Miracle-dz/UniFAR-FTUs huggingface dataset:
Preclinical and clinical evaluation of autonomic function in humans

This review focuses on how to assess autonomic function in humans including various ways to measure heart rate, catecholamines, and sympathetic neural activity. The need to assess autonomic function is paramount in many experimental paradigms because of the following. (1) Autonomic dysfunction is present in common diseases like hypertension, diabetes and heart failure, and the magnitude of this dysfunction is broadly related to morbidity and mortality in these disorders. (2) The relationship between autonomic dysfunction and morbidity and mortality can be causal. (3) Interventions that modulate or reverse autonomic dysfunction can improve outcomes in the affected patients. The techniques discussed are also frequently used to understand the autonomic response to sympathoexcitatory manoeuvres like exercise, the cold pressor test or mental stress. Because these manoeuvres can engage a variety of sensory and efferent pathways, under some circumstances the physiological responses measured by many of the techniques are directionally similar, in others they are divergent. Thus any investigator seeking to study the autonomic nervous system or its contribution to either normal physiology or pathophysiological conditions must carefully balance a number of considerations to ensure that the right technique is used to address the question of interest.
A note on the estimation of the ABO gene frequencies and the coefficient of inbreeding.

Recently, Yasuda (1966a, b) has advanced an argument which he interprets as a demonstration that no estimate of the inbreeding coefficient can be obtained from data on the frequency of individuals with the blood group phenotypes 0, A, B, and AB. We believe this conclusion to be unwarranted and to stem from some confusion regarding tests of hypothesis and problems of estimation. Our argument proceeds as follows: Consider a population wherein the probabilities of individuals of phenotypes 0, A, B, and AB are
An automated methodology for converting OSM data into a Land Use/Cover map

The appearance of OpenStreetMap (OSM) in 2004 sparked a phenomenon known as Volunteered Geographic Information (VGI). Today, VGI comes in many flavours (e.g. toponyms, GPS tracks, geo-tagged photos, micro-blogging or complete topographic maps) and from various sources. One subject that has attracted research interest from the early days of VGI is how good such datasets are and how to combine them with authoritative datasets. To this end, the paper explores three intertwined subjects from a quality point of view First, we examine the topo-semantic consistency of OSM data by evaluating a number of rules between polygonal and linear features and then paying special attention to quality of Points of Interest (POIs). A number of topo-semantic rules will be used to evaluate the valididy of features’ location. The focus then turns to the use of geo-tagged photos to evaluate the location and type of OSM data and to disambiguate topological issues that arise when different OSM layers overlap.
VARIATION IN HOST SPECIFICITY BETWEEN SPECIES OF AVIAN HEMOSPORIDIAN PARASITES: EVIDENCE FROM PARASITE MORPHOLOGY AND CYTOCHROME B GENE SEQUENCES

A parasite's shift to a new host may have serious evolutionary consequences, since host switching usually is associated with a change in virulence and may lead to the evolution of emerging diseases. This phenomenon remains insufficiently studied in wildlife. Here, we combine microscopic examination of blood films and PCR-based methods to investigate the natural host specificity of Haemoproteus and Plasmodium spp. in birds of 4 families of the Passeriformes within a small geographic area. The material was collected on the Curonian Spit in the Baltic Sea between May and July in 2003–2004. A nested-PCR protocol was used for amplifying and sequencing a fragment of 480 nucleotides of the cytochrome b gene of the mtDNA of these parasites. Blood samples from 282 birds, which were positive both by microscopic examination of blood films and mtDNA amplification, were used in this study. We found that Haemoproteus majoris (lineages hPARUS1, hCCF5, hWW2, and hPHSIB1), Haemoproteus sp. (hWW1), Plasmodium (Haemamoeba) sp. (pSGS1), and Plasmodium (Haemamoeba) sp. (pGRW11) are capable of infecting birds belonging to different families of passeriform birds. Some species of Haemoproteus are less specific than have been traditionally believed. Haemoproteus majoris appears to have a genetic predisposition to have a broad host range. The level of host specificity varies markedly among different species of hemosporidian parasites of birds. The natural host range is thus not a reliable taxonomic character in the systematics of these parasites in the form in which it is still accepted in some recent taxonomic studies.
Technical Report : Inference of Principal Road Paths Using GPS Data

