Miracle-dz/UniFAR-FTUs huggingface dataset:
Candida parapsilosis: from Genes to the Bedside

Patients with suppressed immunity are at the highest risk for hospital-acquired infections. Among these, invasive candidiasis is the most prevalent systemic fungal nosocomial infection. SUMMARY Patients with suppressed immunity are at the highest risk for hospital-acquired infections. Among these, invasive candidiasis is the most prevalent systemic fungal nosocomial infection. Over recent decades, the combined prevalence of non-albicans Candida species outranked Candida albicans infections in several geographical regions worldwide, highlighting the need to understand their pathobiology in order to develop effective treatment and to prevent future outbreaks. Candida parapsilosis is the second or third most frequently isolated Candida species from patients. Besides being highly prevalent, its biology differs markedly from that of C. albicans, which may be associated with C. parapsilosis’ increased incidence. Differences in virulence, regulatory and antifungal drug resistance mechanisms, and the patient groups at risk indicate that conclusions drawn from C. albicans pathobiology cannot be simply extrapolated to C. parapsilosis. Such species-specific characteristics may also influence their recognition and elimination by the host and the efficacy of antifungal drugs. Due to the availability of high-throughput, state-of-the-art experimental tools and molecular genetic methods adapted to C. parapsilosis, genome and transcriptome studies are now available that greatly contribute to our understanding of what makes this species a threat. In this review, we summarize 10 years of findings on C. parapsilosis pathogenesis, including the species’ genetic properties, transcriptome studies, host responses, and molecular mechanisms of virulence. Antifungal susceptibility studies and clinician perspectives are discussed. We also present regional incidence reports in order to provide an updated worldwide epidemiology summary.
Perceptions of Economic Inequality Are Related to Children’s Judgments About Access to Opportunities

This study examined how children’s perceptions of economic inequalities impacted their moral judgments about access to opportunities. The sample included ethnically diverse 8- to 14-year-olds (N = 267; M = 11.61 years, SD = 1.88) of middle- to upper-middle-income backgrounds. The larger the economic inequality in access to opportunities children perceived, the more negatively they evaluated granting access to a specific opportunity (an educational summer camp) to high-wealth peers alone, and the more they reasoned about the importance of fair access to learning. Further, children were more supportive of admitting low-wealth peers when they knew they had been excluded from the opportunity in the past, and children who chose to admit low-wealth peers reasoned about the implications of broader economic inequalities. Finally, most children preferred to take an active role in determining who should receive access to this special opportunity rather than leaving the decision to chance. These findings provide evidence for how perceptions of both broad and context specific intergroup relations contribute to moral judgments in childhood.
Prediction intervals for overdispersed binomial data with application to historical controls

Bioassays are highly standardized trials for assessing the impact of a chemical compound on a model organism. In that context, it is standard to compare several treatment groups with an untreated control. If the same type of bioassay is carried out several times, the amount of information about the historical controls rises with every new study. This information can be applied to predict the outcome of one future control using a prediction interval. Since the observations are counts of success out of a given sample size, like mortality or histopathological findings, the data can be assumed to be binomial but may exhibit overdispersion caused by the variability between historical studies. We describe two approaches that account for overdispersion: asymptotic prediction intervals using the quasi‐binomial assumption and prediction intervals based on the quantiles of the beta‐binomial distribution. Both interval types were α‐calibrated using bootstrap methods. For an assessment of the intervals coverage probabilities, a simulation study based on various numbers of historical studies and sample sizes as well as different binomial proportions and varying levels of overdispersion was run. It could be shown that α‐calibration can improve the coverage probabilities of both interval types. The coverage probability of the calibrated intervals, calculated based on at least 10 historical studies, was satisfactory close to the nominal 95%. In a last step, the intervals were computed based on a real data set from the NTP homepage, using historical controls from bioassays with the mice strain B6C3F1.
Energy-Aware Adaptive Cooperative FEC Protocol in MIMO Channel for Wireless Sensor Networks

We propose an adaptive cooperative forward error correction (ACFEC) based on energy efficiency combining Reed-Solomon (RS) coder algorithm and multiple input multiple output (MIMO) channel technology with monitoring signal-to-noise ratio (SNR) in wireless sensor networks. First, we propose a new Markov chain model for FEC based on RS codes and derive the expressions for QoS on the basis of this model, which comprise four metrics: throughput, packet error rate, delay, and energy efficiency. Then, we apply RS codes with the MIMO channel technology to the cross-layer design. Numerical and simulation results show that the joint design of MIMO and adaptive cooperative FEC based on RS codes can achieve considerable spectral efficiency gain, real-time performance, reliability, and energy utility.
Overexpression of microRNA-101 causes anti-tumor effects by targeting CREB1 in colon cancer

