Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel N4-Like Bacteriophage Isolated from a Wastewater Source in South India with Activity against Several Multidrug-Resistant Clinical Pseudomonas aeruginosa Isolates

In India, multidrug resistance determinants are much more abundant in community-associated bacterial pathogens due to the improper treatment of domestic and industrial effluents. In particular, a high bacterial load of the opportunistic pathogen P. aeruginosa in sewage and water bodies in India is well documented. ABSTRACT Multidrug-resistant community-acquired infections caused by the opportunistic human pathogen Pseudomonas aeruginosa are increasingly reported in India and other locations globally. Since this organism is ubiquitous in the environment, samples such as sewage and wastewater are rich reservoirs of P. aeruginosa bacteriophages. In this study, we report the isolation and characterization of a novel P. aeruginosa N4-like lytic bacteriophage, vB_Pae_AM.P2 (AM.P2), from wastewater in Kerala, India. AM.P2 is a double-stranded DNA podovirus that efficiently lyses the model strain, PAO1, at a multiplicity of infection as low as 0.1 phage per bacterium and resistance frequency of 6.59 × 10−4. Synergy in bactericidal activity was observed between AM.P2 and subinhibitory concentrations of the antibiotic ciprofloxacin. Genome sequencing of AM.P2 revealed features similar to those of the N4-like P. aeruginosa phages LUZ7 and KPP21. As judged by two independent assay methods, spot tests and growth inhibition, AM.P2 successfully inhibited the growth of almost 30% of strains from a contemporary collection of multidrug-resistant P. aeruginosa clinical isolates from South India. Thus, AM.P2 may represent an intriguing candidate for inclusion in bacteriophage cocktails developed for various applications, including water decontamination and clinical bacteriophage therapy. IMPORTANCE In India, multidrug resistance determinants are much more abundant in community-associated bacterial pathogens due to the improper treatment of domestic and industrial effluents. In particular, a high bacterial load of the opportunistic pathogen P. aeruginosa in sewage and water bodies in India is well documented. The isolation and characterization of bacteriophages that could target emerging P. aeruginosa strains, representing possible epicenters for community-acquired infections, could serve as a useful alternative tool for various applications, such as phage therapy and environmental treatment. Continuing to supplement the repertoire of broad-spectrum bacteriophages is an essential tool in confronting this problem.
B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells

The long noncoding RNA (lncRNA) XIST establishes X chromosome inactivation (XCI) in female cells in early development and thereafter is thought to be largely dispensable. Here we show XIST is continually required in adult human B cells to silence a subset of X-linked immune genes such as TLR7. XIST-dependent genes lack promoter DNA methylation and require continual XIST-dependent histone deacetylation. XIST RNA-directed proteomics and CRISPRi screen reveal distinctive somatic cell-specific XIST complexes, and identify TRIM28 that mediates Pol II pausing at promoters of X-linked genes in B cells. XIST dysregylation, reflected by escape of XIST-dependent genes, occurs in CD11c+ atypical memory B cells across single-cell transcriptome data in patients with female-biased autoimmunity and COVID-19 infection. XIST inactivation with TLR7 agonism suffices to promote isotype-switched atypical B cells. These results suggest cell-type-specific diversification of lncRNA-protein complexes increase lncRNA functionalities, and expand roles for XIST in sex-differences in biology and medicine. HIGHLIGHTS XIST prevents escape of genes with DNA hypomethylated promoters in B cells. XIST maintains X-inactivation through continuous deacetylation of H3K27ac. XIST ChIRP-MS and allelic CRISPRi screen reveal a B cell-specific XIST cofactor TRIM28. XIST loss and TLR7 stimulation promotes CD11c+ atypical B cell formation.
Roles of oxygen level and hypoxia-inducible factor signaling pathway in cartilage, bone and osteochondral tissue engineering

