Miracle-dz/UniFAR-FTUs huggingface dataset:
CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

ABSTRACT In ecological studies, microbial diversity is nowadays mostly assessed via the detection of phylogenetic marker genes, such as 16S rRNA. However, PCR amplification of these marker genes produces a significant amount of artificial sequences, often referred to as chimeras. Different algorithms have been developed to remove these chimeras, but efforts to combine different methodologies are limited. Therefore, two machine learning classifiers (reference-based and de novo CATCh) were developed by integrating the output of existing chimera detection tools into a new, more powerful method. When comparing our classifiers with existing tools in either the reference-based or de novo mode, a higher performance of our ensemble method was observed on a wide range of sequencing data, including simulated, 454 pyrosequencing, and Illumina MiSeq data sets. Since our algorithm combines the advantages of different individual chimera detection tools, our approach produces more robust results when challenged with chimeric sequences having a low parent divergence, short length of the chimeric range, and various numbers of parents. Additionally, it could be shown that integrating CATCh in the preprocessing pipeline has a beneficial effect on the quality of the clustering in operational taxonomic units.
Cortical Porosity Identifies Women With Osteopenia at Increased Risk for Forearm Fractures

Most fragility fractures arise among the many women with osteopenia, not the smaller number with osteoporosis at high risk for fracture. Thus, most women at risk for fracture assessed only by measuring areal bone mineral density (aBMD) will remain untreated. We measured cortical porosity and trabecular bone volume/total volume (BV/TV) of the ultradistal radius (UDR) using high‐resolution peripheral quantitative computed tomography, aBMD using densitometry, and 10‐year fracture probability using the country‐specific fracture risk assessment tool (FRAX) in 68 postmenopausal women with forearm fractures and 70 age‐matched community controls in Olmsted County, MN, USA. Women with forearm fractures had 0.4 standard deviations (SD) higher cortical porosity and 0.6 SD lower trabecular BV/TV. Compact‐appearing cortical porosity predicted fracture independent of aBMD; odds ratio (OR) = 1.92 (95% confidence interval [CI] 1.10–3.33). In women with osteoporosis at the UDR, cortical porosity did not distinguish those with fractures from those without because high porosity was present in 92% and 86% of each group, respectively. By contrast, in women with osteopenia at the UDR, high porosity of the compact‐appearing cortex conferred an OR for fracture of 4.00 (95% CI 1.15–13.90). In women with osteoporosis, porosity is captured by aBMD, so measuring UDR cortical porosity does not improve diagnostic sensitivity. However, in women with osteopenia, cortical porosity was associated with forearm fractures. © 2014 American Society for Bone and Mineral Research.
How many regional business cycles are there in Spain?: a MS-VAR approach

Este trabajo aplica una moderna aproximacion al analisis de los ciclos economicos, con el objetivo de capturar los hechos estilizados de las diecisiete regiones espanolas y determinar el numero de ciclos existentes. En primer lugar, se aplica un modelo Markov-switching autorregresivo (MS-AR) para estudiar el comportamiento del indice de produccion industrial en cada una de las regiones. Tomando como base estos resultados, obtenemos una clasificacion de los ciclos regionales en tres grupos, el primero es el mas grande -agrupa a diez regiones- y otros dos, que presentan comportamientos mas extremos. Los resultados obtenidos de la aplicacion de un modelo Markov-switching vectorial autorregresivo (MS-VAR) sobre estos tres grupos confirman la existencia de tres ciclos en el pais, que contribuyen a formar el ciclo espanol. Nuestros resultados dejan abierta la posibilidad de utilizar el ciclo economico de algunas regiones -en concreto, las mas representativas o avanzadas- para predecir la actividad economica a nivel nacional, a la vez que previenen contra la puesta en funcionamiento de politicas comunes regionales. Por tanto, la identificacion de los diferentes ciclos economicos en Espana es necesaria para disenar politicas economicas adecuadas para cada region o cluster de regiones.
Enamel matrix derivative: a review of cellular effects in vitro and a model of molecular arrangement and functioning.