Accumulating evidence has demonstrated that aberrantly expressed microRNAs (miRNAs) are involved in the initiation and progression of numerous types of human cancer. Although a number of miRNAs have been demonstrated to be associated with the diagnosis, progression and prognosis of colon cancer, the function of miRNA-101 (miR-101) in colon cancer remains unclear, and the molecular mechanisms underlying the effects of miR-101 in colon cancer require further investigation. The present study investigated the role of miR-101 in colon cancer, and the results suggested that miR-101 expression levels were significantly decreased in colorectal carcinoma tissues and in three types of colorectal cancer cell lines. Furthermore, overexpression of miR-101 inhibited cell proliferation and migration in HT29 cells. The transcription factor cAMP responsive element binding protein 1 (CREB1) was identified to be a direct target of miR-101 using a luciferase reporter assay, reverse transcription-quantitative polymerase chain reaction analysis and western blot assay. miR-101 overexpression in tumor xenografts in vivo decreased the expression levels of proliferating cell nuclear antigen and CREB1, and suppressed tumor growth. The present results suggested that miR-101 may serve a role in colon cancer by directly targeting CREB1. Collectively, the present study may contribute to the development of improved diagnosis and prognostics for colon cancer.
Fabrication of Electrospun Polymer Nanofibers with Diverse Morphologies

Fiber structures with nanoscale diameters offer many fascinating features, such as excellent mechanical properties and high specific surface areas, making them attractive for many applications. Among a variety of technologies for preparing nanofibers, electrospinning is rapidly evolving into a simple process, which is capable of forming diverse morphologies due to its flexibility, functionality, and simplicity. In such review, more emphasis is put on the construction of polymer nanofiber structures and their potential applications. Other issues of electrospinning device, mechanism, and prospects, are also discussed. Specifically, by carefully regulating the operating condition, modifying needle device, optimizing properties of the polymer solutions, some unique structures of core–shell, side-by-side, multilayer, hollow interior, and high porosity can be obtained. Taken together, these well-organized polymer nanofibers can be of great interest in biomedicine, nutrition, bioengineering, pharmaceutics, and healthcare applications.
Priming of Adult Incision Response by Early-Life Injury: Neonatal Microglial Inhibition Has Persistent But Sexually Dimorphic Effects in Adult Rats

Neonatal hindpaw incision primes developing spinal nociceptive circuitry, resulting in enhanced hyperalgesia following reinjury in adulthood. Spinal microglia contribute to this persistent effect, and microglial inhibition at the time of adult reincision blocks the enhanced hyperalgesia. Here, we pharmacologically inhibited microglial function with systemic minocycline or intrathecal SB203580 at the time of neonatal incision and evaluated sex-dependent differences following adult reincision. Incision in adult male and female rats induced equivalent hyperalgesia and spinal dorsal horn expression of genes associated with microglial proliferation (Emr1) and transformation to a reactive phenotype (Irf8). In control adults with prior neonatal incision, the enhanced degree and duration of incision-induced hyperalgesia and spinal microglial responses to reincision were equivalent in males and females. However, microglial inhibition at the time of the neonatal incision revealed sex-dependent effects: the persistent mechanical and thermal hyperalgesia following reincision in adulthood was prevented in males but unaffected in females. Similarly, reincision induced Emr1 and Irf8 gene expression was downregulated in males, but not in females, following neonatal incision with minocycline. To evaluate the distribution of reincision hyperalgesia, prior neonatal incision was performed at different body sites. Hyperalgesia was maximal when the same paw was reincised, and was increased following prior incision at ipsilateral, but not contralateral, sites, supporting a segmentally restricted spinal mechanism. These data highlight the contribution of spinal microglial mechanisms to persistent effects of early-life injury in males, and sex-dependent differences in the ability of microglial inhibition to prevent the transition to a persistent pain state span developmental stages. SIGNIFICANCE STATEMENT Following the same surgery, some patients develop persistent pain. Contributory mechanisms are not fully understood, but early-life experience and sex/gender may influence the transition to chronic pain. Surgery and painful procedural interventions in vulnerable preterm neonates are associated with long-term alterations in somatosensory function and pain that differ in males and females. Surgical injury in neonatal rodents primes the developing nociceptive system and enhances reinjury response in adulthood. Neuroimmune interactions are critical mediators of persistent pain, but sex-dependent differences in spinal neuroglial signaling influence the efficacy of microglial inhibitors following adult injury. Neonatal microglial inhibition has beneficial long-term effects on reinjury response in adult males only, emphasizing the importance of evaluating sex-dependent differences at all ages in preclinical studies.
Population Genetic and Functional Analysis of a cis-Regulatory Polymorphism in the Drosophila melanogaster Metallothionein A gene

