Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the diagnostic accuracy of CEUS in children with benign and malignant liver lesions and portal vein anomalies.

OBJECTIVE Comparison of the diagnostic findings of MRI, CT and CEUS in children with benign and malignant and portal venous anomalies of the liver. MATERIALS/METHODS Retrospective analysis of the diagnostic findings of CEUS, MRI and CT scans in 56 children (age 0-17 years) with a total of 60 benign and malignant liver lesions and anomalies of the portal vein/perfusion. All patients underwent CEUS using sulphur hexafluoride microbubbles and a multi-frequency probe (1-5 MHz, 6-9 MHz). Cine-loops were stored up to 3 minutes. MRI was performed in 38 lesions. CT was performed in 8 lesions. RESULTS Out of the 56 patients 49 liver lesions (48 benign, 1 malignant), 9 anomalies of the portal vein/perfusion and 2 of the biliary system were detected. 16/49 lesions were analyzed histopathologically. Using CEUS, the characterization of the lesions was possible in 45 out of 49 cases. In 32 cases, CEUS provided the exact diagnosis. Only two benign lesions were falsely categorized as malignant.Findings of MRI and CEUS were concordant in 84% of cases (n = 32/38). CEUS considered 1 benign lesion to be malignant. 2 lesions were not detectable and in 3 lesions no definite diagnosis was established using MRI.Findings of CT and CEUS were concordant in 5 of 8 cases. In 21 lesions CEUS as the only imaging modality was found to be sufficient for diagnostics. CONCLUSION Despite the restricted indications for using CEUS in children, it offers a high diagnostic detection rate (93%) for characterization of liver lesions and portal vein anomalies.
A framework toward sustainable ecotourism value chain in the Philippines

ABSTRACT Philippine tourism growth is largely driven by visits to natural attractions. Addressing concerns on sustainability, environmental conservation, and local community involvement has become increasingly challenging. We identify the critical players in the industry and create a value chain framework for Philippine ecotourism that incorporates the quadruple bottom-line strategy to understand how sustainable tourism is being practiced among value chain participants. Findings have implications in the pursuit of sustainable ecotourism development in the country.
The Toll Interleukin-1 Receptor (IL-1R) 8/Single Ig Domain IL-1R-Related Molecule Modulates the Renal Response to Bacterial Infection

ABSTRACT Our immune system has to constantly strike a balance between activation and inhibition of an inflammatory response to combat invading pathogens and avoid inflammation-induced collateral tissue damage. Toll interleukin-1 receptor 8 (IL-1R-8)/single Ig domain IL-1R-related molecule (TIR8/SIGIRR) is an inhibitor of Toll-like receptor (TLR)/IL-1R signaling, which is predominantly expressed in the kidney. The biological role of renal TIR8 during infection is, however, unknown. We therefore evaluated renal TIR8 expression during Escherichia coli pyelonephritis and explored its role in host defense using TIR8−/− versus TIR8+/+ mice. We found that TIR8 protein is abundantly present in the majority of cortical tubular epithelial cells. Pyelonephritis resulted in a significant downregulation of TIR8 mRNA in kidneys of TIR8+/+ mice. TIR8 inhibited an effective host response against E. coli, as indicated by diminished renal bacterial outgrowth and dysfunction in TIR8−/− mice. This correlated with increased amounts of circulating and intrarenal neutrophils at the early phase of infection. TIR8−/− tubular epithelial cells had increased cytokine/chemokine production when stimulated with lipopolysaccharide (LPS) or heat-killed E. coli, suggesting that TIR8 played an anti-inflammatory role during pathogen stimulation by inhibiting LPS signaling. These data suggest that TIR8 is an important negative regulator of an LPS-mediated inflammatory response in tubular epithelial cells and dampens an effective antibacterial host response during pyelonephritis caused by uropathogenic E. coli.
Bacterial proteins pinpoint a single eukaryotic root

