Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum Antibody Response to Five Streptococcus pneumoniae Proteins During Acute Otitis Media in Otitis-prone and Non–otitis-prone Children

Background: Streptococcus pneumoniae (Spn) is one of the common bacteria responsible for episodic acute otitis media (AOM; non–otitis-prone), recurrent AOM (otitis-prone), and AOM treatment failure (AOMTF) in children. Objective: From a population of 268 children, we sought to compare the serum IgG antibody titers of 5 different Spn proteins (PhtD, LytB, PcpA, PhtE, and Ply) that are vaccine candidates in children with episodic AOM (n = 34), who were otitis prone (n = 35) and who had AOMTF (n = 25) caused by Spn. Methods: Antibody was quantitated by enzyme-linked immunosorbent assay. Results: At their AOM visit, anti-PhtD, -LytB, -PhtE, and -Ply IgG antibody titers in otitis-prone children were significantly lower compared with non–otitis-prone children (P < 0.05) and children with AOMTF (P < 0.05). On comparing acute to convalescent geometric mean IgG antibody titers after AOM against the 5 proteins we found that otitis-prone, AOMTF, and non-otitis-prone children had no significant change in titers (except for PhtE in children with AOMTF), but detailed analysis showed that about one-third of the children in each cohort had a 2-fold rise in antibody to the studied antigens. Although non–otitis-prone children had significant increases (P < 0.001) between 6 and 24 months of age in anti-PhtD, PcpA, PhtE, and Ply IgG antibody titers as a consequence of nasopharyngeal colonization and AOM, otitis-prone children either failed to show rises or the rises were significantly less than the non–otitis-prone children. Conclusion: Otitis-prone and AOMTF children mount less of an IgG serum antibody response as compared with non–otitis-prone children to Spn proteins after AOM and nasopharyngeal colonization.
Alteration of Fatty Acid Oxidation in Tubular Epithelial Cells: From Acute Kidney Injury to Renal Fibrogenesis

Renal proximal tubular cells are the most energy-demanding cells in the body. The ATP that they use is mostly produced in their mitochondrial and peroxisomal compartments, by the oxidation of fatty acids. When those cells are placed under a biological stress, such as a transient hypoxia, fatty acid oxidation (FAO) is shut down for a period of time that outlasts injury, and carbohydrate oxidation does not take over. Facing those metabolic constraints, surviving tubular epithelial cells exhibit a phenotypic switch that includes cytoskeletal rearrangement and production of extracellular matrix proteins, most probably contributing to acute kidney injury-induced renal fibrogenesis, thence to the development of chronic kidney disease. Here, we review experimental evidence that dysregulation of FAO profoundly affects the fate of tubular epithelial cells, by promoting epithelial-to-mesenchymal transition, inflammation, and eventually interstitial fibrosis. Restoring physiological production of energy is undoubtedly a possible therapeutic approach to unlock the mesenchymal reprograming of tubular epithelial cells in the kidney. In this respect, the benefit of the use of fibrates is uncertain, but new drugs that could specifically target this metabolic pathway, and, hopefully, attenuate renal fibrosis merit future research.
Injection‐molded high‐density polyethylene–hydroxyapatite–aluminum oxide hybrid composites for hard‐tissue replacement: Mechanical, biological, and protein adsorption behavior

In this article, we report the mechanical and biocompatibility properties of injection-molded high-density polyethylene (HDPE) composites reinforced with 40 wt % ceramic filler [hydroxyapatite (HA) and/or Al2O3] and 2 wt % titanate as a coupling agent. The mechanical property measurements revealed that a combination of a maximum tensile strength of 18.7 MPa and a maximum tensile modulus of about 855 MPa could be achieved with the injection-molded HDPE–20 wt % HA–20 wt % Al2O3 composites. For the same composite composition, the maximum compression strength was determined to be 71.6 MPa and the compression modulus was about 660 MPa. The fractrography study revealed the uniform distribution of ceramic fillers in the semicrystalline HDPE matrix. The cytocompatibility study with osteoblast-like SaOS2 cells confirmed extensive cell adhesion and proliferation on the injection-molded HDPE–20 wt % HA–20 wt % Al2O3 composites. The cell viability analysis with the 3(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay revealed a statistically significant difference between the injection-molded HDPE–20 wt % HA–20 wt % Al2O3 composites and sintered HA for various culture durations of upto 7 days. The difference in cytocompatibility properties among the biocomposites is explained in terms of the difference in the protein absorption behavior. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Evaluation of Mesial Root Canals of Mandibular Molars Obturated with Gutta-Percha and Resilon Techniques