The repair and treatment of articular cartilage injury is a huge challenge of orthopedics. Currently, most of the clinical methods applied in treating cartilage injuries are mainly to relieve pains rather than to cure them, while the strategy of tissue engineering is highly expected to achieve the successful repair of osteochondral defects. Clear understandings of the physiological structures and mechanical properties of cartilage, bone and osteochondral tissues have been established, but the understanding of their physiological heterogeneity still needs further investigation. Apart from the gradients in the micromorphology and composition of cartilage-to-bone extracellular matrixes, an oxygen gradient also exists in natural osteochondral tissue. The response of hypoxia-inducible factor (HIF)-mediated cells to oxygen would affect the differentiation of stem cells and the maturation of osteochondral tissue. This article reviews the roles of oxygen level and HIF signaling pathway in the development of articular cartilage tissue, and their prospective applications in bone and cartilage tissue engineering. The strategies for regulating HIF signaling pathway and how these strategies finding their potential applications in the regeneration of integrated osteochondral tissue are also discussed.
Yeast RNA exosome activity is necessary for maintaining cell wall stability through proper protein glycosylation

Nuclear RNA exosome is the main 3′→5′ RNA degradation and processing complex in eukaryotic cells and its dysregulation therefore impacts gene expression and viability. In this work we show that RNA exosome activity is necessary for maintaining cell wall stability in yeast Saccharomyces cerevisiae. While the essential RNA exosome catalytic subunit Dis3 provides exoribonuclease catalytic activity, the second catalytic subunit Rrp6 has a noncatalytic role in this process. RNA exosome cofactors Rrp47 and Air1/2 are also involved. RNA exosome mutants undergo osmoremedial cell lysis at high temperature or at physiological temperature upon treatment with cell wall stressors. Finally, we show that a defect in protein glycosylation is a major reason for cell wall instability of RNA exosome mutants. Genes encoding enzymes that act in the early steps of the protein glycosylation pathway are down-regulated at high temperature in cells lacking Rrp6 protein or Dis3 exoribonuclease activity and overexpression of the essential enzyme Psa1, that catalyzes synthesis of the mannosylation precursor, suppresses temperature sensitivity and aberrant morphology of these cells. Furthermore, this defect is connected to a temperature-dependent increase in accumulation of noncoding RNAs transcribed from loci of relevant glycosylation-related genes.
Caustic Precipitation of Plutonium and Uranium with Gadolinium as a Neutron Poison

The caustic precipitation of plutonium and uranium from Pu- and U-containing waste solutions has been investigated to determine whether gadolinium could be used as a neutron poison for precipitation with greater than a fissile mass containing both Pu and enriched U. Precipitation experiments were performed using both process solution samples and simulant solutions with a range of 2.6 to 5.16 g/l U and 0 to 4.3:1 U:Pu. Analyses were performed on solutions at intermediate pH to determine the partitioning of elements for accident scenarios. When both Pu and U were present in the solution, precipitation began at pH 4.5 and by pH 7, 99% of Pu and U had precipitated. When complete neutralization was achieved at pH >14 with 1.2 M excess OH-, greater than 99% of Pu, U, and Gd had precipitated. At pH >14, the particle sizes were larger, and the distribution was a single mode. The ratio of hydrogen to fissile atoms in the precipitate was determined after both settling and centrifuging and indicates that sufficient water was associated with the precipitates to provide the needed neutron moderation for Gd to prevent a criticality in solutions containing up to 4.3:1 U:Pu and up to 5.16 g/l U.
Longitudinal Study to Assess the Quantitative Use of Fundus Autofluorescence for Monitoring Disease Progression in Choroideremia