Significance The root of eukaryote phylogeny formally represents the last eukaryotic common ancestor (LECA), but its position has remained controversial. Using new genome sequences, we revised and expanded two datasets of eukaryotic proteins of bacterial origin, which previously yielded conflicting views on the eukaryotic root. Analyses using state-of-the-art phylogenomic methodology revealed that both expanded datasets now support the same root position. Our results justify a new nomenclature for the two main eukaryotic groups and provide a robust phylogenetic framework to investigate the early evolution of the eukaryotic cell. The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between “Unikonta” and “Bikonta,” with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.
Air supply system model with exhaust gas recirculation for improving the life of fuel cell

This paper presents an air supply system model with the exhaust gas recirculation (EGR) function. High potential is one of the key factors for degradation of proton exchange membrane fuel cell. The harmful high voltage always appears when the fuel cell works at small load. The output voltage is greatly affected by the oxygen stoichiometric at the cathode. The high voltage can be lowered down by controlling the oxygen stoichiometric in a suitable range. Based on this concept, an air supply system model with EGR is proposed and modeled. A feasible control strategy for lowering the output voltage is also deployed. Simulation results of the model show that, the oxygen ration in the inlet air can be greatly reduced, as well as the output voltage.
A simple rosette assay for demonstration of complement receptor sites using complement‐coated zymosan beads

In the present article we describe a simple rosette assay for detection of C3 receptor‐bearing B lymphocytes with complement (C)‐coated zymosan (Zy) beads. Zy coated with murine or human C bound to a distinct population of human and mouse lymphocytes as well as to the majority of lymphoblastoid cells of several human established cell lines. Rosette formation was also observed with human red blood cells, with human monocytes and neutrophils. Experiments with anti‐immunoglobulin sera, with other B and T cell markers and with mouse thymocytes proved that the capacity to bind C‐coated Zy is primarily a feature of B lymphocytes. The following findings suggested that C‐coated Zy is bound via receptor sites for the activated components of C3: (a) Zy coated with C3‐deficient serum failed to bind, (b) comparable percentages of various lymphoid and nonlymphoid cells formed rosettes with C‐coated Zy as well as with antibody and C‐coated sheep red bloodcells, and (c) antibodies against human or murine C3 inhibited the binding of C‐coated Zy.
Predicting financial distress: Importance of accounting and firm-specific market variables for Pakistan’s listed firms

Abstract This study is intended to identify the predictors of financial distress for the Pakistani firms. Variables used are the financial ratios representing profitability, liquidity, leverage, and cash flows, as well as two important market factors which are size and idiosyncratic standard deviation of each firm’s stock returns (SIG). The sample consists of 290 firms stretching from 2007 to 2016 and logit regression is applied to predict financial distress. The findings reveal that profitability, liquidity, leverage, cash flow ratios, and firm size are significant, while SIG is insignificant in predicting financial distress. Results of the estimated logit model I, model II, and holdout model reveal that the models perform consistently. This study contributes to the literature by testing the market variables in relation to financial distress as these variables were ignored by the previous studies in Pakistan. Findings of this study are precise as the study covers a longer time horizon and a larger sample size.
Low Rates of Pseudomonas aeruginosa Misidentification in Isolates from Cystic Fibrosis Patients

ABSTRACT Pseudomonas aeruginosa is an important cause of pulmonary infection in cystic fibrosis (CF). Its correct identification ensures effective patient management and infection control strategies. However, little is known about how often CF sputum isolates are falsely identified as P. aeruginosa. We used P. aeruginosa-specific duplex real-time PCR assays to determine if 2,267 P. aeruginosa sputum isolates from 561 CF patients were correctly identified by 17 Australian clinical microbiology laboratories. Misidentified isolates underwent further phenotypic tests, amplified rRNA gene restriction analysis, and partial 16S rRNA gene sequence analysis. Participating laboratories were surveyed on how they identified P. aeruginosa from CF sputum. Overall, 2,214 (97.7%) isolates from 531 (94.7%) CF patients were correctly identified as P. aeruginosa. Further testing with the API 20NE kit correctly identified only 34 (59%) of the misidentified isolates. Twelve (40%) patients had previously grown the misidentified species in their sputum. Achromobacter xylosoxidans (n = 21), Stenotrophomonas maltophilia (n = 15), and Inquilinus limosus (n = 4) were the species most commonly misidentified as P. aeruginosa. Overall, there were very low rates of P. aeruginosa misidentification among isolates from a broad cross section of Australian CF patients. Additional improvements are possible by undertaking a culture history review, noting colonial morphology, and performing stringent oxidase, DNase, and colistin susceptibility testing for all presumptive P. aeruginosa isolates. Isolates exhibiting atypical phenotypic features should be evaluated further by additional phenotypic or genotypic identification techniques.
Co-morbidities and Hyperinflation Are Independent Risk Factors of All-cause Mortality in Very Severe COPD

