Miracle-dz/UniFAR-FTUs huggingface dataset:
Stepped wedge designs: insights from a design of experiments perspective

Stepped wedge designs (SWDs) have received considerable attention recently, as they are potentially a useful way to assess new treatments in areas such as health services implementation. Because allocation is usually by cluster, SWDs are often viewed as a form of cluster‐randomized trial. However, since the treatment within a cluster changes during the course of the study, they can also be viewed as a form of crossover design. This article explores SWDs from the perspective of crossover trials and designed experiments more generally. We show that the treatment effect estimator in a linear mixed effects model can be decomposed into a weighted mean of the estimators obtained from (1) regarding an SWD as a conventional row‐column design and (2) a so‐called vertical analysis, which is a row‐column design with row effects omitted. This provides a precise representation of “horizontal” and “vertical” comparisons, respectively, which to date have appeared without formal description in the literature. This decomposition displays a sometimes surprising way the analysis corrects for the partial confounding between time and treatment effects. The approach also permits the quantification of the loss of efficiency caused by mis‐specifying the correlation parameter in the mixed‐effects model. Optimal extensions of the vertical analysis are obtained, and these are shown to be highly inefficient for values of the within‐cluster dependence that are likely to be encountered in practice. Some recently described extensions to the classic SWD incorporating multiple treatments are also compared using the experimental design framework.
Similar prediction of decreased total mortality , diabetes incidence or cardiovascular events using relative-and absolute-component Mediterranean diet score : The SUN cohort

Please cite this article in press as: D vascular events using relativeand a cular Diseases (2011), doi:10.1016/j. 0939-4753/$ see front matter a 201 doi:10.1016/j.numecd. 2011.10. 009 Abstract Background and Aim: Accumulated evidence supports the effectiveness of Mediterranean-type diets (MeDiet) in reducing mortality and preventing several chronic diseases. Widely used scores to assess adherence to MeDiet are based on specific sample characteristics; alternatively, they might be built according to absolute/normative cut-off points for the consumption of specific food groups (pre-defined servings/day or/week). The aim of this study was to compare sample-specific MeDiet adherence scores (MDS) versus absolutenormative scores (Mediterranean Diet Adherence Screener e MEDAS) on their association with macronutrient intake, total mortality and incidence of chronic diseases. Design: SUN (Seguimiento Universidad de Navarra) dynamic prospective cohort study (60.5% women; mean age 38.4 years). Methods and Results: In cross-sectional analyses (nZ 20,155) we evaluated macronutrient distribution according to MDS (based on 136-item FFQ), MEDAS (based on 13 questions), and variants of both. In prospective analyses (nZ 9109; mean follow-up: 6.2 years), we evaluated disease incidence or mortality. Adherence to MeDiet increased with age and, as expected, was associated with higher fiber intake, lower total fat intake but higher monounsaturated/saturated fat ratio, using all scores. Among subjects initially free of cancer, diabetes, and cardiovascular disease (CVD), adherence to MeDiet appraised with an absolute-normative score (MEDAS) similarly predicted macronutrient distribution and disease incidence or mortality
Diagnosis and Treatment of Depression in Late Life: Consensus Statement Update

Objective. —To reexamine the conclusions of the 1991 National Institutes of Health Consensus Panel on Diagnosis and Treatment of Depression in Late Life in light of current scientific evidence. Participants. —Participants included National Institutes of Health staff and experts drawn from the Planning Committee and presenters of the 1991 Consensus Development Conference. Evidence. —Participants summarized relevant data from the world scientific literature on the original questions posed for the conference. Process. —Participants reviewed the original consensus statement and identified areas for update. The list of issues was circulated to all participants and amended to reflect group agreement. Selected participants prepared first drafts of the consensus update for each issue. All drafts were read by all participants and were amended and edited to reflect group consensus. Conclusions. —The review concluded that, although the initial consensus statement still holds, there is important new information in a number of areas. These areas include the onset and course of late-life depression; comorbidity and disability; sex and hormonal issues; newer medications, psychotherapies, and approaches to long-term treatment; impact of depression on health services and health care resource use; late-life depression as a risk factor for suicide; and the importance of the heterogeneous forms of depression. Depression in older people remains a significant public health problem. The burden of unrecognized or inadequately treated depression is substantial. Efficacious treatments are available. Aggressive approaches to recognition, diagnosis, and treatment are warranted to minimize suffering, improve overall functioning and quality of life, and limit inappropriate use of health care resources.
A Novel Class of Vascular Endothelial Growth Factor-responsive Genes That Require Forkhead Activity for Expression*