Background: Characterisation of preserved autofluorescence (PAF) area in choroideremia (CHM) and its validity for monitoring disease progression in clinical trials is of importance. Methods: Eighty patients with molecularly confirmed CHM were recruited. PAF area was measured manually by 2 graders and half-life was calculated based on exponential decay model. Results: Mean age at baseline and follow-up examination was 38.1 (range, 10–69) and 40.7 (range, 11–70) years. Mean follow-up interval was 29 months (range, 6–104). The median LogMAR visual acuity was 0.10 (OD) and 0.18 (OS). Interobserver repeatability for PAF area was −0.99 to 1.03 mm2 (−6.46 to 6.49% of area). There was a statistically significant relationship between age and rate of PAF area loss (r2 = 0.28, p = 0.012). The half-life for PAF area was 13.7 years (range, 1.7–216.0 years). The correlation between half-life and age was stronger than between half-life and log transformed baseline PAF area, although neither was statistically significant. Conclusions: The intra- and inter-observer PAF area measurement variability provides a baseline change, which must be overcome in a clinical trial if this metric were to be used. Treatments must slow progression to alter the exponential decay in a timely manner accounting for naturally slow progression patterns.
Presumed Consent With Opt-Out: An Ethical Consent Approach to Automatically Refer Patients With Cancer to Tobacco Treatment Services.

Continued smoking after cancer diagnosis increases the risk of cancer recurrence, treatment-related toxic-ities, treatment failure, and death. 1-9 Apart from disease site and stage, continued smoking is the strongest predictor of mortality in patients with cancer. 9,10 Quitting smoking can increase long-term survival, reduce total symptom burden, decrease treatment toxicity, optimize postoperative outcomes in patients requiring surgery, and improve quality of life.
Effect of Hydrolyzable Tannins on Glucose-Transporter Expression and Their Bioavailability in Pig Small-Intestinal 3D Cell Model

Intestinal transepithelial transport of glucose is mediated by glucose transporters, and affects postprandial blood-glucose levels. This study investigates the effect of wood extracts rich in hydrolyzable tannins (HTs) that originated from sweet chestnut (Castanea sativa Mill.) and oak (Quercus petraea) on the expression of glucose transporter genes and the uptake of glucose and HT constituents in a 3D porcine-small-intestine epithelial-cell model. The viability of epithelial cells CLAB and PSI exposed to different HTs was determined using alamarBlue®. qPCR was used to analyze the gene expression of SGLT1, GLUT2, GLUT4, and POLR2A. Glucose uptake was confirmed by assay, and LC–MS/ MS was used for the analysis of HT bioavailability. HTs at 37 µg/mL were found to adversely affect cell viability and downregulate POLR2A expression. HT from wood extract Tanex at concentrations of 4 µg/mL upregulated the expression of GLUT2, as well as glucose uptake at 1 µg/mL. The time-dependent passage of gallic acid through enterocytes was influenced by all wood extracts compared to gallic acid itself as a control. These results suggest that HTs could modulate glucose uptake and gallic acid passage in the 3D cell model.
A Serial-Mediation Model to Link Entrepreneurship Education and Green Entrepreneurial Behavior: Application of Resource-Based View and Flow Theory

Eco-conscious behaviors have become a global imperative for entrepreneurs, as the consumer demand for products and services has become increasingly green. Hence, the purpose of this study is to identify the role of entrepreneurship education in environmental sustainability as measured by the launch of green ventures. This study also aims at extending the literature of resource-based view and flow theory by highlighting their application into the green venturing context. Data were collected from 420 Pakistani students having studied an entrepreneurship course in their university life by using the convenience sampling technique. The covariance based structural equation modeling (CB-SEM) was used to test the hypothesized relationships, and it was identified that entrepreneurship education evokes commitment to the environment, subsequently leading towards university green entrepreneurial support, environmental motivation, and green entrepreneurial behavior. University green entrepreneurial support also significantly influences green venturing; however, environmental motivation does not affect green entrepreneurial behavior. The findings of this study can be useful for policymakers in higher educational institutions, regulatory bodies, and diverse-government agencies dealing with UN sustainable development goals.
Combination of CA19-9 and Blood Free-Circulating Methylated RUNX3 May Be Useful to Diagnose Stage I Pancreatic Cancer