BACKGROUND Enamel matrix derivative (EMD), the active component of Emdogain®, is a viable option in the treatment of periodontal disease owing to its ability to regenerate lost tissue. It is believed to mimic odontogenesis, though the details of its functioning remain the focus of current research. OBJECTIVE The aim of this article is to review all relevant literature reporting on the composition/characterization of EMD as well as the effects of EMD, and its components amelogenin and ameloblastin, on the behavior of various cell types in vitro. In this way, insight into the underlying mechanism of regeneration will be garnered and utilized to propose a model for the molecular arrangement and functioning of EMD. METHODS A review of in vitro studies of EMD, or components of EMD, was performed using key words "enamel matrix proteins" OR "EMD" OR "Emdogain" OR "amelogenin" OR "ameloblastin" OR "sheath proteins" AND "cells. " Results of this analysis, together with current knowledge on the molecular composition of EMD and the structure and regulation of its components, are then used to present a model of EMD functioning. RESULTS Characterization of the molecular composition of EMD confirmed that amelogenin proteins, including their enzymatically cleaved and alternatively spliced fragments, dominate the protein complex (>90%). A small presence of ameloblastin has also been reported. Analysis of the effects of EMD indicated that gene expression, protein production, proliferation, and differentiation of various cell types are affected and often enhanced by EMD, particularly for periodontal ligament and osteoblastic cell types. EMD also stimulated angiogenesis. In contrast, EMD had a cytostatic effect on epithelial cells. Full-length amelogenin elicited similar effects to EMD, though to a lesser extent. Both the leucine-rich amelogenin peptide and the ameloblastin peptides demonstrated osteogenic effects. A model for molecular structure and functioning of EMD involving nanosphere formation, aggregation, and dissolution is presented. CONCLUSIONS EMD elicits a regenerative response in periodontal tissues that is only partly replicated by amelogenin or ameloblastin components. A synergistic effect among the various proteins and with the cells, as well as a temporal effect, may prove important aspects of the EMD response in vivo.
A comparison of the performance of the EQ-5D and SF-6D for individuals aged > 45 years

We sought to compare the performance of the EQ-5D and SF-6D with regard to the criteria of practicality, convergent validity, and construct validity, the level of agreement between the two measures was also assessed. Responses from 1865 individuals aged > 45 years in one general practice were analysed. Of these, 93.1% completed the EQ-5D, compared with 86.4% for the SF-6D, where individuals who were older, female, of a lower occupational skill level, from an area of lower deprivation, or used prescribed medication were significantly less likely to complete the SF-6D. The performance of both measures was comparable with regard to both convergent and construct validities, as both the EQ-5D and SF-6D scores were closely related to scores on the EuroQol visual analogue scale (VAS) (p
Breast self-examination: self-reported frequency, quality, and associated outcomes.

BACKGROUND There is little information on the quality of breast self-examination (BSE) and associated outcomes. METHOD We conducted a retrospective cohort study of 27,421 women enrolled in a Pacific Northwest health plan. We linked responses regarding BSE quality from a questionnaire to subsequent screening and diagnostic efforts. RESULTS A total of 75% of the women performed BSE. We rated BSE quality as adequate in 27%. Women who reported higher BSE duration, frequency, and quality were more likely to have diagnostic mammograms. Participants ultimately diagnosed with breast cancer (N = 300) were significantly less likely to report performing BSE. Tumor size and stage were not associated with BSE behavior. CONCLUSION A high proportion of women perform BSE, but few do so adequately. We found no evidence for benefit of BSE. It is time to ask whether systematic BSE performance should continue to be encouraged.
Relationships between dendritic morphology and cytochrome oxidase compartments in monkey striate cortex

