Miracle-dz/UniFAR-FTUs huggingface dataset:
Congenital heart disease and cardiac surgery in childhood: effects on cognitive function and academic ability

OBJECTIVE To evaluate changes in cognitive and academic functioning following cardiac surgery in children with congenital heart disease. DESIGN A prospective cross sectional study in which patients were assessed immediately before treatment and 12 months later. PATIENTS Three groups of children aged 3.5–17 years: a group with congenital heart disease awaiting surgery, another awaiting bone marrow transplantation, and a healthy comparison group. MAIN OUTCOME MEASURES Intelligence quotient and measures of academic attainment, evaluated with the British Ability Scales. RESULTS Preoperatively, children with cyanotic lesions showed deficits in comparison with those with acyanotic lesions. Postoperatively, children with cyanotic lesions showed a deterioration in performance and achieved significantly lower scores than those with acyanotic lesions. While there were significant differences between the congenital heart disease and bone marrow transplantation groups preoperatively, these were no longer apparent at follow up. CONCLUSIONS In contrast to previously published findings, the present results suggest that cardiac surgery does not result in early postoperative improvements in cognitive function for children with congenital heart disease. The nature of the cardiac lesion continues to affect cognitive and academic performance, even after surgery.
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.
Social and Language Skills in Adolescent Boys with Asperger Syndrome

Twenty-one adolescent boys with Asperger syndrome and 21 boys matched on age and an estimate of IQ were assessed using standardized measures of social perception (Child and Adolescent Social Perception Measure, CASP), social skills (parent, teacher, and student forms of the Social Skills Rating System, SSRS), number of close friends and frequency of contact (Child Behavior Checklist) and expressive and receptive language (Clinical Evaluation of Language Fundamentals-Revised). There were significant differences between groups on CASP scores, SSRS scores, number of friends, frequency of contact and social competence. There was also a significant difference on receptive language. The clinically and statistically significant differences between the groups on the measures of social skills help us understand the nature of the social deficits in Asperger syndrome and suggest the need to focus on specific deficits. These findings are discussed in relation to diagnostic criteria and intervention.
Selection of nonfastidious adenovirus species in 293 cells inoculated with stool specimens containing adenovirus 40

Of 35 stool specimens isolated and examined in 293 cells, 15 isolates contained adenovirus species 40 (Ad40), and 4 of these 15 isolates also contained a nonfastidious adenovirus species (Ad1 in two cases, Ad18 or Ad31) which was selected over Ad40 during serial passage in the 293 cells. The selection of Ad1 over Ad40 was examined in detail. Restriction analysis of intracellular DNA and the relative infectivity titers of Ad40 and Ad1 at each passage level after the inoculation of 293 cells with a particular stool specimen demonstrated that although the amount of Ad40 DNA synthesized far exceeded that of Ad1, the relative infectivity titer of Ad40 was low. The growth characteristics of Ad40 were then compared with those of Ad1, Ad18, and Ad41 in singly infected 293 cell cultures. One-step growth curves showed the same growth rate in each case, with a latent period of 12 h and a maximum titer at 24 to 36 h postinfection. Yields of infectious Ad40 virus were consistently 100- to 1,000-fold lower than those of Ad1. This difference was reflected by a reduced yield of total AD40 virions (p1.34) as determined by 35S labeling experiments. However, the 3- to 10-fold reduction in total yield of Ad40 virions did not account for the 100- to 1,000-fold reduction in the yield of infectious virus.
Short Implant to Support Maxillary Restorations: Bone Stress Analysis Using Regular and Switching Platform

Purpose The aim of this study was to evaluate stress distribution on peri-implant bone simulating the influence of implants with different lengths on regular and switching platforms in the anterior maxilla by means of three-dimensional finite element analysis. Materials and Methods Four mathematical models of a central incisor supported by an external hexagon implant (diameter, 5.0 mm) were created, varying the length (15.0 mm for long implants [L] and 7.0 mm for short implants [S]) and the diameter of the abutment platform (5.0 mm for regular models [R] and 4.1 mm for switching models [S]). The models were created using the Mimics 11.11 (Materialise) and SolidWorks 2010 (Inovart) software. Numerical analysis was performed using ANSYS Workbench 10.0 (Swanson Analysis System). Oblique forces (100 N) were applied to the palatine surface of the central incisor. The bone/implant interface was considered perfectly integrated. Maximum (&sgr;max) and minimum (&sgr;min) principal stress values were obtained. Results For the cortical bone, the highest stress values (&sgr;max) were observed in the SR (73.7 MPa) followed by LR (65.1 MPa), SS (63.6 MPa), and LS (54.2 MPa). For the trabecular bone, the highest stress values (&sgr;max) were observed in the SS (8.87 MPa) followed by the SR (8.32 MPa), LR (7.49 MPa), and LS (7.08 MPa). Conclusions The influence of switching platform was more evident for the cortical bone in comparison with the trabecular bone for the short and long implants. The long implants showed lower stress values in comparison to the short implants, mainly when the switching platform was used.
Toxic anterior segment syndrome