Objective: The aim of this study was to evaluate the obturation of mesial root canals of mandibular first molars performed with different filling techniques and materials (gutta-percha and resilon). Methods: Seventy-eight mesial root canals of human mandibular first molars were prepared using the K3 rotary system, and the apical preparation was set up to size 35.04. The root canals were obturated with single cone, System B, Thermafil and Real Seal 1 techniques using either gutta-percha/ThermaSeal Plus (n=13) or Resilon/Real Seal SE (n=13). Rhodamine B dye was incorporated into the sealers. Each specimen was horizontally sectioned at 2 milimeters (mm), 4 mm and 6 mm from the apex, and the samples were examined under a stereomicroscope to evaluate the presence and type of isthmuses and the percentage areas of gutta-percha/Resilon, sealer and voids. Confocal laser scanning microscopy (CLSM) was used to evaluate the sealer penetration into dentinal tubules. The Kruskal-Wallis and Dunn’s tests were used to analyse the stereomicroscope data, while the ANOVA and Tukey tests were used to analyse the CLSM data (P<0.05). Results: Thermafil and Real Seal 1 fillings showed more gutta-percha/Resilon and less sealer (P<0.05) at the 2 mm level, but the percentage of voids was similar in all groups (P>0.05). At the 4 mm level, more sealer (P<0.05) was found in the single cone groups using both materials. The System B groups exhibited better performance at the 6 mm level. The percentage of sealer penetration showed no statistically significant differences among the obturation techniques for all evaluated levels. Similar results (P>0.05) were found for both material/sealers. Conclusion: None of the materials or techniques completely filled the mesial root canals of mandibular molars, but the plasticised techniques were more efficient. The obturations using both materials and sealers were similar.
Prediction of adverse health outcomes in older people using a frailty index based on routine primary care data.

BACKGROUND A general frailty indicator could guide general practitioners (GPs) in directing their care efforts to the patients at highest risk. We investigated if a Frailty Index (FI) based on the routine health care data of GPs can predict the risk of adverse health outcomes in community-dwelling older people. METHODS This was a retrospective cohort study with a 2-year follow-up period among all patients in an urban primary care center aged 60 and older: 1,679 patients (987 women [59%], median age, 73 years [interquartile range, 65-81]). For each patient, a baseline FI score was computed as the number of health deficits present divided by the total number of 36 deficits on the FI. Adverse health outcomes were defined as the first registered event of an emergency department (ED) or after-hours GP visit, nursing home admission, or death. RESULTS In total, 508 outcome events occurred within the sample population. Kaplan-Meier survival curves were constructed according to FI tertiles. The tertiles were able to discriminate between patients with low, intermediate, and high risk for adverse health outcomes (p value < .001). With adjustments for age, consultation gap, and sex, a one deficit increase in the FI score was associated with an increased hazard for adverse health outcomes (hazard ratio, 1.166; 95% confidence interval [CI], 1.129-1.210) and a moderate predictive ability for adverse health outcomes (c-statistic, 0.702; 95% CI, 0.680-0.724). CONCLUSIONS An FI based on International Classification of Primary Care (ICPC)-encoded routine health care data does predict the risk of adverse health outcomes in elderly population.
Immunoinhibitory Pathway Aged Mice through Blockade of an T Cell Responses in + Virus-Specific CD8 Augmentation of Primary Influenza A