Abstract Background: COPD is a multi-component disease that is not sufficiently reflected by FEV1 alone. We studied in patients with very severe COPD, which dimensions of the disease, including co-morbidities, dominate prognosis. Methods: In patients with FEV1 < 30% predicted, anthropometric, laboratory, spirometric and body plethysmographic data, smoking status, alcohol consumption, the level of dyspnoea and exercise performance were assessed. Co-morbidities were categorized by the Charlson-index and the COPD-specific co-morbidity test (COTE). The prognostic value of multiple dimensions was explored using uni- and multivariate survival analyses regarding death from any or respiratory cause. Results: Among 209 patients included (58/151 female/male; FEV1 25.0 (22.0–26.9)%predicted), arterial hypertension (54.1%), hyperlipidemia (38.3%) and diabetes (19.6%) were most common, 57.9% showing a COTE-index of ≥1 point. During follow-up (28 (14–45) months), 121 patients had died, mostly (56.2%) due to respiratory causes. Age, BMI, the ratio of residual volume to total lung capacity (RV/TLC), co-morbidities in terms of the COTE- and Charlson-index, but not FEV1, were significantly associated with all-cause and respiratory mortality. The association of the median values of the Charlson- (HR 1.911 [95%-CI 1.338–2.730]) and COTE-index (HR 1.852 [95%-CI 1.297–2.644], p < 0.001 each) with mortality was similar and stronger when combined with age. In multivariate analyses, only RV/TLC and co-morbidities were independent risk factors of all-cause mortality (p < 0.05 each). Conclusion: In very severe COPD, resting hyperinflation and co-morbidities provide the major prognostic information, whereas the association of the recently introduced COTE-index with mortality was similar to that of the established Charlson-index and even stronger when including age.
Small intestinal development in the young chick: Crypt formation and enterocyte proliferation and migration

1. Post-natch mucosal development was examined in the chick small intestinal epithelium using immunostaining with proliferating cell nuclear antigen (PCNA) and 5-bromo-2-deoxyuridine (BrdU). 2. On the day of hatching jejunal crypts were small and a single crypt per villus was observed. However, during the 108 h post-hatch crypts developed rapidly, branching and increasing in size, cell numbers and cell size. 3. Almost all epithelial cells in the small intestine of the hatching chick were proliferating, as indicated by PCNA and BrdU, while more than 80% of proliferating cells were localised in the crypts after 108 h post hatch. 4. Estimate of villus cell transit time using BrdU was only possible from 48 h post-hatch when villus transit time was 72 h in the jejunum, whereas at 336 h transit time was 96 h. 5. In the 108 h post hatch a rapid transition occurs from total jejunal epithelial cell proliferation and immature crypts to a defined proliferative zone in the crypts, with constant division and migration.
Physical model for membrane protrusions during spreading

During cell spreading onto a substrate, the kinetics of the contact area is an observable quantity. This paper is concerned with a physical approach to modeling this process in the case of ameboid motility where the membrane detaches itself from the underlying cytoskeleton at the leading edge. The physical model we propose is based on previous reports which highlight that membrane tension regulates cell spreading. Using a phenomenological feedback loop to mimic stress-dependent biochemistry, we show that the actin polymerization rate can be coupled to the stress which builds up at the margin of the contact area between the cell and the substrate. In the limit of small variation of membrane tension, we show that the actin polymerization rate can be written in a closed form. Our analysis defines characteristic lengths which depend on elastic properties of the membrane–cytoskeleton complex, such as the membrane–cytoskeleton interaction, and on molecular parameters, the rate of actin polymerization. We discuss our model in the case of axi-symmetric and non-axi-symmetric spreading and we compute the characteristic time scales as a function of fundamental elastic constants such as the strength of membrane–cytoskeleton adherence.
Bilateral breast carcinoma– a rare case report