Toxic anterior segment syndrome (TASS) is an acute postoperative sterile inflammatory reaction that occurs 12–48 h following uneventful cataract surgery. In the past this condition was known by many names, such as postoperative uveitis and sterile endophthalmitis. Even though the expression ‘toxic anterior segment inflammation’ was used by Monson et al in 1992,1 the term TASS has only become well-known over the last 8–10 years. The characteristic clinical features are diffuse limbus to limbus corneal oedema secondary to toxic damage to corneal endothelial cells, fibrin in the anterior chamber (most often with hypopyon) due to the breakdown of the blood–aqueous barrier, secondary glaucoma due to trabecular meshwork damage, and damage to the iris resulting in an irregular or dilated pupil. Sometimes the reaction is mainly limited to corneal endothelial cell damage, when it is termed toxic endothelial cell destruction. Typically such eyes respond to intensive steroid therapy and may recover well. However in severe cases, residual sequelae such as permanent corneal oedema and glaucoma can persist.2 Any discussion on TASS raises the following questions. 1. Is it …
Bi-Directional Exchange of Membrane Components Occurs during Co-Culture of Mesenchymal Stem Cells and Nucleus Pulposus Cells

Mesenchymal stem cell (MSC)-based therapies have been proposed as novel treatments for intervertebral disc (IVD) degeneration. We have previously demonstrated that when MSCs are co-cultured with nucleus pulposus (NP) cells with direct cell-cell contact, they differentiate along the NP lineage and simultaneously stimulate the degenerate NP cell population to regain a normal (non-degenerate) phenotype, an effect which requires cell-cell communication. However, the mechanisms by which NP cells and MSCs interact in this system are currently unclear. Thus, in this study we investigated a range of potential mechanisms for exchange of cellular components or information that may direct these changes, including cell fusion, gap-junctional communication and exchange of membrane components by direct transfer or via microvesicle formation. Flow cytometry of fluorescently labeled MSCs and NP cells revealed evidence of some cell fusion and formation of gapjunctions, although at the three timepoints studied these phenomena were detectable only in a small proportion of cells. While these mechanisms may play a role in cell-cell communication, the data suggests they are not the predominant mechanism of interaction. However, flow cytometry of fluorescently dual-labeled cells showed that extensive bi-directional transfer of membrane components is operational during direct co-culture of MSCs and NP cells. Furthermore, there was also evidence for secretion and internalization of membrane-bound microvesicles by both cell types. Thus, this study highlights bi-directional intercellular transfer of membrane components as a possible mechanism of cellular communication between MSC and NP cells.
Evaluating the efficiency of the association football transfer market using regression based player ratings

In recent times, the use of quantitative methods to improve decisions within sports has increased. In association football, large amounts of match data has become available. This work first shows how simple match data describing the players on pitch and the time for events such as goals and red cards, can be used to derive an objective player rating. The rating is based on solving a large linear regression model. The resulting player ratings are in turn used as input to a regression model for analyzing transfer fees. It is shown that the performance of players, as reflected in the player ratings, is an important predictor of transfer fees. At the same time, several other important factors that determine the size of transfer fees are identified.
Cross-sectional associations of resistin, coronary heart disease, and insulin resistance.