Recently, we have shown that transient phosphorylation and inhibition of the pro-apoptotic transcription factor, forkhead, by vascular endothelial growth factor (VEGF) is essential for endothelial cell (EC) survival and proliferation. The goal of the present study was to determine whether forkhead (FKHR) also plays a positive role in agonist-mediated gene induction. Human coronary artery ECs were transduced with adenovirus overexpressing constitutively active phosphorylation-resistant triple mutant FKHR or transfected with small interference RNA (siRNA) against FKHR. The cells were then treated in the absence or presence of VEGF and assayed for gene expression using quantitative real-time PCR and Northern blots analyses. The data revealed a novel set of VEGF-responsive genes that require FKHR activity for optimal expression in ECs, including bone morphogenic protein 2, cbp/p300-interacting transactivator 2, decay accelerating factor (DAF), vascular cell adhesion molecule-1 (VCAM-1), manganese superoxide dismutase, endothelial-specific molecule-1, RING1 and YY1-binding protein, and matrix metalloproteinase-10. Consistent with a positive role for FKHR in mediating VEGF induction of DAF and VCAM-1 mRNA, siRNA against FKHR attenuated the effect of VEGF on complement-mediated EC lysis and monocyte adhesion, respectively. VEGF induction of the forkhead-dependent genes was down-regulated by the NF-κB inhibitor, constitutively active Ad-IκB, and in some cases by the nuclear factor of activated T-cells (NF-AT) inhibitor, cyclosporin. Together, these findings suggest that the VEGF-forkhead signaling axis plays an important functional role in ECs beyond the regulation of cell survival/apoptosis and cell cycle.
Studying brain cytoarchitecture with MRI—Present, future and promises of high field

This review surveys the efforts that have been done so far to use magnetic resonance imaging (MRI) and other related methods to investigate the complex microstructural features of brain tissue in a quantitative and semiquantitative manner. Emphasis is put on diffusion and diffusion/relaxation methods, which were borrowed from the field of porous media nuclear magnetic resonance (NMR), and which are those that allow the most direct link between the measured NMR signal and the microscopic geometry of the investigated medium. Other methods that allow compartment‐specific measurements with MR, such as multiple quantum filtered NMR of quadrupolar nuclei, are also discussed. The potential contribution of high field MRI to these methods and possible future directions are lastly discussed. © 2010 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 20, 57–61, 2010
Winter precipitation and snow accumulation drive the methane sink or source strength of Arctic tussock tundra