In primate striate cortex, staining for the mitochondrial enzyme cytochrome oxidase reveals a regular pattern of intense staining, the blobs, which are surrounded by the lighter stained interblob regions. Neurons in both compartments exhibit profound functional differences: blob cells have color selective, unoriented receptive fields, whereas interblob cells are usually not color selective and have oriented receptive fields, Neuroanatomical tracing studies have shown that blob and interblob cells receive different inputs and participate in different projections. It is not known, however, whether this compartmental organization is also reflected in the dendritic morphology of individual cells. We therefore combined intracellular staining with cytochrome oxidase histochemistry to study the relationship between cell morphology and blob pattern in layers 2 and 3 of macaque striate cortex. Single cells were injected with the fluorescent dye lucifer yellow in lightly fixed tangential sections. Adjacent sections were reacted for cytochrome oxidase to reveal the blobs. The spatial relationship between stained cells and the pattern of the blobs were subsequently determined by aligning the sections by using radially running blood vessels as landmarks.
CagA in Barrett’s oesophagus in Colombia, a country with a high prevalence of gastric cancer

Background: In the USA, atrophic gastritis and gastric cancer are rare, whereas gastro-oesophageal reflux disease (GERD) is common. Infection with Helicobacter pylori, especially a CagA positive strain, is unusual in patients with GERD/Barrett’s oesophagus in the USA. Aim: To examine the relation between Barrett’s oesophagus and CagA positive H pylori in Colombia, a country with a high prevalence of CagA positive H pylori associated atrophic gastritis and gastric cancer. Methods:Helicobacter pylori and CagA status was determined among Colombian patients with long segment Barrett’s oesophagus and a control group with simple H pylori gastritis. Helicobacter pylori status was determined using a triple stain and CagA status was determined by immunohistochemistry using a specific rabbit anti-CagA serum. Results: Gastric and oesophageal mucosal biopsies were obtained from 51 patients—39 men (mean age, 57.8 years; SD, 13.1) and 12 women (mean age, 51.8 years; SD, 14.4)—with documented long segment Barrett’s oesophagus. The results were compared with 24 Colombian patients with H pylori gastritis without oesophageal disease. Thirty two patients with Barrett’s oesophagus had active H pylori infection. CagA status was evaluated in a subset of 23 H pylori infected patients with Barrett’s oesophagus, and was positive in eight of these patients compared with 19 of 24 controls (p = 0.01). Conclusions: Although most Colombian patients with Barrett’s oesophagus had H pylori infection, CagA positive infections were unusual. These data illustrate how consistent corpus inflammation reduces acid secretion, which prevents Barrett’s oesophagus among those with abnormal gastro-oesophageal reflux barriers.
Regional odontodysplasia: report of a case in the mandible crossing the midline.

AIM This report presents an unusual case of regional odontodysplasia (RO) in the mandible which crosses the midline along with its clinical management. BACKGROUND RO is an uncommon, nonhereditary unilateral developmental anomaly involving the dental hard tissues, most frequently affecting the maxillary teeth. REPORT RO was diagnosed in a 12-year-old. The dysplastic teeth were the mandibular canines, lateral incisors, central incisors, and the right premolars. The treatment was extraction of the affected teeth followed by provisory prosthetic rehabilitation. SUMMARY The etiology of RO remains obscure. In this case a possible association with pre-natal trauma is suspected. The literature is not unanimous as to the management of RO. Nevertheless, the presence of a dental abscess is an indication for extraction. Since general bone quality is not affected, a provisory prosthesis was fabricated as the patient waits for future implant rehabilitation. The executed treatment met the expectations of the patient and her mother as it improved the patient's masticatory function, esthetics, and quality of life. CLINICAL SIGNIFICANCE The general practitioner must be prepared to deal with different situations in the dental office. The diagnosis of RO relies mainly on clinical and radiographic findings, and its treatment depends on the affected teeth, the severity of the dysplasia, the presence of infection, and the patient's age.
Lived Experiences of Adolescent Athletes Following Sport-Related Concussion

