Miracle-dz/UniFAR-FTUs huggingface dataset:
Knowledge discovery in spatial databases: the PADRÃO’s qualitative approach

Knowledge discovery in databases is a complex process concerned with the discovery of relationships and other descriptions from data. Knowledge discovery in spatial databases represents a particular case of discovery, allowing the discovery of relationships that exist between spatial and non-spatial data, and other data characteristics that aren’t explicitly stored in spatial databases. This paper describes the conception and implementation of PADRÃO, a system for knowledge discovery in spatial databases. PADRÃO presents a new approach to this process, which is based on qualitative spatial reasoning. The spatial semantic knowledge and the principles of qualitative spatial reasoning needed for the spatial reasoning process are available in the PADRÃO’s geographic database and PADRÃO’s spatial knowledge base, allowing the integration of the geo-spatial component, associated with the analysed non-geographic data, in the process of knowledge discovery. Maribel Santos, Luís Amaral Information Systems Department and Algoritmi Research Centre University of Minho, Campus de Azurém 4800-019 Guimarães, PORTUGAL Telf. :+351 253 510259 Fax:+351 253 510250 e-mail: maribel@dsi.uminho. pt, amaral@dsi.uminho. pt
The Clinical Outcomes of Antimicrobial Therapy in Pediatric Patients With Nontyphoid Salmonellosis With Different Levels of Severity

Background. To evaluate if a severity score could differentiate the severity of children with nontyphoid salmonellosis; clinical outcomes of antimicrobial therapy in nontyphoid salmonellosis children with different severities. Methods. Admitted children with nontyphoid salmonellosis from 1996 to 2009 were monitored. Enrolled patients were divided into no antibiotics, concordant, and discordant therapies. Besides, the patients were classified into mild, moderate, and severe group according to the severity score. Clinical outcomes were compared among them. Results. A total of 558 patients were enrolled. In no therapy subset, compared with mild group, patients had worse clinical outcomes and more complications in severe group. Patients receiving no therapy had better clinical outcomes in mild group. However, patients receiving concordant therapy (ceftriaxone) had better clinical outcomes in severe group. Conclusions. The severity score and local antibiotic susceptibility could serve as guides for antibiotic prescription for severe nontyphoid salmonellosis in children. Inappropriate antibiotic use would worsen clinical outcomes in children with mild nontyphoid salmonellosis.
The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

ABSTRACT The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA− mutant is unable to grow under photosynthetic conditions, when a ppsR mutation was present, photosynthetic growth occurred. An examination of the double mutant under anaerobic-dark-dimethyl sulfoxide conditions using microarray analysis revealed the existence of an “extended” PpsR regulon and new physiological roles. To characterize the PpsR regulon and to better ascertain the significance of degeneracy within the PpsR binding sequence in vivo, we adapted the chromatin immunoprecipitation technique to R. sphaeroides. We demonstrated that in vivo there was direct and significant binding by PpsR to newly identified genes involved in microaerobic respiration and periplasmic stress resistance, as well as to photosynthesis genes. The new members of the PpsR regulon are located outside the photosynthesis gene cluster and have degenerate PpsR binding sequences. The possible interaction under physiologic conditions with degenerate binding sequences in the presence of other biologically relevant molecules is discussed with respect to its importance in physiological processes and to the existence of complex phenotypes associated with regulatory mutants. This study further defines the DNA structure necessary for PpsR binding in situ.
Phenotypic and functional characterization of Bst+/− mouse retina

ABSTRACT The belly spot and tail (Bst+/−) mouse phenotype is caused by mutations of the ribosomal protein L24 (Rpl24). Among various phenotypes in Bst+/− mice, the most interesting are its retinal abnormalities, consisting of delayed closure of choroid fissures, decreased ganglion cells and subretinal vascularization. We further characterized the Bst+/− mouse and investigated the underlying molecular mechanisms to assess the feasibility of using this strain as a model for stem cell therapy of retinal degenerative diseases due to retinal ganglion cell (RGC) loss. We found that, although RGCs are significantly reduced in retinal ganglion cell layer in Bst+/− mouse, melanopsin+ RGCs, also called ipRGCs, appear to be unchanged. Pupillary light reflex was completely absent in Bst+/− mice but they had a normal circadian rhythm. In order to examine the pathological abnormalities in Bst+/− mice, we performed electron microscopy in RGC and found that mitochondria morphology was deformed, having irregular borders and lacking cristae. The complex activities of the mitochondrial electron transport chain were significantly decreased. Finally, for subretinal vascularization, we also found that angiogenesis is delayed in Bst+/− associated with delayed hyaloid regression. Characterization of Bst+/− retina suggests that the Bst+/− mouse strain could be a useful murine model. It might be used to explore further the pathogenesis and strategy of treatment of retinal degenerative diseases by employing stem cell technology. Summary: We characterized Bst+/− mice and found that pupillary light reflex was completely absent, which could be used as a readout for the efficacy of stem cell therapy in this model.
A Bayesian Generative Model for Surface Template Estimation