We are presenting a rare case of bilateral breast cancer. A 65–year–old female reported to us with complaint of lump in the left breast. There was positive family history. The patient was diagnosed with carcinoma breast of left side on edge biopsy and of right side by ultrasonography, which was confirmed on fine needle aspiration cytology. At the time of admission, ultrasonography of the abdomen and right breast were normal. After 1 month, the patient was readmitted with redness over the inner quadrant of the right breast skin
All‐trans 3,4‐didehydroretinoic acid equals all‐trans retinoic acid in support of chick neuronal development

All‐trans 3,4‐didehydroretinoic acid (at‐ddRA) has been identified as a biologically important retinoid in avian, but not mammalian, embryonic development. In this report, we show that at‐ddRA, like all‐trans retinoic acid (atRA), supports the survival and differentiation of sympathetic neurons of the embryonic chick. Furthermore, the expression of the retinoid‐responsive gene RARβ2 is increased in neurons exposed to either at‐ddRA or atRA. The mechanism whereby at‐ddRA exerts its effects in chick neurons may involve binding to and activation of nuclear retinoid receptors. For this reason, the binding of recombinant chick RARβ2 to at‐ddRA and to receptor‐specific DNA response elements was examined and compared with the binding characteristics of recombinant murine RARβ2. The chick RARβ2, like the mammalian RAR, binds to [3H]atRA with high affinity (Kd=0.7‐2 nM). Furthermore, both chick and murine RARβ2 bind equally well to at‐ddRA, atRA, and 9‐cis RA, but neither receptor shows appreciable binding to 13‐cis RA. The chick RARβ2 recognizes previously described retinoic acid response elements of mammalian gene promoters and, like mammalian RARβ2, shows enhanced binding in the presence of RXR. This study provides evidence that at‐ddRA, like atRA, supports neuronal development in the chick by its interaction with nuclear retinoid receptors. —Repa, J. J., Plum, L. A. , Tadikonda, P. K. , Clagett‐Dame, M. All‐trans 3,4‐didehydroretinoic acid equals all‐trans retinoic acid in support of chick neuronal development. FÁSEBJ. 10,1078‐1084 (1996)
A Prospective Randomized Study Comparing Open versus Laparoscopy-Assisted D2 Radical Gastrectomy in Advanced Gastric Cancer

