wide germline predicted sites used two recently identified transgenerational sperm epimutation signature sets from the pesticides dichlorodiphenyltrichloroethane (DDT) and methoxychlor (MXC) exposure lineage F3 generation. Analysis of this positive validation data set showed a 100% prediction accuracy for all the DDT-MXC sperm epimutations. Observations further elucidate the genomic features associated with transgenerational germline epimutations and identify a genome-wide set of potential epimutations that can be used to facilitate identification of epigenetic diagnostics for ancestral environmental exposures and disease susceptibility.
Effect of intra‐alveolar meconium on pulmonary surface tension properties

To evaluate the effect of meconium on pulmonary surface tension properties, the mechanics of 30 excised, separated canine pulmonary lobes were studied. Meconia were blended in normal saline to produce solutions of 10% and 20%. Solutions were filtered to remove large particles and instilled endobronchially into the canine lobes. The static pressure-volume deflation curve of each lobe was determined before and 4 h after instillation of either normal saline or meconium solution. In the saline control group (eight lobes), the curve was essentially unchanged before and after instillation. In the 10% meconium group (14 lobes), the curve was significantly depressed after instillation, especially at a transpulmonary airway pressure of 10 cm H2O (p <.05) and 5 cm H20 (p <.005). In the 20% meconium group (eight lobes), the depression of the pressure-volume curve was essentially the same as that of the 10% solution group. It is concluded that meconium depresses the surface-active properties of the alveolar linings.
A Weighted Passenger Flow Evolving Model for the High-Speed Rail Network Based on the City Attractiveness

As the rapid development of the high-speed rail, its carrying traffic is growing constantly. In order to research and analyses the traffic development trend of the high-speed rail, We make full use of the complex networks theory this tool, combining the special characteristics of the high-speed rail network, and then build a weighted traffic evolving model of the high-speed rail network based on the city attractiveness. Through the theoretical derivation and simulation, we confirm that this model has a distinct power-law distribution property and a better robustness. Besides, we find that the attractiveness of the city has an obvious impact on the traffic in accord with the reality, so it has a valid practical reference value.
ATP and NO dually control migration of microglia to nerve lesions

Microglia migrate rapidly to lesions in the central nervous system (CNS), presumably in response to chemoattractants including ATP released directly or indirectly by the injury. Previous work on the leech has shown that nitric oxide (NO), generated at the lesion, is both a stop signal for microglia at the lesion and crucial for their directed migration from hundreds of micrometers away within the nerve cord, perhaps mediated by a soluble guanylate cyclase (sGC). In this study, application of 100 μM ATP caused maximal movement of microglia in leech nerve cords. The nucleotides ADP, UTP, and the nonhydrolyzable ATP analog AMP‐PNP (adenyl‐5′‐yl imidodiphosphate) also caused movement, whereas AMP, cAMP, and adenosine were without effect. Both movement in ATP and migration after injury were slowed by 50 μM reactive blue 2 (RB2), an antagonist of purinergic receptors, without influencing the direction of movement. This contrasted with the effect of the NO scavenger cPTIO (2‐(4‐carboxyphenyl)‐4,4,5,5‐teramethylimidazoline‐oxyl‐3‐oxide), which misdirected movement when applied at 1 mM. The cPTIO reduced cGMP immunoreactivity without changing the immunoreactivity of eNOS (endothelial nitric oxide synthase), which accompanies increased NOS activity after nerve cord injury, consistent with involvement of sGC. Moreover, the sGC‐specific inhibitor LY83583 applied at 50 μM had a similar effect, in agreement with previous results with methylene blue. Taken together, the experiments support the hypothesis that ATP released directly or indirectly by injury activates microglia to move, whereas NO that activates sGC directs migration of microglia to CNS lesions. © 2008 Wiley Periodicals, Inc. Develop Neurobiol, 2009
Behavior and survival of Mytilus congeners following episodes of elevated body temperature in air and seawater