Immune responses diminish with age resulting in an increased susceptibility of the elderly to infectious agents and an inability to mount protective immune responses to vaccines. Immunosenescence affects multiple aspects of the immune system, including CD8 + T cells, which control viral infections and are assumed to prevent the development of cancers. In this study, we tested if CD8 + T cell responses in aged mice could be enhanced through a vaccine that concomitantly expresses Ag and a molecule that blocks an immunoinhibitory pathway. Speciﬁcally, we tested a vaccine based on a replication-defective chimpanzee-derived adenovirus vector expressing the nucleoprotein (NP) of inﬂuenza A virus as a fusion protein with the HSV type 1 glycoprotein D, which through binding to the herpes virus entry mediator, blocks the immunoinhibitory herpes virus entry mediator B and T lymphocyte attenuator/CD160 pathways. Our results show that the vaccine expressing a fusion protein of NP and glycoprotein D induces signiﬁcantly higher NP-speciﬁc CD8 + T cell responses in young and aged mice compared with the vaccine expressing NP only. The Journal of Immunology , 2010, 184: 5475–5484.
CUL4B: a novel epigenetic driver in Wnt/β‐catenin‐dependent hepatocarcinogenesis

Emerging evidence indicates that Cullin 4B (CUL4B), a major component of ubiquitin ligase complexes, is over‐expressed in diverse cancer types with pro‐tumourigenic effects. In this issue of the Journal of Pathology, Yuan and colleagues [6] elucidated the oncogenic activity of CUL4B in hepatocellular carcinoma (HCC) and delineated its role in driving Wnt/β‐catenin signalling. In addition to the stabilization of β‐catenin protein against proteasomal degradation, CUL4B also acts in concert with enhancer of Zeste homologue 2 (EZH2) to concordantly silence multiple Wnt inhibitors. These findings provide significant mechanistic insights into the epigenetic activation of the Wnt/β‐catenin pathway in HCC and shed light on the functional importance of ubiquitination in this intricate regulatory system. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Mechanisms of paracrine cardioprotection by cord blood mesenchymal stromal cells.

OBJECTIVES Among the mechanisms by which somatic stem cells may improve left ventricular function in ischaemic heart disease are pro-survival stimuli mediated by secreted factors. This phenomenon is frequently referred to, but remains poorly understood. We therefore investigated the non-regenerative cardioprotective effects of cord blood mesenchymal stromal cells (CBMSCs) in vitro and sought to identify relevant intracellular signalling pathways. METHODS Conditioned medium from CBMSCs and fibroblasts was prepared, and secreted factors were analysed by Luminex(®) immunobead assay. Murine cardiomyocyte-derived HL-1 cells were subjected to simulated ischaemia by glucose and serum deprivation and hypoxia in CBMSC-conditioned or cell-free control medium or in medium conditioned by foreskin fibroblasts. The proportions of vital, apoptotic and necrotic cells (poly-caspase activity, annexin V and ethidium homodimer-III staining) were quantified using a high-content imaging system. Metabolic activity and proliferation rate were determined via 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium and 5-bromo-2-deoxyuridine assays. Phosphorylation of Akt, extracellular-signal-regulated kinase (ERK)1/2, signal transducer and activator of transcription 3 (STAT3) and glycogen synthase kinase 3β was determined by western blot, and experiments were repeated in the presence of specific small-molecule inhibitors (Wortmannin, UO126 and Stattic). RESULTS CBMSC medium reduced the proportion of dead HL-1 cardiomyocytes from 39 ± 3 to 28 ± 1% (P < 0.05) and the rate of late apoptotic cells to 68 ± 2% of that in control medium (P < 0.001). Metabolic activity was increased by 12 ± 1% compared with control (P < 0.05), while in fibroblast medium it was not (5 ± 2%, P = 1). This was associated with increased phosphorylation of Akt (2-fold, P < 0.05), ERK1/2 (3-fold, P < 0.01) and STAT3 (12-fold, P < 0.001). Combined blocking of the phosphatidylinositol-4,5-bisphosphate 3-kinase/Akt and mitogen-activated protein kinase/ERK signalling abolished the protective CBMSC effect, while blocking the pathways individually had no effect. Inhibition of STAT3 phosphorylation drastically lowered HL-1 cell viability in control medium, but not in medium conditioned by CBMSCs. CONCLUSIONS The factors released by CBMSCs protect cardiomyocyte-like HL-1 cells from simulated ischaemia more than those released from fibroblasts. While CBMSC-triggered Akt and ERK1/2 activation provides protection in a compensatory manner, STAT3 is crucial for cardiomyocyte survival in ischaemia, but is not a key mediator of cytoprotective stem cell actions.
Dental students' perceived barriers in geriatric dental care active involvement.