3D surfaces are important geometric models for many objects of interest in image analysis and Computational Anatomy. In this paper, we describe a Bayesian inference scheme for estimating a template surface from a set of observed surface data. In order to achieve this, we use the geodesic shooting approach to construct a statistical model for the generation and the observations of random surfaces. We develop a mode approximation EM algorithm to infer the maximum a posteriori estimation of initial momentum μ, which determines the template surface. Experimental results of caudate, thalamus, and hippocampus data are presented.
A framework for the identification of full-field structural dynamics using sequences of images in the presence of non-ideal operating conditions

Recent developments in the ability to automatically and efficiently extract natural frequencies, damping ratios, and full-field mode shapes from video of vibrating structures has great potential for reducing the resources and time required for performing experimental and operational modal analysis at very high spatial resolution. Furthermore, these techniques have the added advantage that they can be implemented remotely and in a non-contact fashion. Emerging full-field imaging techniques therefore have potential to allow the identification of the modal properties of structures in regimes that used to be challenging. For instance, these techniques suggest that the high spatial resolution structural identification could be performed on an aircraft during flight using a ground or aircraft-based imager. They also have the potential to identify the dynamics of microscopic systems. In order to realize this capability it will be necessary to develop techniques that can extract full-field structural dynamics in the presence of non-ideal operating conditions. In this work, we develop a framework for the deployment of emerging algorithms that allow the automatic extraction of high-resolution, full-field modal parameters in the presence of non-ideal operating conditions. One of the most notable non-ideal operating conditions is the rigid body motion of both the structure being measured as well as the imager performing the measurement. We demonstrate an instantiation of the framework by showing how it can be used to address, in-plane, translational, rigid body motion. The development of a frame-to-frame keypoint–based technique for identifying full-field structural dynamics in the presence of either rigid body motion is presented and demonstrated in the context of the framework for the deployment of full-field structural identification techniques in the presence of non-ideal operating conditions. It is expected that this framework will ultimately help enable the collection of full-field structural dynamics using measurement platforms including unmanned aerial vehicles, robotic telescopes, satellites, imagers mounted in high-vibration environments (seismic, industrial, harsh weather), characterization of microscopic structures, and human-carried imagers. If imager-based structural identification techniques mature to the point that they can be used in non-ideal field conditions, it could open up the possibility that the structural health monitoring community will be able to think beyond monitoring individual structures, to full-field structural integrity monitoring at the city scale.
Increased breast cancer risk at high plasma folate concentrations among women with the MTHFR 677T allele.

BACKGROUND Folate is involved in DNA synthesis and methylation and may thereby influence carcinogenesis. OBJECTIVES We examined plasma folate (P-folate) concentration in relation to genotypes of the folate-metabolizing enzyme methylenetetrahydrofolate reductase [MTHFR 677C-->T (rs1801133) and 1298A-->C (rs1801131)]. We also explored whether P-folate was associated with risk of postmenopausal breast cancer overall and in subgroups with genetic variants of the MTHFR single nucleotide polymorphisms (SNPs). DESIGN This nested case-control study included 313 cases (age 55-73 y at baseline) with invasive breast cancer and 626 control subjects, matched on age and blood-sample date, from the population-based Malmö Diet and Cancer cohort. P-folate and MTHFR genotypes were determined for 310 cases and 611 controls. P-folate according to genotype was calculated by using analysis of variance. Odds ratios were obtained by using logistic regression. All tests were 2-sided. RESULTS The variant 677T allele was associated with lower P-folate. In women with the 677T allele, a high P-folate concentration was associated with increased breast cancer risk (P for trend across P-folate tertiles = 0.03). Interaction was seen between the 677C-->T SNP and P-folate (P = 0.002). A positive association, which was seen between P-folate and breast cancer risk in 1298AA women (P = 0.01), was probably due to linkage between the 2 SNPs. Overall, and in women with other genotypes, no significant associations were observed. CONCLUSIONS Our results suggest an association of high P-folate concentration with increased risk of postmenopausal breast cancer in carriers of the 677T allele. The findings underline the importance of genetic variation of MTHFR in the complex relation between folate and cancer.
Open-angle glaucoma.