SUMMARY Coping with environmental stress may involve combinations of behavioral and physiological responses. We examined potential interactions between adult mussels' simple behavioral repertoire – opening/closing of the shell valves – and thermal stress physiology in common-gardened individuals of three Mytilus congeners found on the West Coast of North America: two native species (M. californianus and M. trossulus) and one invasive species from the Mediterranean (M. galloprovincialis). We first continuously monitored valve behavior over three consecutive days on which body temperatures were gradually increased, either in air or in seawater. A temperature threshold effect was evident between 25 and 33°C in several behavioral measures. Mussels tended to spend much less time with the valves in a sealed position following exposure to 33°C body temperature, especially when exposed in air. This behavior could not be explained by decreases in adductor muscle glycogen (stores of this metabolic fuel actually increased in some scenarios), impacts of forced valve sealing on long-term survival (none observed in a second experiment), or loss of contractile function in the adductor muscles (individuals exhibited as many or more valve adduction movements following elevated body temperature compared with controls). We hypothesize that this reduced propensity to seal the valves following thermal extremes represents avoidance of hypoxia–reoxygenation cycles and concomitant oxidative stress. We further conjecture that prolonged valve gaping following episodes of elevated body temperature may have important ecological consequences by affecting species interactions. We then examined survival over a 90 day period following exposure to elevated body temperature and/or emersion, observing ongoing mortality throughout this monitoring period. Survival varied significantly among species (M. trossulus had the lowest survival) and among experimental contexts (survival was lowest after experiencing elevated body temperature in seawater). Surprisingly, we observed no cumulative impact on survival of 3 days relative to 1 day of exposure to elevated body temperature. The delayed mortality and context-specific outcomes we observed have important implications for the design of future experiments and for interpretation of field distribution patterns of these species. Ultimately, variation in the catalog of physiological and behavioral capacities among closely related or sympatric species is likely to complicate prediction of the ecological consequences of global change and species invasions.
Why do we fail to deliver evidence-based practice in critical care medicine?

Purpose of review The use of evidence-based practices in clinical practice is frequently inadequate. Recent research has uncovered many barriers to the implementation of evidence-based practices in critical care medicine. Using a comprehensive conceptual framework, this review identifies and classifies the barriers to implementation of several major critical care evidence-based practices. Recent findings The many barriers that have been recently identified can be classified into domains of the consolidated framework for implementation research (CFIR). Barriers to the management of patients with acute respiratory distress syndrome (ARDS) include ARDS under-recognition. Barriers to the use of the awakening and breathing coordination, delirium monitoring/management, and early exercise/mobility (ABCDE) bundle for mechanically ventilated patients and the sepsis bundle include patient-related, clinician-related, protocol-related, contextual-related, and intervention-related factors. Although these many barriers can be classified into all five CFIR domains (intervention, outer setting, inner setting, individuals, and process), most barriers fall within the individuals and inner setting domains. Summary There are many barriers to the implementation of evidence-based practice in critical care medicine. Systematically classifying these barriers allows implementation researchers and clinicians to design targeted implementation strategies, giving them the greatest chance of success in improving the use of evidence-based practice.
Robust Clipping for OFDM Transmissions over Memoryless Impulsive Noise Channels

The detriment arising from strong and frequently occurring impulses over an Orthogonal Frequency Division Multiplexing system is paramount because signals on sub-carriers appear to be corrupted simultaneously. To overcome this obstacle, clipping has been reported as an effective approach. Unlike previous works, this work derived the clipping threshold without assuming the a priori knowledge of the probability density function (PDF) of impulsive noise, which is usually unobtainable in precise measure in most practical scenarios, and may change rapidly over time. Then, a decoding metric accommodated to the clipping effect was derived to realize coding gain. To attest the proposed scheme, this study conducted computer simulations in compliance with the IEEE 1901 standard. For various impulse noise models under consideration, the proposed scheme was promisingly on par with its conventional counterpart, the clipping threshold of which, however, relies on an assumed PDF.