CONTEXT Recently, resistin was found to be present in atherosclerotic lesions in apoE(-/-) mice. Resistin may be associated with inflammation and atherosclerosis in humans; however, the role of resistin in human disease remains controversial. OBJECTIVE This study assesses cross-sectional relationships of resistin with coronary heart disease (CHD). DESIGN, SETTING, AND PARTICIPANTS Blood samples from the third examination of the Strong Heart Study (SHS)--the largest study of CHD in American Indians--were used. Cases who had suffered previous myocardial infarction (n = 100) were selected randomly from the three SHS sites and matched for study site and sex with controls who had no history of cardiovascular disease (CHD or stroke) (n = 100). MAIN OUTCOME MEASURE Resistin levels by enzyme-linked immunosorbent assay method in cases and controls was the main outcome measure. RESULTS Resistin levels were higher in cases than controls [median (interquartile range): 3.4 (2.5-4.7) vs. 2.8 (2.1-4.0) ng/ml; P = 0.003] and had univariate correlations with age (Spearman r = 0.21; P < 0.002), fasting insulin (r = 0.21; P = 0.003), insulin resistance by homeostasis model (r = 0.22; P = 0.04), albumin to creatinine ratio (r = 0.19; P = 0.01), and fibrinogen (r = 0.34; P < 0.0001). Cases were more likely to have diabetes (cases 67%; controls 41%; P < 0.0001) but had similar body mass index (cases 31.4 +/- 5.4; controls 30.7 +/- 6.3; P = 0.85). Resistin levels were higher in participants with established nephropathy (albumin to creatinine ratio >300 mg/g, n = 26) compared with those with normo- (n = 122) or microalbuminuria (n = 42). In multivariate analysis, nephropathy (P = 0.0013) but not previous myocardial infarction (P = 0.12) was significantly associated with resistin. CONCLUSIONS Resistin is not independently associated with CHD. Resistin is elevated in survivors of myocardial infarction; however, this reflects a novel association of raised resistin with diabetic nephropathy.
Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPARγ has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPARγ has been validated through two supporting biological assays.
Income and Physical Activity among Adults: Evidence from Self-Reported and Pedometer-Based Physical Activity Measurements

This study examined the relationship between income and physical activity by using three measures to illustrate daily physical activity: the self-reported physical activity index for leisure-time physical activity, pedometer-based total steps for overall daily physical activity, and pedometer-based aerobic steps that reflect continuous steps for more than 10 min at a time. The study population consisted of 753 adults from Finland (mean age 41.7 years; 64% women) who participated in 2011 in the follow-up of the ongoing Young Finns study. Ordinary least squares models were used to evaluate the associations between income and physical activity. The consistency of the results was explored by using register-based income information from Statistics Finland, employing the instrumental variable approach, and dividing the pedometer-based physical activity according to weekdays and weekend days. The results indicated that higher income was associated with higher self-reported physical activity for both genders. The results were robust to the inclusion of the control variables and the use of register-based income information. However, the pedometer-based results were gender-specific and depended on the measurement day (weekday vs. weekend day). In more detail, the association was positive for women and negative or non-existing for men. According to the measurement day, among women, income was positively associated with aerobic steps despite the measurement day and with totals steps measured on the weekend. Among men, income was negatively associated with aerobic steps measured on weekdays. The results indicate that there is an association between income and physical activity, but the association is gender-specific and depends on the measurement type of physical activity.
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

Various databases have harnessed the wealth of publicly available microarray data to address biological questions ranging from across-tissue differential expression to homologous gene expression. Despite their practical value, these databases rely on relative measures of expression and are unable to address the most fundamental question—which genes are expressed in a given cell type. The Gene Expression Barcode is the first database to provide reliable absolute measures of expression for most annotated genes for 131 human and 89 mouse tissue types, including diseased tissue. This is made possible by a novel algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results in a matter of seconds. The raw data, curated annotation, and code used to create our resource are also available at http://rafalab.jhsph. edu/barcode.
Quantitative photoacoustic imaging: fitting a model of light transport to the initial pressure distribution

Photoacoustic imaging, which generates a map of the initial acoustic pressure distribution generated by a short laser pulse, has been demonstrated by several authors. Quantitative photoacoustic imaging takes this one stage further to produce a map of the distribution of an optical property of the tissue, in this case absorption, which can then be related to a physiological parameter. In this technique, the initial pressure distribution is assumed to be proportional to the absorbed laser energy density. A model of light transport in scattering media is then used to estimate the distribution of optical properties that would result in such a pattern of absorbed energy. The light model used a finite element implementation of the diffusion equation (with the delta-E(3) approximation included to improve the accuracy at short distances inside the scattering medium). An algorithm which applies this model iteratively and converges on a quantitative estimate of the optical absorption distribution is described. 2D examples using simulated data (initial pressure maps) with and without noise are shown to converge quickly and accurately.
Rational normal scrolls and the defining equations of Rees algebras