Over the last few years, electronic vehicle guidance systems have become increasingly more popular. However, despite their ubiquity, performance will always be subject to the availability of detailed digital road maps. Most current digital maps are still inadequate for advanced applications in unstructured environments. Lack of up-to-date information and insufficient refinement of the road geometry are among the most important shortcomings. The massive use of inexpensive GPS receivers, combined with the rapidly increasing availability of wireless communication infrastructure, suggests that large amounts of data combining both modalities will be available in a near future. The approach presented here draws on machine learning techniques and processes logs of position traces to consistently build a detailed and fine-grained representation of the road network by extracting the principal paths followed by the vehicles. Although this work addresses the road building problem in very dynamic environments such as open-pit mines, it is also applicable to urban environments. New contributions include a fully unsupervised segmentation method for sampling roads and inferring the network topology, a general technique for extracting detailed information about road splits, merges and intersections, and a robust algorithm that articulates these two. Experimental results with data from large mining operations are presented to validate the new algorithm. Digital road maps, data mining, machine learning, GPS, road safety.
The Fibronectin-Binding Proteins of Staphylococcus aureus May Promote Mammary Gland Colonization in a Lactating Mouse Model of Mastitis

ABSTRACT The fibronectin-binding proteins (FnBPs) of Staphylococcus aureus are believed to be implicated in the pathogen's adherence to and colonization of bovine mammary glands, thus leading to infectious mastitis. In vitro studies have shown that FnBPs help the adhesion of the pathogen to bovine mammary epithelial cells. However, the importance of FnBPs for the infection of mammary glands has never been directly established in vivo. In this study with a mouse model of mastitis, the presence of FnBPs on the surface of S. aureus increased the capacity of the bacterium to colonize mammary glands under suckling pressure compared to that of a mutant lacking FnBPs.
Role of extent of resection in the long-term outcome of low-grade hemispheric gliomas.

PURPOSE The prognostic role of extent of resection (EOR) of low-grade gliomas (LGGs) is a major controversy. We designed a retrospective study to assess the influence of EOR on long-term outcomes of LGGs. PATIENTS AND METHODS The study population (N = 216) included adults undergoing initial resection of hemispheric LGG. Region-of-interest analysis was performed to measure tumor volumes based on fluid-attenuated inversion-recovery (FLAIR) imaging. RESULTS Median preoperative and postoperative tumor volumes and EOR were 36.6 cm(3) (range, 0.7 to 246.1 cm(3)), 3.7 cm(3) (range, 0 to 197.8 cm(3)) and 88.0% (range, 5% to 100%), respectively. There was no operative mortality. New postoperative deficits were noted in 36 patients (17%); however, all but four had complete recovery. There were 34 deaths (16%; median follow-up, 4.4 years). Progression and malignant progression were identified in 95 (44%) and 44 (20%) cases, respectively. Patients with at least 90% EOR had 5- and 8-year overall survival (OS) rates of 97% and 91%, respectively, whereas patients with less than 90% EOR had 5- and 8-year OS rates of 76% and 60%, respectively. After adjusting each measure of tumor burden for age, Karnofsky performance score (KPS), tumor location, and tumor subtype, OS was predicted by EOR (hazard ratio [HR] = 0.972; 95% CI, 0.960 to 0.983; P < .001), log preoperative tumor volume (HR = 4.442; 95% CI, 1.601 to 12.320; P = .004), and postoperative tumor volume (HR = 1.010; 95% CI, 1.001 to 1.019; P = .03), progression-free survival was predicted by log preoperative tumor volume (HR = 2.711; 95% CI, 1.590 to 4.623; P <or= .001) and postoperative tumor volume (HR = 1.007; 95% CI, 1.001 to 1.014; P = .035), and malignant progression-free survival was predicted by EOR (HR = 0.983; 95% CI, 0.972 to 0.995; P = .005) and log preoperative tumor volume (HR = 3.826; 95% CI, 1.632 to 8.969; P = .002). CONCLUSION Improved outcome among adult patients with hemispheric LGG is predicted by greater EOR.
Orientation Disparity, Deformation, and Stereoscopic Slant Perception