Background: Although serum carbohydrate antigen 19-9 (CA19-9) is widely used as a useful biomarker of pancreatic cancer for monitoring the response to therapy, it is not recommended for screening of early pancreatic cancer because of its limited sensitivity for small tumors. Thus, it is critical to discover novel serum biomarkers to complement CA19-9 in order to improve sensitivity. Although methylated runt-related transcription factor 3 (RUNX3) is a biomarker of pancreatic cancer, its detection by conventional bisulfite-based methylation assays from a small serum sample amount is very difficult. Therefore, we developed a new methylation assay, the combined restriction digital PCR (CORD) assay, that enables counting of even one copy of a methylated gene in a small DNA sample amount without DNA bisulfite treatment. Objectives: We evaluated the sensitivity and specificity of serum DNA testing of methylated RUNX3 by the CORD assay in combination with and without CA19-9 for the detection of pancreatic cancer in 55 patients with pancreatic cancer, 12 patients with benign pancreatic disease, and 80 healthy individuals. Results: The CORD assay of methylated RUNX3 had a sensitivity of 50.9% (28/55) and specificity of 93.5% (86/92). Combination of the CORD assay of methylated RUNX3 and CA19-9 resulted in a sensitivity of 85.5% (47/55) and specificity of 93.5% (86/92) for all stages of pancreatic cancer and a sensitivity of 77.8% (7/9) for stage I pancreatic cancer. Conclusions: ombination of the CORD assay and CA19-9 may provide an alternative screening strategy for detecting early-stage pancreatic cancer.
Relationship between Time-dependent Signal Changes in Parasagittal Perivenous Cysts and Leakage of Gadolinium-based Contrast Agents into the Subarachnoid Space

Purpose To investigate the association between signal changes over time in perivenous cystic structures near the superior sagittal sinus and leakage of a gadolinium-based contrast agent (GBCA) into the subarachnoid space in patients with suspected endolymphatic hydrops. Methods Fifty-one cystic structures in 27 cases were evaluated. The signal intensity of the cystic structures was measured on 3D real inversion recovery (3D-real IR) images obtained at pre-, and at 10 min, 4 hrs and 24 hrs post-intravenous administration (IV) of GBCA. Signal enhancement of the cystic structures from the pre-contrast images at each time point was compared in subjects with leakage (positive) versus those without leakage (negative) using an ANOVA. Fisher’s exact probability test was used to compare the maximum contrast-enhanced time point between positive and negative groups. We used 5% as a threshold to determine statistical significance. Results In leakage positive subjects, mean signal enhancement of the cysts was significantly greater at 4 and 24 hrs compared to 10 min. However, although there was a trend of an increase from 4 to 24 hrs, the difference was not significant. In the leakage negative group, mean signal enhancement of the cysts was significantly higher at 4 hrs compared to 10 min and 24 hrs. There was no significant difference between 10 min and 24 hrs. In the positive group, the maximum signal increase was found in 10/38 and 28/38 cysts at 4 and 24 hrs after IV-GBCA, respectively. In the leakage negative group, the maximum signal increase was found in 10/13 and 3/13 cysts at 4 and 24 hrs, respectively (P = 0.0019). Conclusion There was an association between signal changes over time after IV-GBCA in perivenous cystic structures and leakage of GBCA. Further research to clarify the impact of cystic structures on the function of the waste clearance system of the brain is warranted.
Comparison of Prognostic Scores in Patients With Hepatocellular Carcinoma Treated With Sorafenib

INTRODUCTION: Prognostic classifications for patients treated with sorafenib for hepatocellular carcinoma (HCC) facilitate stratification in trials and inform clinical decision making. Recently, 3 different prognostic models (hepatoma arterial-embolization prognosis [HAP] score, sorafenib advanced HCC prognosis [SAP] score, and Prediction Of Survival in Advanced Sorafenib-treated HCC [PROSASH]-II) have been proposed specifically for patients treated with sorafenib. This study aimed to compare the prognostic performance of different scores. METHODS: We analyzed a large prospective database gathering data of 552 patients treated with sorafenib from 7 Italian centers. The performance of the HAP, SAP, and PROSASH–II models were compared with those of generic HCC prognostic models (including the Barcelona Clinic for Liver Cancer and Italian Liver Cancer staging systems, albumin–bilirubin grade, and Child-Pugh score) to verify whether they could provide additional information. RESULTS: The PROSASH-II model improved discrimination (C-index 0.62) compared with existing prognostic scores (C-index ≤0.59). Its stratification significantly discriminated patients, with a median overall survival of 21.5, 15.3, 9.3, and 6.0 months for risk group 1, 2, 3, and 4, respectively. The HAP and SAP score were also validated but with a poorer performance compared with the PROSASH-II. DISCUSSION: Although suboptimal, PROSASH-II is the most effective prognostic classification model among other available scores in a large Italian population of patients treated with sorafenib.
Copper Release Behavior in Two Calcareous Soils Amended with Three Organic Materials