Abstract Consider a height two ideal, I, which is minimally generated by m homogeneous forms of degree d in the polynomial ring R = k[x, y]. Suppose that one column in the homogeneous presenting matrix φ of I has entries of degree n and all of the other entries of φ are linear. We identify an explicit generating set for the ideal which defines the Rees algebra ℛ = R[It]; so for the polynomial ring S = R[T 1, . , Tm ]. We resolve ℛ as an S-module and Is as an R-module, for all powers s. The proof uses the homogeneous coordinate ring, A = S/H, of a rational normal scroll, with . The ideal is isomorphic to the n th symbolic power of a height one prime ideal K of A. The ideal K (n) is generated by monomials. Whenever possible, we study A/K (n) in place of because the generators of K (n) are much less complicated then the generators of . We obtain a filtration of K (n) in which the factors are polynomial rings, hypersurface rings, or modules resolved by generalized Eagon–Northcott complexes. The generators of I parameterize an algebraic curve in projective m – 1 space. The defining equations of the special fiber ring ℛ/(x, y)ℛ yield a solution of the implicitization problem for .
NF2/Merlin in hereditary neurofibromatosis 2 versus cancer: biologic mechanisms and clinical associations

Inactivating germline mutations in the tumor suppressor gene NF2 cause the hereditary syndrome neurofibromatosis 2, which is characterized by the development of neoplasms of the nervous system, most notably bilateral vestibular schwannoma. Somatic NF2 mutations have also been reported in a variety of cancers, but interestingly these mutations do not cause the same tumors that are common in hereditary neurofibromatosis 2, even though the same gene is involved and there is overlap in the site of mutations. This review highlights cancers in which somatic NF2 mutations have been found, the cell signaling pathways involving NF2/merlin, current clinical trials treating neurofibromatosis 2 patients, and preclinical findings that promise to lead to new targeted therapies for both cancers harboring NF2 mutations and neurofibromatosis 2 patients.
Circulatory Response to Laryngoscopy and Tracheal Intubation With or Without Prior Oropharyngeal Viscous Lidocaine

Oropharyngeal topical anesthesia with viscous lidocaine (25 ml of 2% as a “mouthwash and gargle” 10 min before laryngoscopy) attenuated the pressor but not heart rate (HR) response during laryngoscopy and tracheal intubation. Compared with control patients, mean arterial pressure (MAP) increased less in response to tracheal intubation (23 ± 5 torr versus 39 ± 4 torr, p <0.05) and returned toward awake levels sooner in patients receiving viscous lidocaine. MAP increased more than 40 torr in response to intubation in 6/20 patients treated with viscous lidocaine, while 12/20 control patients manifested this degree of blood pressure elevation. HR increased about 20 bpm (p< 0.05) with or without viscous lidocaine. Arterial lidocaine concentrations were less than 0.5 μg/ml after oropharyngeal anesthesia. Prior topical anesthesia of the oropharynx with viscous lidocaine should be considered when pressor responses during tracheal intubation would be particularly likely or hazardous.
An Efficient Mutual Authentication and Access Control Scheme for Wireless Sensor Networks in Healthcare

Wireless sensor networks (WSNs) will play an active role in the 21th Century Healthcare IT to reduce the healthcare cost and improve the quality of care. The protection of data confidentiality and patient privacy are the most critical requirements for the ubiquitous use of WSNs in healthcare environments. This requires a secure and lightweight user authentication and access control. Symmetric key - based access control is not suitable for WSNs in healthcare due to dynamic network topology, mobility, and stringent resource constraints. In this paper, we propose a secure, lightweight public key - based security scheme, Mutual Authentication and Access Control based on Elliptic curve cryptography (MAACE). MAACE is a mutual authentication protocol where a healthcare professional can authenticate to an accessed node (a PDA or medical sensor) and vice versa. This is to ensure that medical data is not exposed to an unauthorized person. On the other hand, it ensures that medical data sent to healthcare professionals did not originate from a malicious node. MAACE is more scalable and requires less memory compared to symmetric key-based schemes. Furthermore, it is much more lightweight than other public key-based schemes. Security analysis and performance evaluation results are presented and compared to existing schemes to show advantages of the proposed scheme.