OBJECTIVES The present study assessed dental students' perceived barriers to geriatric dental care provision. METHODS Out of 512 dental students in Iranian dental schools were participated in the study 464 were completed the questionnaire. The mean age of the dental students was 25.5 ± 2.8 years; 67% were women. RESULTS Most of the participants (79%) did not have any training focused on geriatric dental care, and the vast majority (more than 83%) had no experience with geriatric dental care. The primary barriers to provide dental care to the elderly that dental student mentioned included insufficient knowledge of geriatric dental care and perceived lack of communication skills and self-confidence in managing elderly patients. CONCLUSION Increased emphasis on geriatric dental education in the undergraduate dental curriculums needed to minimize the barriers and improving dental students' willingness to serve older people.
Looking through glassfish: marine genetic structure in an estuarine species

Through the use of mitochondrial DNA (ATP8 gene), the prediction of intermediate genetic structuring was investigated in two species of estuarine glassfish (Ambassis marianus and Ambassis jacksoniensis) (Perciformes : Ambassidae) to determine the possibility of a generalised ‘estuarine’ genetic structure. Individuals were collected from estuaries in eastern Australia between Tin Can Bay (Queensland) in the north and Kempsey (New South Wales) in the south. Analysis of the haplotype frequencies found in this region suggested panmictic populations with star-like phylogenies with extremely high levels of genetic diversity, but with no correlation between geographic distance and genetic distance. Non-significant FST and ΦST suggested extensive dispersal among estuaries. However, Tajima’s D and Fu’s FS values suggest ‘mutation–genetic drift equilibrium’ has not been reached, and that population expansions occurring 262 000 (A. marianus) and 300 000 (A. jacksoniensis) years ago may obscure any phylogeographic structuring or isolation by distance. The finding of panmixia was contrary to the prediction of genetic structuring intermediate between that of marine fish (shallowly structured) and freshwater fish (highly structured), suggesting high dispersal capabilities in these species.
Mapping the Organization of Axis of Motion Selective Features in Human Area MT Using High-Field fMRI

Functional magnetic resonance imaging (fMRI) at high magnetic fields has made it possible to investigate the columnar organization of the human brain in vivo with high degrees of accuracy and sensitivity. Until now, these results have been limited to the organization principles of early visual cortex (V1). While the middle temporal area (MT) has been the first identified extra-striate visual area shown to exhibit a columnar organization in monkeys, evidence of MT's columnar response properties and topographic layout in humans has remained elusive. Research using various approaches suggests similar response properties as in monkeys but failed to provide direct evidence for direction or axis of motion selectivity in human area MT. By combining state of the art pulse sequence design, high spatial resolution in all three dimensions (0.8 mm isotropic), optimized coil design, ultrahigh field magnets (7 Tesla) and novel high resolution cortical grid sampling analysis tools, we provide the first direct evidence for large-scale axis of motion selective feature organization in human area MT closely matching predictions from topographic columnar-level simulations.
Morphogenesis of koi herpesvirus observed by electron microscopy.

Koi herpesvirus (KHV or cyprinid herpesvirus 3) was inoculated onto three fish cell lines derived from carp, Cyprinus carpio L. , and the process of virion formation observed with electron microscopy. Essentially, similar features of virus particles were observed in all three cell lines. The nucleus of infected cells was characterized by margination of chromatin and often contained many capsids of about 110 nm in diameter with varying morphology. The morphological variation of the capsids was very similar to that of mammalian herpesviruses. Some capsids protruded from the inner nuclear membrane, and others, with envelopes, were located in the perinuclear space between the inner and outer nuclear membrane, suggesting budding of capsids at the inner nuclear membrane. Naked capsids and envelopment of capsids by budding into vesicles were also observed in the cytoplasm. Mature, enveloped virions 170-200 nm in diameter were seen in cytoplasmic vesicles or outside the cell. These observations suggest KHV virions mature through a complex morphological pathway including two distinct envelopments, which have been found only in herpesviruses. These observations support the inclusion of KHV in the family Herpesviridae.
A step-up approach or open necrosectomy for necrotizing pancreatitis.