Background: Previous studies have identified the effect of sport-related concussion on health-related quality of life through the use of patient-reported outcome measures. However, there has been little research exploring the underlying mechanisms that influence these perceptions of health-related quality of life among adolescent athletes who have sustained a sport-related concussion. Purpose: To explore the psychosocial aspects of concussion among adolescent athletes. Study Design: Case series; Level of evidence, 4. Methods: A total of 12 interscholastic athletes (4 girls, 8 boys; mean ± SD age, 15.7 ± 1.7 years; grade level, 10.2 ± 1.4) were interviewed via a semistructured interview protocol between 15 and 30 days postinjury. Data analysis was guided by the consensual qualitative research tradition. Themes and categories emerged through consensus by a 3-person research team, and bias was minimized through the use of multiple-analyst triangulation. Results: Participants identified numerous postconcussion symptoms that resulted in increasing difficulty with emotions (eg, irritable, easily frustrated), roles at school (eg, concentration difficulties, fatigue), and roles in their social environment (eg, letting the team down, not being able to contribute to sport). As a result, participants expressed how they tried to minimize or mask symptoms to decrease the potential of being viewed differently by their peers. Conclusion: Adolescent athletes perceived a significant effect of sport-related concussion on numerous areas of psychosocial and emotional health and well-being. Anticipatory guidance—with education regarding the possible signs and symptoms, risk factors, and recovery expectations following a concussion—is important to include in postinjury management. A better understanding of sport-related concussion and expected recovery could help to improve perceptions of this injury among interscholastic athletes. Additionally, best practices should be identified to assist health care professionals and school personnel in the development of temporary adjustments or formal academic adjustment policies in the secondary school setting, therefore ensuring that the patients receive the support that they need to maintain their roles as students.
Interaction Between Fluids and Vasoactive Agents on Mortality in Septic Shock: A Multicenter, Observational Study*

Objective:Fluids and vasoactive agents are both used to treat septic shock, but little is known about how they interact or the optimal way to administer them. We sought to determine how hospital mortality was influenced by combined use of these two treatments. Design:Retrospective evaluation using multivariable logistic regression to evaluate the association between hospital mortality and categorical variables representing initiation of vasoactive agents and volumes of IV fluids given 0–1, 1–6, and 6–24 hours after onset, including interactions and adjusting for potential confounders. Setting:ICUs of 24 hospitals in 3 countries. Patients:Two thousand eight hundred forty-nine patients who survived more than 24 hours after after onset of septic shock, admitted between 1989 and 2007. Interventions:None. Measurements and Main Results:Fluids and vasoactive agents had strong, interacting associations with mortality (p < 0.0001). Mortality was lowest when vasoactive agents were begun 1–6 hours after onset, with more than 1 L of fluids in the initial hour after shock onset, more than 2.4 L from hours 1–6, and 1.6–3.5 L from 6 to 24 hours. The lowest mortality rates were associated with starting vasoactive agents 1–6 hours after onset. Conclusions:The focus during the first hour of resuscitation for septic shock should be aggressive fluid administration, only thereafter starting vasoactive agents, while continuing aggressive fluid administration. Starting vasoactive agents in the initial hour may be detrimental, and not all of that association is due to less fluids being given with such early initiation of vasoactive agents.
Anti‐Asthma Simplified Herbal Medicine Intervention‐induced long‐lasting tolerance to allergen exposure in an asthma model is interferon‐γ, but not transforming growth factor‐β dependent

Background Chronic allergic asthma is the result of a T‐helper type 2 (Th2)‐biased immune status. Current asthma therapies control symptoms in some patients, but a long‐lasting therapy has not been established. Anti‐Asthma Simplified Herbal Medicine Intervention (ASHMI™), a Chinese herbal formula improved symptoms and lung function, and reduced Th2 responses in a controlled trial of patients with persistent moderate to severe asthma.
Evolution and progression of atherosclerotic lesions in coronary arteries of children and young adults.

In an autopsy study of the evolution of atherosclerotic lesions in young people, we obtained the coronary arteries and aortas of 1160 male and female subjects who died between full-term birth and age 29 years. In this article, we report the light and electron microscopic observations of the coronary arteries of 565 of these subjects in which we fixed the coronary arteries by perfusion with glutaraldehyde under pressure. From birth, the intima was always thicker in the half of the coronary artery circumference opposite the flow-divider wall of a bifurcation (eccentric thickening). In cases where we found lipid in the intima, there was always more in eccentric thickening. Isolated macrophage foam cells in the intima of infants were the earliest sign of lipid retention. These cells occurred in 45% of infants in the first 8 months of life but decreased subsequently. At puberty, more substantial accumulations of macrophage foam cells reappeared in more children. Foam cells were now accompanied by lipid droplets in existing smooth muscle cells and by thinly scattered extracellular lipid. Sixty-five percent of children between ages 12 and 14 years had such lesions. An additional 8% of children had progressed beyond this early stage and had developed advanced preatheroma or atheroma stages. Such advanced lesions, located only in areas of eccentric thickening, were characterized by the addition of massive extracellular lipid that displaced normal cells and matrix and, thus, damaged and weakened the arterial wall. (ABSTRACT TRUNCATED AT 250 WORDS)
Lissencephaly and LIS1: insights into the molecular mechanisms of neuronal migration and development