significance. It seems absurd to think of two separate diseases occurring in those patients with classical low tension glaucoma in one eye and overt glaucoma in the other. It seerrms unreasonable to find family histories of classical open-angle glaucoma (with high pressures) in patients showing typical low tension glaucoma unless a single disease is involved. It seems unreasonable to label a patient as having glaucoma when he has had low tension glaucoma for years, just because he later develops a small rise in intraocular pressure or an "abnormal" outflow facility. Chronic simple glaucoma and low tension glaucoma are much more likely to be manifestations of a disease process in which many factors assume varying importance in interfering with perfusion of the optic nerve head. A clearer recognition and understanding of the factors concerned in producing low tension glaucoma--some of which have been identified-and the significance of intraocular pressure as an important but by no means the only factor leading to ischaemia of the optic nerve head, may help to answer some of the enigmas of chronic simple glaucoma itself.
Asian Spine Journal Asian Spine Journal Low Back Pain: Current Surgical Approaches

which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Low back pain (LBP) is a worldwide phenomenon. The UK studies place LBP as the largest single cause of absence from work; up to 80% of the population will experience LBP at least once in their lifetime. Most individuals do not seek medical care and are not disabled by their pain once it is managed by nonoperative measures. However, around 10% of patients go on to develop chronic pain. This review outlines the basics of the traditional approach to spinal surgery for chronic LBP secondary to osteoarthritis of the lumbar spine as well as explains the novel concepts and terminology of back pain surgery. Traditionally, the stepwise approach to surgery starts with local anaesthetic and steroid injection followed by spinal fusion. Fusion aims to alleviate pain by preventing movement between affected spinal segments; this commonly involves open surgery, which requires large soft tissue dissection and there is a possibility of blood loss and prolonged recovery time. Established minimally invasive spine surgery techniques (MISS) aim to reduce all of these complications and they include laparoscopic anterior lumbar interbody fusion and MISS posterior instrumentation with pedicle screws and rods. Newer MISS techniques include extreme lateral interbody fusion and axial interbody fusion. The main problem of fusion is the disruption of the biomechanics of the rest of the spine; leading to adjacent level disease. Theoretically, this can be prevented by performing motion-preserving surgeries such as total disc replacement, facet arthroplasty, and non fusion stabilisation. We outline the basic concepts of the procedures mentioned above as well as explore some of the novel surgical therapies available for chronic LBP.
What Psychiatry Means to Me

Moving in early career from public health physician to psychiatrist gives me a public health view of psychiatry and an interest in pursuing the goals of widening access to community-based services for people with mental disorders and promoting mental health in communities. Training in social medicine in the UK and psychiatry in Australia lead to studies of homelessness in people living with psychotic disorders, the health of family caregivers, assessing quality of life and mental health promotion. Work with the World Health Organization (WHO) in the Western Pacific Region and the World Psychiatric Association (WPA) worldwide has given me opportunities to work with psychiatrists, mental health workers, service users and others in governments and non-government organisations implementing the recommendations of the World Health Report 2001 in countries with limited resources. My work as WPA Secretary for Publications seeks to improve information exchange in countries irrespective of their wealth. This is an exciting time to be working in a global village with technical capacity to reach into its furthest corners. Psychiatrists supported by WPA can help ensure that vulnerable people and communities and people living with mental disorders are well served in this new environment and no longer left out and left behind.
PlatinumCNV: A Bayesian Gaussian mixture model for genotyping copy number polymorphisms using SNP array signal intensity data

We present a statistical model for allele‐specific patterns of copy number polymorphisms (CNPs) in commercial single nucleotide polymorphism (SNP) array data. This model is based on the observation that fluorescent signal intensities tend to cluster into clouds of similar allele‐specific copy number (ASCN) genotypes at each SNP locus. To capture the tendency of this clustering to be made vague by instrumental errors, our model allows for cluster memberships to overlap each other, according to a Bayesian Gaussian mixture model (GMM). This approach is flexible, allowing for both absolute scale differences and X/Y scale imbalances of fluorescent signal intensities. The resulting model is also robust toward unobserved ASCN genotypes, which can be problematic for ordinary GMMs. We illustrated the utility of the model by applying it to commercial SNP array intensity data obtained from the Illumina HumanHap 610K platform. We retrieved more than 4,000 allele‐specific CNPs, though 99% of them showed rather simple allele‐specific CNP patterns with only a single aneuploid haplotype among the normal haplotypes. The genotyping accuracy was assessed by two approaches, quantitative PCR and replicated subjects. The results of both of these approaches demonstrated mean genotyping error rates of 1%. We demonstrated a preliminary genome‐wide association study of three hematological traits. The result exhibited that it could form the foundation for new, more effective statistical methods for the mapping of both disease genes and quantitative trait loci with genome‐wide CNPs. The methods described in this work are implemented in a software package, PlatinumCNV, available on the Internet. Genet. Epidemiol. 35:831–844, 2011. © 2011 Wiley Periodicals, Inc.
New Prebiotic Blend of Polydextrose and Galacto-oligosaccharides Has a Bifidogenic Effect in Young Infants