Background: In recent years, many clinical studies have confirmed the value of laparoscopy-assisted gastrectomy (LAG) in gastric cancer surgery, especially in early stages. But the safety and oncologic adequacy of laparoscopy-assisted D2 radical gastrectomy for advanced gastric cancer are still in debate. We conducted a prospective randomized trial to compare open versus laparoscopy-assisted D2 radical gastrectomy in advanced gastric cancer. Methods: For this study, 123 patients who had been diagnosed endoscopically with gastric cancer were randomly assigned to either LAG (n = 61) or open gastrectomy (OG) (n = 62) which ran from March 2008 to December 2009. Clinical characteristics, operative findings, postoperative recovery, morbidity, pathological report and survival rate were compared. D2 lymph node dissection was performed in 49 patients in the LAG group and 47 patients in the OG group with advanced gastric cancer. We adopt sub-group analysis in this paper. Results: The clinical characteristics of patients in the LAG and OG groups who were in the advanced stage, included age, sex, BMI and concurrent illness, and their ECOG scores were well matched. Operative findings, postoperative recovery, morbidity, pathological findings including tumor location, depth of invasion, TNM stage, histological grade and surgical extension in the two groups were also similar. Compared to the OG group, the mean operating time was significantly longer for the LAG group (267.88 ± 54.284 min in the LAG group vs. 182.02 ± 41.016 min in the OG group, p = 6.383 × 10–13); the mean number of days when body temperature exceeded 37°C was significantly shorter in the LAG group (p = 6.34 × 10–8). There were no postoperative deaths in both the groups. The postoperative morbidity rate was 12.24% in the LAG group and 19.15% in the OG group with no significant difference (p = 0.357). However, pulmonary infection was observed more frequently in the OG group (p = 0.038). After a mean follow-up of 22.1354 months (from 4 to 36 months), 14 and 15 patients died of gastric cancer in the LAG and OG groups, respectively. Two and one patient died of nongastric cancer in the LAG and OG groups, respectively. The overall survival rates were 67.1% and 53.8% in the LAG and OG groups, respectively. The estimated mean survival time was 29.387 months in the LAG group and 28.978 months in the OG group. There was no statistically significant difference in the overall survival rate for patients in both groups – LAG and OG (log-rank test, p = 0.911, Tarone Ware test, p = 0.994, and Breslow test, p = 0. 961). Conclusion: LAG with D2 lymph node dissection is a safe and feasible procedure with adequate lymphadenectomy, good curability and survival rate for the treatment of advanced gastric cancer.
Interleukin-8 levels in human lung epithelial cells are increased in response to coal fly ash and vary with the bioavailability of iron, as a function of particle size and source of coal.

Particulate air pollution contains iron, and some of the pathological effects after inhalation may be due to radical species produced by iron-catalyzed reactions. We tested the hypothesis that iron present in coal fly ash (CFA) could induce the expression and synthesis of the inflammatory cytokine interleukin-8 (IL-8). CFA, containing as much as 14% iron, was used as a model combustion source particle. Three coal types were used to generate three size fractions enriched in particles [submicron (<1 micrometer), fine (<2.5 micrometer), or coarse (2.5-10 micrometer]), as well as the fraction of >10 micrometer. Treatment of human lung epithelial (A549) cells for 4 h with CFA from Utah enriched in <1 micrometer particles (20 microgram/cm(2)) resulted in a 2.6-fold increase in mRNA levels for IL-8. IL-8 levels were increased in the medium by as much as 8-fold when cells were treated with the fraction enriched in the smallest size Utah CFA for 24 h. IL-8 production was completely inhibited when the CFA was pretreated with the metal chelator desferrioxamine B, suggesting that a transition metal was responsible for the induction, probably iron. Treatment with a soluble form of iron, ferric ammonium citrate (FAC), mimicked the IL-8 level increase observed with CFA. There was a direct relationship, above a threshold level of bioavailable iron, between the levels of IL-8 and bioavailable iron in A549 cells treated with CFA or FAC. Further, the relationship between IL-8 and bioavailable iron for CFA was indistinguishable from that for FAC. These results strongly suggest that iron can induce IL-8 in A549 cells and that iron was the likely component of CFA that induced IL-8. CFA-induced IL-8 production was inhibited by tetramethylthiourea or dimethyl sulfoxide, suggesting that radical species were involved in the induction. These results demonstrate that iron present in CFA may be responsible for production and release of inflammatory mediators by the lung epithelium through generation of radical species and suggest that iron may contribute to the exacerbation of respiratory problems by particulate air pollution.
Exact analytical loop closure in proteins using polynomial equations

Loop closure in proteins has been studied actively for over 25 years. Using spherical geometry and polynomial equations, several loop‐closure problems in proteins are solved exactly by reducing them to the determination of the real roots of a polynomial. Loops of seven, eight, and nine atoms are treated explicitly, including the tripeptide and disulfide‐bonded loop‐closure problems. The number of valid loop closures can be evaluated by the method of Sturm chains, which counts the number of real roots of a polynomial. Longer loops can be treated by three methods: by sampling enough dihedral angles to reduce the problem to a soluble loop‐closure problem; by applying the loop‐closure algorithm hierarchically; or by decimating the chain into independently moving rigid elements that can be reconnected using loop‐closure algorithms. Applications of the methods to docking, homology modeling and NMR problems are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 819–844, 1999