Koenderink and van Doorn's theory, that the basis of stereoscopic slant perception is the deformation component of the disparity, field, was tested for slant around a horizontal axis, which produces images with a vertical ramp of horizontal disparity (horizontal shear) characterised by a global orientation disparity at the vertical meridian. The disparity field in this case can be parsed into two components, deformation and curl, which each contribute half of the orientation disparity. This case was compared with similar random-dot stimuli in which the deformation component was doubled and the curl component eliminated or vice versa. All three types of stimuli had identical orientation disparity at the vertical meridian. A condition in which there was no such orientation disparity, but deformation was present, was also included. It was found that perceived slant was not related to the deformation present, as Koenderink and van Doorn's theory would predict, but was predictable from the orientation disparity at the vertical meridian per se.
Cardiac troponins in chest pain

Despite a fall in the age adjusted prevalence of cardiovascular disease in the developed world,1 the number of patients presenting with chest pain is rising. Greater public awareness of the importance of chest pain has lowered the threshold for seeking medical help, while improvements in our ability to manage acute coronary syndromes necessitate prompt and accurate identification of ischaemic cardiac pain. Most patients who present to accident and emergency departments will have non-cardiac pain and others, with ischaemic pain, will be at low risk of serious adverse events in the short term. In contrast, many of those at high risk have no diagnostic clinical or electrocardiographic findings at presentation (about 50% of patients ultimately diagnosed as having an acute myocardial infarction, and 65% of those with unstable angina, present with non-diagnostic electrocardiograms). 2 The major challenge is therefore determining the risk of an individual patient. There are two components to such risk. “Acute risk” is determined by the volume and severity of ischaemic myocardium (usually reflected in electrocardiographic changes) and the extent of myocardial injury (indicated by troponins and cardiac enzymes). “Prognostic risk” is influenced by prior cardiac damage, confounding …
Analysis of myocardial deformation based on pixel tracking in two dimensional echocardiographic images enables quantitative assessment of regional left ventricular function

Objective: To evaluate whether myocardial strain and strain rate calculated from two dimensional echocardiography by automatic frame-by-frame tracking of natural acoustic markers enables objective description of regional left ventricular (LV) function. Methods: In 64 patients parasternal two dimensional echocardiographic views at the apical, mid-ventricular and basal levels were obtained. An automatic frame-by-frame tracking system of natural acoustic echocardiographic markers was used to calculate radial strain, circumferential strain, radial strain rate and circumferential strain rate for each LV segment in a 16 segment model. Cardiac magnetic resonance imaging (cMRI) was performed to define segmental LV function as normokinetic, hypokinetic or akinetic. Results: Image quality was sufficient for adequate strain and strain-rate analysis from two dimensional echocardiographic images obtained from parasternal views in 88% of segments. Obtained radial strain data were highly reproducible and analysis was affected by only small intraobserver (mean 4.4 (SD 1.6)%) and interobserver variabilities (7.3 (2.5)%). Each of the analysed strain and strain-rate parameters was significantly different between segments defined as normokinetic, hypokinetic or akinetic by cMRI (radial strain 36.8 (10.5)%, 24.1 (7.5)% and 13.4 (4.8)%, respectively, p < 0.001). Peak systolic radial strain enabled detection of hypokinesis or akinesis with a sensitivity of 83.5% and a specificity of 83.5% (cut off value 29.1%, receiver operating characteristic (ROC) curve area 0.905, 95% CI 0.883 to 0.923). Peak systolic radial strain analysis also enabled detection of akinesis versus hypokinesis with a sensitivity of 82.7% and a specificity of 94.5% (cut off value 21.0%, ROC curve area 0.946). Peak systolic radial strain-rate analysis was less accurate than peak systolic radial strain analysis to detect cMRI-defined segmental function abnormalities. The accuracy of peak systolic circumferential strain and strain rate was similar to that of corresponding radial parameters. Conclusions: Frame-by-frame tracking of acoustic markers in two dimensional echocardiographic images enables accurate analysis of regional systolic LV function.
Epidermolysis bullosa acquisita associated with vesicular cystitis