Arctic winter precipitation is projected to increase with global warming, but some areas will experience decreases in snow accumulation. Although Arctic CH4 emissions may represent a significant climate forcing feedback, long‐term impacts of changes in snow accumulation on CH4 fluxes remain uncertain. We measured ecosystem CH4 fluxes and soil CH4 and CO2 concentrations and 13C composition to investigate the metabolic pathways and transport mechanisms driving moist acidic tundra CH4 flux over the growing season (Jun–Aug) after 18 years of experimental snow depth increases and decreases. Deeper snow increased soil wetness and warming, reducing soil %O2 levels and increasing thaw depth. Soil moisture, through changes in soil %O2 saturation, determined predominance of methanotrophy or methanogenesis, with soil temperature regulating the ecosystem CH4 sink or source strength. Reduced snow (RS) increased the fraction of oxidized CH4 (Fox) by 75–120% compared to Ambient, switching the system from a small source to a net CH4 sink (21 ± 2 and −31 ± 1 mg CH4 m−2 season−1 at Ambient and RS). Deeper snow reduced Fox by 35–40% and 90–100% in medium‐ (MS) and high‐ (HS) snow additions relative to Ambient, contributing to increasing the CH4 source strength of moist acidic tundra (464 ± 15 and 3561 ± 97 mg CH4 m−2 season−1 at MS and HS). Decreases in Fox with deeper snow were partly due to increases in plant‐mediated CH4 transport associated with the expansion of tall graminoids. Deeper snow enhanced CH4 production within newly thawed soils, responding mainly to soil warming rather than to increases in acetate fermentation expected from thaw‐induced increases in SOC availability. Our results suggest that increased winter precipitation will increase the CH4 source strength of Arctic tundra, but the resulting positive feedback on climate change will depend on the balance between areas with more or less snow accumulation than they are currently facing.
Vaccination Strategies in the Treatment of Lymphomas

Malignant lymphomas are clonal neoplasms of lymphoid origin. By definition, all cells of the malignant clone have undergone the same rearrangement of antigen receptor genes and express identical antigen receptor molecules (immunoglobulin for B cell lymphomas, T cell receptor for T cell lymphomas). The hypervariable stretches within the variable regions of these receptors are considered true tumor-specific antigens (‘idiotypes’). In several animal models, protective humoral or cellular immunity can be induced against the malignant lymphoma by vaccination with the tumor-derived idiotype. Successful experimental immunization strategies in animals include idiotype protein vaccines combined with various adjuvants, genetically or immunologically modified lymphoma cells, idiotype-presenting dendritic cells, idiotype-encoding viral vectors, and DNA immunization. Firm evidence for the induction of lymphoma-specific immunity has also been obtained from human idiotype vaccination trials. Furthermore, some trials have provided strong but hitherto formally unproven evidence for clinical benefit of idiotype-vaccinated patients. Alternative vaccination approaches are based on immunologically modified tumor cells. Current research efforts concentrate on the identification of the most efficacious vaccination route, on definitive proof of clinical efficacy, and on the development of convenient methods to manufacture individual idiotype vaccines.
Design of Escherichia coli-Expressed Stalk Domain Immunogens of H1N1 Hemagglutinin That Protect Mice from Lethal Challenge

ABSTRACT The hemagglutinin protein (HA) on the surface of influenza virus is essential for viral entry into the host cells. The HA1 subunit of HA is also the primary target for neutralizing antibodies. The HA2 subunit is less exposed on the virion surface and more conserved than HA1. We have previously designed an HA2-based immunogen derived from the sequence of the H3N2 A/HK/68 virus. In the present study, we report the design of an HA2-based immunogen from the H1N1 subtype (PR/8/34). This immunogen (H1HA0HA6) and its circular permutant (H1HA6) were well folded and provided complete protection against homologous viral challenge. Antisera of immunized mice showed cross-reactivity with HA proteins of different strains and subtypes. Although no neutralization was observable in a conventional neutralization assay, sera of immunized guinea pigs competed with a broadly neutralizing antibody, CR6261, for binding to recombinant Viet/04 HA protein, suggesting that CR6261-like antibodies were elicited by the immunogens. Stem domain immunogens from a seasonal H1N1 strain (A/NC/20/99) and a recent pandemic strain (A/Cal/07/09) provided cross-protection against A/PR/8/34 viral challenge. HA2-containing stem domain immunogens therefore have the potential to provide subtype-specific protection.
Programming for humans : a new paradigm for domain-specific languages