Understanding time-dependent copper (Cu) desorption behavior is critical for improving the prediction of Cu availability in soils. This study was conducted to evaluate the influence of municipal waste compost, sheep manure, and wheat straw on desorption characteristics of Cu and to evaluate the suitability of different kinetic models to describe the Cu release pattern in two calcareous soils. Diethylenetriaminepentaacetic acid (DTPA) and ethylenediaminetetraacetic acid (EDTA) were employed to extract Cu from soils. Best-fitted kinetic models including Elovich, simple Elovich, two-constant rate, and parabolic diffusion were selected based on their low standard error and high coefficient of determination. Extractable copper significantly decreased with increasing rates of sheep manure and wheat straw but increased with increasing rates of municipal waste compost amendment. Results revealed that copper was more readily desorbed from clay soil compared to silt loam soil. The copper desorption patterns were almost similar for both extractants; however, EDTA extracted more Cu from soils.
Spatial variation of microtubule depolymerization in large asters

Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.
Bacteria Adhesion of Textiles Influenced by Wettability and Pore Characteristics of Fibrous Substrates

Bacteria adhesion on the surface is an initial step to create biofouling, which may lead to a severe infection of living organisms and humans. This study is concerned with investigating the textile properties including wettability, porosity, total pore volume, and pore size in association with bacteria adhesion. As model bacteria, Gram-negative, rod-shaped Escherichia coli and the Gram-positive, spherical-shaped Staphylococcus aureus were used to analyze the adhesion tendency. Electrospun webs made from polystyrene and poly(lactic acid) were used as substrates, with modification of wettability by the plasma process using either O2 or C4F8 gas. The pore and morphological characteristics of fibrous webs were analyzed by the capillary flow porometer and scanning electron microscopy. The substrate’s wettability appeared to be the primary factor influencing the cell adhesion, where the hydrophilic surface resulted in considerably higher adhesion. The pore volume and the pore size, rather than the porosity itself, were other important factors affecting the bacteria adherence and retention. In addition, the compact spatial distribution of fibers limited the cell intrusion into the pores, reducing the total amount of adherence. Thus, superhydrophobic textiles with the reduced total pore volume and smaller pore size would circumvent the adhesion. The findings of this study provide informative discussion on the characteristics of fibrous webs affecting the bacteria adhesion, which can be used as a fundamental design guide of anti-biofouling textiles.
Motives for Empathy among Clinical Nurses in China: A Qualitative Study.

PURPOSE This study aimed to explore the motives of clinical nurses for experiencing empathy with patients and their families based on a self-determination theory framework. METHODS Semi-structured face-to-face interviews with twenty-one nurses at four tertiary hospitals in Anhui, China, were conducted, recorded and transcribed. A content analysis with a directed approach was performed. RESULTS An analysis of the interview transcripts revealed three categories of empathy motivation: autonomous motivation, controlled motivation and a lack of empathy motivation. Autonomous motivation included personal interests, enjoyment and a sense of value, pure altruism, assimilation, and recognition of the importance of empathy. Controlled motivation highlighted pressures from oneself and others, the possibility of tangible or intangible rewards, and avoidance of adverse effects. Finally, a lack of empathy motivation referred to a lack of intention for empathy and denial of the value of empathy. CONCLUSION This study provides a deep understanding of the motives underlying empathy in nurses. The results reveal the reasons for empathy and may support the development of effective strategies to foster and promote empathy in nurses.