A 55‐year‐old woman with epidermotysis bullosa acquisita (EBA) who had associated vesicular cystitis is described. The clinical, histological and immunohistological features of the skin and mucous membranes were in accordance with previous reports of this disease. The patient also had symptoms of cystitis, and a cystoscopic examination showed areas of erosions and vesicles in the wall of the urinary bladder, Histological and immunopathological studies of the urinary bladder demonstrated sub‐mucosal vesicles, and linear deposits of IgG and C3 along the mucosal‐lamina propria junction. These bladder changes may be induced by the autoantibodies present in EBA.
Lakes as sensors in the landscape: Optical metrics as scalable sentinel responses to climate change

As the lowest point in the surrounding landscape, lakes act as sensors in the landscape to provide insights into the response of both terrestrial and aquatic ecosystems to climate change. Here a novel suite of climate forcing optical indices (CFOI) from lakes across North America is found to respond to changes in air temperature, precipitation, and solar radiation at timescales ranging from a single storm event to seasonal changes to longer‐term interdecadal trends with regression r2 values ranging from 0.73 to 0.89. These indices are based on two optical metrics of dissolved organic carbon (DOC) quality: DOC specific absorbance (a*320) and spectral slope (S275–295), where the ratio a*320 to S275–295 gives a composite climate forcing index. These indices of DOC quality are more responsive to climate forcing than is DOC concentration. A similar relationship between the component indices a*320 and S275–295 is observed across a wide range of lake types. A conceptual model is used to examine the similarities and differences in DOC‐related mechanisms and ecological consequences due to increased temperature vs. precipitation. While both warmer and wetter conditions increase thermal stratification, these two types of climate forcing will have opposite effects on water transparency as well as many ecological consequences, including oxygen depletion, the balance between autotrophy and heterotrophy, and depth distributions of phytoplankton and zooplankton.
Effects of Estrogen Therapy on the Serotonergic System in an Animal Model of Perimenopause Induced by 4-Vinylcyclohexen Diepoxide (VCD)

Abstract Chronic exposure to 4-vinylcycloxene diepoxide (VCD) in rodents accelerates the natural process of ovarian follicular atresia modelling perimenopause in women. We investigated why estrogen therapy is beneficial for symptomatic women despite normal or high estrogen levels during perimenopause. Female rats (28 d) were injected daily with VCD or oil for 15 d; 55-65 d after the first injection, pellets of 17β-estradiol or oil were inserted subcutaneously. Around 20 d after, the rats were euthanized (control rats on diestrus and estradiol-treated 21 d after pellets implants). Blood was collected for hormone measurement, the brains were removed and dorsal raphe nucleus (DRN), hippocampus (HPC), and amygdala (AMY) punched out for serotonin (5-HT), estrogen receptor β (ERβ), and progesterone receptor (PR) mRNA level measurements. Another set of rats was perfused for tryptophan hydroxylase (TPH) immunohistochemistry in the DRN. Periestropausal rats exhibited estradiol levels similar to controls and a lower progesterone level, which was restored by estradiol. The DRN of periestropausal rats exhibited lower expression of PR and ERβ mRNA and a lower number of TPH cells. Estradiol restored the ERβ mRNA levels and number of serotonergic cells in the DRN caudal subregion. The 5-HT levels were lower in the AMY and HPC in peristropausal rats, and estradiol treatment increased the 5-HT levels in the HPC and also increased ERβ expression in this area. In conclusion, estradiol may improve perimenopause symptoms by increasing progesterone and boosting serotonin pathway from the caudal DRN to the dorsal HPC potentially through an increment in ERβ expression in the DRN.
Structure-Preserving $H^2$ Optimal Model Reduction Based on the Riemannian Trust-Region Method