Objective: The aim of the study was to evaluate the effect of infant formula with polydextrose (PDX) and galacto-oligosaccharides (GOS) on fecal microbiota and secretory IgA (sIgA). Materials and Methods: In the present double-blind, randomized study, term infants received control (Enfamil Lipil) or the same formula with PDX/GOS (4 g/L, 1:1 ratio; PDX/GOS) for 60 days; a reference breast-fed group was included. Formula intake, tolerance, and stool characteristics were collected via electronic diary and analyzed by repeated measures analysis of variance. Anthropometric measurements and stool samples were obtained at baseline and after 30 and 60 days of feeding. Fecal sIgA was measured by enzyme-linked immunosorbent assay and fecal bacteria by fluorescent in situ hybridization and quantitative real-time polymerase chain reaction (qPCR); both were analyzed by Wilcoxon rank sum test. Results: Two hundred thirty infants completed the study. Infants consuming PDX/GOS had softer stools than control at all times (P < 0.001). Using qPCR, counts in PDX/GOS were closer to the breast-fed group, tended to be higher than control for total bifidobacteria (P = 0.069) and Bifidobacterium longum (P = 0.057) at 30 days, and were significantly higher for total bifidobacteria and B longum at 60 days and B infantis at 30 days (P = 0.002). No significant differences were detected between PDX/GOS and control in changes from baseline to 30 or 60 days for sIgA or total bifidobacteria by fluorescent in situ hybridization or qPCR; however, significantly higher changes from baseline were detected between PDX/GOS and control for B infantis at 30 days and B longum at 60 days (P ⩽ 0.035). Conclusions: Infant formula with PDX/GOS produces soft stools and a bifidogenic effect closer to breast milk than formula without PDX/GOS.
Identification of New Dystroglycan Complexes in Skeletal Muscle

The dystroglycan complex contains the transmembrane protein β-dystroglycan and its interacting extracellular mucin-like protein α-dystroglycan. In skeletal muscle fibers, the dystroglycan complex plays an important structural role by linking the cytoskeletal protein dystrophin to laminin in the extracellular matrix. Mutations that affect any of the proteins involved in this structural axis lead to myofiber degeneration and are associated with muscular dystrophies and congenital myopathies. Because loss of dystrophin in Duchenne muscular dystrophy (DMD) leads to an almost complete loss of dystroglycan complexes at the myofiber membrane, it is generally assumed that the vast majority of dystroglycan complexes within skeletal muscle fibers interact with dystrophin. The residual dystroglycan present in dystrophin-deficient muscle is thought to be preserved by utrophin, a structural homolog of dystrophin that is up-regulated in dystrophic muscles. However, we found that dystroglycan complexes are still present at the myofiber membrane in the absence of both dystrophin and utrophin. Our data show that only a minority of dystroglycan complexes associate with dystrophin in wild type muscle. Furthermore, we provide evidence for at least three separate pools of dystroglycan complexes within myofibers that differ in composition and are differentially affected by loss of dystrophin. Our findings indicate a more complex role of dystroglycan in muscle than currently recognized and may help explain differences in disease pathology and severity among myopathies linked to mutations in DAPC members.
A HLA based simulator architecture for co-simulating ICT based power system control and protection systems

Power systems and especially Smart Grids increasingly apply Information and Communication Technologies (ICT) for exchanging information over wide area networks. Here, the performance of the ICT has become crucial for the development of new Wide Area Monitoring, Protection And Control (WAMPAC) [1] systems. In this context, simulations are a common way for evaluation, but power systems and communication networks are usually analysed with dedicated simulators. Therefore a combined simulation for analysing the dynamics and mutual impacts of both domains is needed. In this paper we present a generic hybrid simulation architecture based on the IEEE standard 1516 - High Level Architecture [2] to enable a combined simulation of power systems and communication networks in an integrated simulation environment. First, we introduce our hybrid simulator architecture, along with the communication and synchronization process between sub-simulators. Secondly, we present our communication networks architecture for modelling the network traffic caused by the information transmitted by control and protection algorithms within the electrical transmission system. Finally, we introduce our modelling approach for mapping entities between the power systems and the communication networks. For this purpose, we introduce our concept of a Substation Data Processing Unit, which represents entities on substation level by providing an IEC 61850 [3] based model for mapping logical functions for local process control, implementing decentralized protection and control algorithms and providing additional components for the power systems (e.g Phasor Measurement Units (PMUs) [4]).