Although gene expression can vary extensively within and among populations, the genetic basis of this variation and the evolutionary forces that maintain it are largely unknown. In Drosophila melanogaster, a 49-bp insertion/deletion (indel) polymorphism in the Metallothionein A (MtnA) gene is associated with variation in MtnA expression and oxidative stress tolerance. To better understand the functional and evolutionary significance of this polymorphism, we investigated it in several worldwide populations. In a German population, the deletion was present at a high and stable frequency over multiple seasons and years, and was associated with increased MtnA expression. There was, however, no evidence that the polymorphism was maintained by overdominant, seasonally fluctuating, or sexually antagonistic selection. The deletion was rare in a population from the species’ ancestral range in sub-Saharan Africa and is likely the result of non-African admixture, suggesting that it spread to high frequency following the species’ out-of-Africa expansion. Using data from a North American population, we found that the deletion was associated with MtnA expression and tolerance to oxidative stress induced by menadione sodium bisulfite. Our results are consistent with the deletion being selectively favored in temperate populations due to the increased MtnA expression and oxidative stress tolerance that it confers.
Fungi in the Marine Environment: Open Questions and Unsolved Problems

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. ABSTRACT Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.
Multi-Functional Laccase Immobilized Hydrogel Microparticles for Efficient Removal of Bisphenol A

Hghly stable, reusable, and multi-functional biocatalytic microparticles with Laccase (Lac) enzyme (Lac/particles) were synthesized for bisphenol A (BPA) removal from aqueous solution. The Lac/particles were prepared by encapsulating Lac enzymes into poly ethylene glycol (PEG) hydrogel via the UV assisted emulsion polymerization method followed by cross linking with glutaraldehyde (GA). The obtained Lac/particles were spherical and micron sized (137–535 μm), presenting high enzyme entrapment efficiency of 100%, high activity recovery of 18.9%, and great stability at various pHs (3–7) than the free Lac. The Lac/particles could adsorb the BPA into the catalytic particles in a short time, promoting contact between BPA and enzyme, and further enzymatically degrade them without the shaking process and independent surrounding buffer solution. The Lac/particles could be reused for another round BPA adsorption and biotranformation by maintaining over 90% of BPA removal efficiency after seven times reuse. The synergistic effects of adsorption and biocatalytical reaction of Lac/particles have significant values in high efficient and cost-effective BPA removal.
Realizing the Clinical Potential of Immunogenic Cell Death in Cancer Chemotherapy and Radiotherapy

Immunogenic cell death (ICD), which is triggered by exposure of tumor cells to a limited range of anticancer drugs, radiotherapy, and photodynamic therapy, represents a recent innovation in the revitalized and burgeoning field of oncoimmunnotherapy. ICD results in the cellular redistribution and extracellular release of damage-associated molecular patterns (DAMPs), which have the potential to activate and restore tumor-targeted immune responses. Although a convincing body of evidence exists with respect to the antitumor efficacy of ICD in various experimental systems, especially murine models of experimental anticancer immunotherapy, evidence for the existence of ICD in the clinical setting is less compelling. Following overviews of hallmark developments, which have sparked the revival of interest in the field of oncoimmunotherapy, types of tumor cell death and the various DAMPs most prominently involved in the activation of antitumor immune responses, the remainder of this review is focused on strategies which may potentiate ICD in the clinical setting. These include identification of tumor- and host-related factors predictive of the efficacy of ICD, the clinical utility of combinatorial immunotherapeutic strategies, novel small molecule inducers of ICD, novel and repurposed small molecule immunostimulants, as well as the critical requirement for validated biomarkers in predicting the efficacy of ICD.
Procalcitonin and Midregional Proatrial Natriuretic Peptide as Biomarkers of Subclinical Cerebrovascular Damage: The Northern Manhattan Study