ion gradient Our notation requires the user to work at a fairly low level of abstraction. Crucially, there is no procedure for packaging up a collection of nodes in a graph as a reusable node, unlike how a function can be created in most programming languages. This abstraction-hating is close to the level of abstraction possible in Excel, where formulas must be copied if they are to be used repeatedly. We do support structured data types as tables which, when compared to Excel, are an abstraction over multiple cells. The amount of abstraction required by the user seems acceptable compared to Excel, and less than the programming language. Closeness of mapping The notation maps quite well to the problem domain. In particular, our WYSIWYG editor enables the user to put programs directly into web pages. The use of tables as the pervasive data structure forces a tight mapping between the notation and the possible problems that can be expressed. This could make it much Note that these dimensions are not orthogonal, so a change in one dimension will affect other dimensions. Additionally, whilst the dimensions are not intrinsically good or bad, we organise them according to the preferred direction of each dimension for end-users, for example, low abstraction and high visibility are considered good.
Positivity Conditions for Quartic Polynomials

Simple necessary and sufficient conditions that a quartic polynomial f(z) be non-negative for z greater than or equal to 0 or a is less than or equal to z and z is less than or equal to b are derived, and illustrated geometrically. The geometry provides considerable insight and suggests various approximations and computational simplifications. The theory is applied to monotone quintic spline interpolations, giving necessary and sufficient conditions and an algorithm for monotone Hermite quintic interpolation.
A Broad Phylogenetic Analysis of Boraginaceae: Implications for the Relationships of Mertensia

Abstract The phylogenetic relationships of Mertensia (Boraginaceae), which comprises approximately 45 species in both Asia and North America, have been uncertain, and taxonomists have placed the genus in various tribes of subfamily Boraginoideae, with the most recent placements in Trigonotideae and Cynoglosseae. Our study applies molecular phylogenetic methods to test the monophyly and relationships of Mertensia. We used DNA sequence data from the nuclear ribosomal nrITS region and four cpDNA regions (matK, ndhF, rbcL, trnL-trnF) to examine the placement of Mertensia among a sampling of accessions from approximately 70% of the genera of Boraginaceae s. l. Phylogeny reconstructions using maximum parsimony, maximum likelihood, and Bayesian inference were largely congruent with previous molecular phylogenetic analyses of Boraginaceae that had applied far fewer taxa. We recovered five deep clades that correspond to Boraginaceae subfamilies Boraginoideae, Cordioideae, Heliotropioideae, Hydrophylloideae, and Ehretioideae (including Lennoa and Pholisma). In subfamily Boraginoideae, we recovered clades that correspond to the tribes Echiochilieae, Lithospermeae, Cynoglosseae, and Boragineae, although several tribes previously circumscribed on the basis of morphological data were not recovered as monophyletic in our results. Based on the sister relationship between the genus Codon and subfamily Boraginoideae found in our phylogeny reconstructions, we propose Codoneae as a new tribe of Boraginoideae. We recovered strong support for the monophyly of Mertensia and the placement of the monotypic genus Asperugo as its sister. Mertensia and Asperugo were strongly supported as members of Cynoglosseae.
Word Vector Enrichment of Low Frequency Words in the Bag-of-Words Model for Short Text Multi-class Classification Problems

The bag-of-words model is a standard representation of text for many linear classifier learners. In many problem domains, linear classifiers are preferred over more complex models due to their efficiency, robustness and interpretability, and the bag-of-words text representation can capture sufficient information for linear classifiers to make highly accurate predictions. However in settings where there is a large vocabulary, large variance in the frequency of terms in the training corpus, many classes and very short text (e.g., single sentences or document titles) the bag-of-words representation becomes extremely sparse, and this can reduce the accuracy of classifiers. A particular issue in such settings is that short texts tend to contain infrequently occurring or rare terms which lack class-conditional evidence. In this work we introduce a method for enriching the bag-of-words model by complementing such rare term information with related terms from both general and domain-specific Word Vector models. By reducing sparseness in the bag-of-words models, our enrichment approach achieves improved classification over several baseline classifiers in a variety of text classification problems. Our approach is also efficient because it requires no change to the linear classifier before or during training, since bag-of-words enrichment applies only to text being classified.
Percutaneous vertebroplasty for pain management in malignant fractures of the spine with epidural involvement.