This paper studies stability- and symmetry-preserving $H^2$ optimal model reduction problems of linear systems, which include linear gradient systems as a special case. The problem is formulated as a nonlinear optimization problem on the product manifold of the manifold of symmetric positive-definite matrices and two Euclidean spaces. To solve the problem by using the trust-region method, the gradient and Hessian of the objective function are derived. Furthermore, it is shown that if we restrict our systems to gradient systems, the gradient and Hessian can be obtained more efficiently. More concretely, by symmetry, we can reduce linear matrix equations to be solved. In addition, by a simple example, we show that the solutions to our problem and a similar problem in some literature works are not unique, and the solution sets of both problems do not contain each other in general. Also, it is revealed that the attained optimal values do not coincide. Numerical experiments show that the proposed method gives a reduced system with the same structure with the original system although the balanced truncation method does not.
A single tablet regimen is associated with higher adherence and viral suppression than multiple tablet regimens in HIV+ homeless and marginally housed people

Background:Although, single-tablet regimen (STR) efavirenz, emtricibine, and tenofovir disoproxil fumarate (EFV/FTC/TDF) may be appealing in HIV-infected persons who are at high risk for nonadherence, the degree to which this simplified formulation affects adherence is not known. The virologic effectiveness of this STR in a potentially nonadherent population remains a concern, given the rapid selection of drug resistance seen with these drugs. Method:We performed a prospective observational study assessing adherence and virologic response to EFV/FTC/TDF STR among a cohort of homeless and marginally housed individuals. We compared adherence and viral suppression to historical controls followed in the same cohort. Results:Adherence was higher in EFV/FTC/TDF STR regimen compared to non-one-pill-once-daily therapy (P = 0.006) after controlling for multiple confounders. Viral suppression (HIV RNA <50 copies/ml) was greater in EFV/ FTC/TDF STR than non-one-pill-once-daily regimens (69.2 versus 46.5%; P = 0.02), but there was no difference in viral suppression after controlling for adherence. Conclusion:Once-daily EFV/TNF/FTC STR appears to be a reasonable option for individuals with multiple barriers to adherence. Randomized clinical trials addressing various therapeutic strategies for this patient population are needed.
H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast

The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition. DOI: http://dx.doi. org/10.7554/eLife.06845. 001
Hyperactivité musculaire dans les douleurs myofasciales orofaciales

Bien que tres frequente, la douleur musculaire chronique reste mal comprise. Les deux travaux presentes dans ce memoire portent sur l'etude electrophysiologique des muscles masticateurs chez les patients souffrant de douleurs orofaciales chroniques (myofasciales et neuropathiques) et chez des sujets non-douloureux (derengements internes de l'articulation temporo-mandibulaire et controles). La premiere etude evalue la relation entre une douleur orofaciale spontanee chronique, moderee ou severe, et deux variables electrophysiologiques : l'activite electromyographique (EMG) au repos et l'amplitude du reflexe masseterin. En presence de douleurs orofaciales, myofasciales ou neuropathiques, les muscles temporaux et masseters presentent une "hyperactivite EMG" tonique et une reduction majeure de l'amplitude du reflexe masseterin. Quand les douleurs sont unilaterales, ces signes sont identiques du cote douloureux et non douloureux. Nous en deduisons que la modulation de l'activite musculaire en presence de douleurs orofaciales chroniques n'est pas la consequence directe d'un mecanisme nociceptif peripherique et nous discutons l'hypothese d'un mecanisme d'origine central. La seconde etude montre en l'effet d'une butee anterieur (JIG) sur cette "hyperactivite" EMG : le JIG reduit transitoirement l'activite EMG des muscles masticateurs dans les douleurs myofasciales mais pas dans les douleurs neuropathique. Si le premier travail suggere que la douleur myofasciale pourrait etre une "douleur neuropathique du muscle" le second montre que les deux entites pathologiques different sur certains mecanismes. Par ailleurs, la seconde etude confirme l'interet de l'utilisation transitoire du JIG en pratique odontologique (rapports intermaxillaires, ajustements occlusaux). Ce travail ouvre sur deux projets en cours d'inclusion. La premiere etude, exploratoire, fait l'objet d'un Projet Hospitalier de Recherche Clinique regional, la seconde est un essai therapeutique non pharmacologique.