Background and Purpose— Chronic infections and cardiac dysfunction are risk factors for stroke. We hypothesized that blood biomarkers of infection (procalcitonin) and cardiac dysfunction (midregional proatrial natriuretic peptide [MR-proANP]), previously associated with small vessel stroke and cardioembolic stroke are also associated with subclinical cerebrovascular damage, including silent brain infarcts and white matter hyperintensity volume. Methods— The NOMAS (Northern Manhattan Study) was designed to assess risk factors for incident vascular disease in a multiethnic cohort. A subsample underwent brain magnetic resonance imaging and had blood samples available for biomarker measurement (n=1178). We used logistic regression models to estimate the odds ratios and 95% confidence intervals (95% CIs) for the association of these biomarkers with silent brain infarcts after adjusting for demographic, behavioral, and medical risk factors. We used linear regression to assess associations with log-white matter hyperintensity volume. Results— Mean age was 70±9 years; 60% were women, 66% Hispanic, 17% black, and 15% were white. After adjusting for risk factors, subjects with procalcitonin or MR-proANP in the top quartile, compared with the lowest quartile were more likely to have silent brain infarcts (adjusted odds ratio for procalcitonin, 2.2; 95% CI, 1.3–3.7 and for MR-proANP, 3.3; 95% CI, 1.7–6.3) and increased white matter hyperintensity volume (adjusted mean change in log-white matter hyperintensity volume for procalcitonin, 0.29; 95% CI, 0.13–0.44 and for MR-proANP, 0.18; 95% CI, 0.004–0.36). Conclusions— Higher concentrations of procalcitonin, a marker of infection, and MR-proANP, a marker of cardiac dysfunction, are independently associated with subclinical cerebrovascular damage. If further studies demonstrate an incremental value for risk stratification, biomarker-guided primary prevention studies may lead to new approaches to prevent cerebrovascular disease.
Complete mitochondrial genome of the palemargin grouper Epinephelus bontoides (Pisces: Perciformes)

Abstract The complete mitogenome of the palemargin grouper, Epinephelus bontoides, was presented in this study. This mitochondrial genome consists of 16 903 bp, follow the typical gene arrangement with 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (CR). The overall base composition was A, 28.7%; G, 16.1%; C, 28.0%; and T, 27.2%. The control region was 1200 bp in length, which located between tRNAPro and tRNAPhe, rich in A + T (69.2%) content. Based on the Neighbor-Joining (NJ) tree, E. bontoides was grouped with E. trimaculatus, E. quoyanus, E. areolatus, and E. bleekeri, and then combined with E. merra formed a clade. This complete mitogenome of E. bontoides can provide essential phylogenetic information of Epinephelus.
Impact of repeated hospital accreditation surveys on quality and reliability, an 8-year interrupted time series analysis

Objective To evaluate whether hospital re-accreditation improves quality, patient safety and reliability over three accreditation cycles by testing the accreditation life cycle model on quality measures. Design The validity of the life cycle model was tested by calibrating interrupted time series (ITS) regression equations for 27 quality measures. The change in the variation of quality over the three accreditation cycles was evaluated using the Levene’s test. Setting A 650-bed tertiary academic hospital in Abu Dhabi, UAE. Participants Each month (over 96 months), a simple random sample of 10% of patient records was selected and audited resulting in a total of 388 800 observations from 14 500 records. Intervention(s) The impact of hospital accreditation on the 27 quality measures was observed for 96 months, 1-year preaccreditation (2007) and 3 years postaccreditation for each of the three accreditation cycles (2008, 2011 and 2014). Main outcome measure(s) The life cycle model was evaluated by aggregating the data for 27 quality measures to produce a composite score (YC) and to fit an ITS regression equation to the unweighted monthly mean of the series. Results The results provide some evidence for the validity of the four phases of the life cycle namely, the initiation phase, the presurvey phase, the postaccreditation slump and the stagnation phase. Furthermore, the life cycle model explains 87% of the variation in quality compliance measures (R2=0.87). The best-fit ITS model contains two significant variables (β1 and β3) (p≤0.001). The Levene’s test (p≤0.05) demonstrated a significant reduction in variation of the quality measures (YC) with subsequent accreditation cycles. Conclusion The study demonstrates that accreditation has the capacity to sustain improvements over the accreditation cycle. The significant reduction in the variation of the quality measures (YC) with subsequent accreditation cycles indicates that accreditation supports the goal of high reliability.