BACKGROUND Necrotizing pancreatitis with infected necrotic tissue is associated with a high rate of complications and death. Standard treatment is open necrosectomy. The outcome may be improved by a minimally invasive step-up approach. METHODS In this multicenter study, we randomly assigned 88 patients with necrotizing pancreatitis and suspected or confirmed infected necrotic tissue to undergo primary open necrosectomy or a step-up approach to treatment. The step-up approach consisted of percutaneous drainage followed, if necessary, by minimally invasive retroperitoneal necrosectomy. The primary end point was a composite of major complications (new-onset multiple-organ failure or multiple systemic complications, perforation of a visceral organ or enterocutaneous fistula, or bleeding) or death. RESULTS The primary end point occurred in 31 of 45 patients (69%) assigned to open necrosectomy and in 17 of 43 patients (40%) assigned to the step-up approach (risk ratio with the step-up approach, 0.57; 95% confidence interval, 0.38 to 0.87; P=0.006). Of the patients assigned to the step-up approach, 35% were treated with percutaneous drainage only. New-onset multiple-organ failure occurred less often in patients assigned to the step-up approach than in those assigned to open necrosectomy (12% vs. 40%, P=0.002). The rate of death did not differ significantly between groups (19% vs. 16%, P=0.70). Patients assigned to the step-up approach had a lower rate of incisional hernias (7% vs. 24%, P=0.03) and new-onset diabetes (16% vs. 38%, P=0.02). CONCLUSIONS A minimally invasive step-up approach, as compared with open necrosectomy, reduced the rate of the composite end point of major complications or death among patients with necrotizing pancreatitis and infected necrotic tissue. (Current Controlled Trials number, ISRCTN13975868.)
JHKL Photometry and the K-Band Luminosity Function at the Galactic Center

J, H, K, and L photometry for the stars in the central 2' (5 pc) of the Galaxy are presented. Using the observed J-H, H-K, and K-L colors and assumed intrinsic colors, we determine the interstellar extinction at 2.2 mic (A_K) for approximately 1100 individual stars. The mean A_K (= 3.3 mag) is similar to previous results, but we find that the reddening is highly variable and some stars are likely to be seen through A_K > 6 mag. The de-reddened K-band luminosity function points to a significantly brighter component to the stellar population (> 1.5 mag at K) than found in the stellar population in Baade's window, confirming previous work done at lower spatial resolution. The observed flux of all Galactic center stars with estimated Ko (de-reddened magnitude) </= 7.0 mag is approx 25 % of the total in the 2' X 2' field. Our observations confirm the recent finding that several bright M stars in the Galactic center are variable. Our photometry also establishes the near-infrared variability of the M1-2 supergiant, IRS 7.
Genome-Scale Analysis of the Uses of the Escherichia coli Genome: Model-Driven Analysis of Heterogeneous Data Sets

ABSTRACT The recent availability of heterogeneous high-throughput data types has increased the need for scalable in silico methods with which to integrate data related to the processes of regulation, protein synthesis, and metabolism. A sequence-based framework for modeling transcription and translation in prokaryotes has been established and has been extended to study the expression state of the entire Escherichia coli genome. The resulting in silico analysis of the expression state highlighted three facets of gene expression in E. coli: (i) the metabolic resources required for genome expression and protein synthesis were found to be relatively invariant under the conditions tested; (ii) effective promoter strengths were estimated at the genome scale by using global mRNA abundance and half-life data, revealing genes subject to regulation under the experimental conditions tested; and (iii) large-scale genome location-dependent expression patterns with approximately 600-kb periodicity were detected in the E. coli genome based on the 49 expression data sets analyzed. These results support the notion that a structured model-driven analysis of expression data yields additional information that can be subjected to commonly used statistical analyses. The integration of heterogeneous genome-scale data (i.e., sequence, expression data, and mRNA half-life data) is readily achieved in the context of an in silico model.
Software Unit Test Coverage and Adequacy HONG

Objective measurement of test quality is one of the key issues in software testing. It has been a major research focus for the last two decades. Many test criteria have been proposed and studied for this purpose. Various kinds of rationales have been presented in support of one criterion or another. We survey the research work in this area. The notion of adequacy criteria is examined together with its role in software dynamic testing. A review of criteria classification is followed by a summary of the methods for comparison and assessment of criteria.