PURPOSE To evaluate the feasibility, efficacy, and safety of percutaneous vertebroplasty (PV) in the treatment of pathologic fractures owing to malignancy with epidural involvement, with or without neurologic symptoms of spinal cord or cauda equina compression. MATERIALS AND METHODS This study was approved by the local ethics committee; informed consent was obtained from all patients. This retrospective review was performed for 51 consecutive patients with metastatic disease or multiple myeloma treated by means of vertebroplasty, who presented with at least one vertebral lesion with epidural involvement, with or without clinical symptoms of spinal cord or cauda equina compression. All patients with neurologic deficit were terminally ill. A neurologic examination was performed before and after treatment in all patients. All imaging examinations and treatments were reviewed, and chi(2), Mann Whitney, or Fisher exact testing was performed for univariate analysis of variables. RESULTS A total of 74 vertebrae were treated in 51 patients, 22 women and 29 men with a mean age of 62.5 years (range, 28-85 years). Fifteen (29%) patients presented symptoms of complete or incomplete spinal cord or cauda equina compression before vertebroplasty and no further clinical deterioration was observed after treatment. The analgesic efficacy of vertebroplasty was satisfactory for 94% (48 of 51) of patients after 1 day, 86% (31 of 36) patients after 1 month, and 92% (11 of 12) patients after 1 year. One patient with no clinical neurologic deficit before treatment experienced symptoms of cauda equina compression 2 days after vertebroplasty. No other major complication was observed. CONCLUSION The feasibility, efficacy, and safety of PV were confirmed in patients experiencing pain related to malignant spinal tumors with epidural extension, with a low complication rate. PV should become part of the palliative analgesic treatment for such patients. (c) RSNA, 2010.
Correlation between incidences of hospitalised accidental burns and deprivation scores: an ecological study

Several studies have reported a positive relationship between injury rates and social deprivation.1–3 The relationship between the incidence of accidental burns and increasing social deprivation has been reported.4 Gaps in our present knowledge about socioeconomic status and incidence of injuries need to be filled using data from different countries with different levels of development, because injuries, including burns, occur with widening inequalities with different epidemiological aspects in the world. In this article, I will analyse the incidences of hospitalised cases of accidental burns in relation to deprivation scores of areas using data from two referral burns centres in Bushehr …
L'exception française : L'école maternelle face à la diversité des formes préscolaires : Le préscolaire en question : sur les pratiques

La France vit le paradoxe d'un systeme prescolaire qui, bien que recevant des enfants a partir de deux ans, se pense comme ecole, mais cette situation assez exceptionnelle au regard de ce qui se passe ailleurs semble plus consideree comme une norme universalisable que comme un trait culturel specifique. A travers des comparaisons mettant en evidence les valeurs culturelles sous-jacentes a differents systemes prescolaires (Japon, USA, Allemagne) et la notion de forme scolaire et prescolaire nous essayons de comprendre cette dimension culturelle propre au systeme francais. Il s'agit de proposer une recherche capable de penser la singularite de la configuration denommee ecole maternelle en analysant les choix sous-jacents a cette forme normale ici, rejetee dans d'autres contextes.
Distribution and status of the large Branchiopoda (Crustacea) in Corsica, France

Knowledge of the Branchiopoda of Corsica is limited. Their distribution is updated, on the basis of eight years of investigations on 20 ponds. To date, three species of Anostraca and one species of Notostraca have been reported (Tanymastix stagnalis, Chirocephalus salinus, Branchipus schaefferi and Triops cancriformis cancriformis). B. schaefferi (recorded for the first time in Corsica) occurs in a single locality, C. salinus and T. cancriformis cancriformis are limited to restricted distributions, while T. stagnalis is common in temporary ponds of Corsica. Their status is assessed according to IUCN Red List criteria. Temporary habitats are endangered by human activities and require a proper conservation management.