Lissencephaly is a severe human neuronal migration defect characterized by a smooth cerebral surface, mental retardation and seizures. LIS1 was first gene cloned in an organism important for neuronal migration, as it was deleted or mutated in patients with lissencephaly in a heterozygous fashion. Studies in model organisms, particularly Aspergillus nidulans, as well as those in the mouse, have uncovered an evolutionarily conserved pathway that involves LIS1 and cytoplasmic dynein. This pathway codes for proteins in a complex with cytoplasmic dynein and positively regulates its conserved function in nuclear migration. This complex appears to be important for proliferation and neuronal survival as well as neuronal migration. One of the components of this complex, NDEL1, is a phosphoprotein that is a substrate for CDK5 (or CDK2 in fibroblasts) and Aurora‐A, two mitotic kinases. CDK5‐phosphorylated NDEL1 binds to 14‐3‐3ɛ, which protects it from phosphatase attack. Interestingly, 14‐3‐3ɛ is located 1 Mb from LIS1 and is heterozygously deleted with LIS1 in patients with a severe form of lissencephaly, Miller–Dieker syndrome. Mouse models confirm that 14‐3‐3ɛ plays an important role in neuronal migration, and mice that are double heterozygotes for mutations in Lis1 and 14‐3‐3ɛ, display more severe neuronal migration defects. The identification of LIS1 as the first lissencephaly gene, and the first gene required for neuronal migration has revealed the importance of the regulation of cytoplasmic dynein in the control of neuronal migration by modulating nuclear migration in a pathway conserved in virtually all eukaryotes.
Treatment of Wilson's Disease with Triethylene Tetramine Hydrochloride (Trientine)

Penicillamine is the drug of choice for the treatment of Wilson's disease, whatever the stage of the illness. Toxic manifestations may preclude the use of this life-saving drug in some patients and discontinuation of penicillamine therapy usually leads to death. We report our experience with Trientine in seven patients, aged 13 to 33 years, with Wilson's disease who developed toxic manifestations with penicillamine that required discontinuation of therapy. These include two with nephrosis, one with neutropenia, two with thrombocytopenia, and one each with a SLE-like and a Henoch-Schonlein-like syndrome. The patients were treated for periods from 6 weeks to 16 years with a dose of 0.5 to 2 g/day. Trientine proved to be an effective alternative copper chelating agent in the treatment of Wilson's disease in patients with penicillamine-induced neutropenia, thrombocytopenia, SLE, and nephrosis. No serious untoward side effects were noted.
Comparing Supervised Exercise Therapy to Invasive Measures in the Management of Symptomatic Peripheral Arterial Disease

Peripheral arterial disease (PAD) is associated with considerable morbidity and mortality. Consensus rightly demands the incorporation of supervised exercise training (SET) into PAD treatment protocols. However, the exact role of SET particularly its relationship with intervention requires further clarification. While supervised exercise is undoubtedly an excellent tool in the conservative management of mild PAD its use in more advanced disease as an adjunct to open or endovascular intervention is not clearly defined. Indeed its use in isolation in this cohort is incompletely reported. The aim of this review is to clarify the exact role of SET in the management of symptomatic PAD and in particular to assess its role in comparison with or as an adjunct to invasive intervention. A systematic literature search revealed a total 11 randomised studies inclusive of 969 patients. All studies compared SET and intervention with monotherapy. Study results suggest that exercise is a complication-free treatment. Furthermore, it appears to offer significant improvements in patients walk distances with a combination of both SET and intervention offering a superior walking outcome to monotherapy in those requiring invasive measures.