Miracle-dz/UniFAR-FTUs huggingface dataset:
Biclustering Via Sparse Clustering

In many situations it is desirable to identify clusters that differ with respect to only a subset of features. Such clusters may represent homogeneous subgroups of patients with a disease, such as cancer or chronic pain. We define a bicluster to be a submatrix U of a larger data matrix X such that the features and observations in U differ from those not contained in U. For example, the observations in U could have different means or variances with respect to the features in U. We propose a general framework for biclustering based on the sparse clustering method of Witten and Tibshirani (2010). We develop a method for identifying features that belong to biclusters. This framework can be used to identify biclusters that differ with respect to the means of the features, the variance of the features, or more general differences. We apply these methods to several simulated and real-world data sets and compare the results of our method with several previously published methods. The results of our method compare favorably with existing methods with respect to both predictive accuracy and computing time.
Transketolase of Staphylococcus aureus is involved in the control 1 of master regulators of stress response during infection 2

cause of both and chronic infections in of (PPP) PPP transketolase. We showed that inactivation of the unique gene encoding transketolase activity in S. aureus led to drastic metabolomic changes. Using time-lapse video imaging and mice infection, we observed a major defect of the ∆ tkt strain compared to wild-type strain in early intracellular proliferation and in the ability to colonise kidneys. Transcriptional activity of the two master regulators Sigma B and RpiRc was drastically reduced in the ∆ tkt mutant during host cells invasion. The concomitant increased RNAIII transcription, suggests that TKT -or a functional PPP- strongly influences the ability of S. aureus to proliferate within host cells by modulating key transcriptional regulators. tkt genes are found in a wide range of organisms including bacteria, plants and mammals, underlining the ubiquitous role 77 of this enzyme in biology. We show here that tkt inactivation in S. aureus USA300 leads to dysregulation of whole cell metabolism. This correlates with impaired proliferation of intracellular staphylococci in vitro and kidney colonisation defect in infected mice.
Maintaining the stem cell niche in multicellular models of epithelia

The maintenance of the stem cell niche is critical to epithelial tissue morphology and function. In this paper we investigate how current modelling methods can result in the erroneous loss of stem cells from the stem cell niche. Using an established model of the inter-follicular epidermis we find there is a limit to the stem cell densities that can be maintained in the basal layer (the niche) if we do not include additional mechanisms to stop the loss of stem cells from the niche. We suggest a new methodology that enables maintenance of a desired homeostatic population of stem cells in the niche: a rotational force is applied to the two daughter cells during the mitotic phase of division to enforce a particular division direction. We demonstrate that this new methodology achieves this goal. This methodology reflects the regulation of orientation of the mitotic spindle during the final phase of the cell cycle.
Assessing Endogenous Pain Inhibition: Test-Retest Reliability of Exercise-Induced Hypoalgesia in Local and Remote Body Parts After Aerobic Cycling.

OBJECTIVE Acute exercise can trigger a hypoalgesic response (exercise-induced hypoalgesia [EIH]) in healthy subjects. Despite promising application possibilities of EIH in the clinical context, its reliability has not been sufficiently examined. This study therefore investigated the between-session and within-subject test-retest reliability of EIH at local and remote body parts after aerobic cycling at a heart rate-controlled intensity. METHODS Thirty healthy adults (15 women) performed 15 minutes of aerobic cycling in two sessions. Pressure pain thresholds (PPTs) were assessed at the leg (local), the back (semilocal), and the hand (remote) before, immediately after, and 15 minutes after exercise. Intraclass correlation coefficients (ICCs) were calculated for absolute and percent changes in PPT from baseline to immediately postexercise, and between-session agreement of EIH responders was examined. RESULTS PPTs significantly increased at the leg during both sessions (all P < 0.001) and at the back during session 2 (P < 0.001), indicating EIH. Fair between-session reliability was shown for absolute changes at the leg (ICC = 0.54) and the back (ICC = 0.40), whereas the reliability of percent changes was poor (ICC < 0.33). Reliability at the hand was poor for both absolute and percent changes (ICC < 0.33). Agreement in EIH responders was not significant for EIH at the leg or the back (all P > 0.05). CONCLUSIONS Our results suggest fair test-retest reliability of EIH after aerobic cycling for local and semilocal body parts, but only in men, demonstrating the need for more standardized methodological approaches to improve EIH as a clinical parameter.
Contagion and Differentiation in Unethical Behavior

In a world where encounters with dishonesty are frequent, it is important to know if exposure to other people's unethical behavior can increase or decrease an individual's dishonesty. In Experiment 1, our confederate cheated ostentatiously by finishing a task impossibly quickly and leaving the room with the maximum reward. In line with social-norms theory, participants' level of unethical behavior increased when the confederate was an in-group member, but decreased when the confederate was an out-group member. In Experiment 2, our confederate instead asked a question about cheating, which merely strengthened the saliency of this possibility. This manipulation decreased the level of unethical behavior among the other group members. These results suggest that individuals' unethicality does not depend on the simple calculations of cost-benefit analysis, but rather depends on the social norms implied by the dishonesty of others and also on the saliency of dishonesty.
Identifying causal paths between health and socio-economic status: Evidence from European older workforce surveys

relationship. In addition, such a relationship takes place early in life and keeps on evolving over time so that both one’s health and SES at a given point in time result from the cumulative effects of this spiral. Thus, only by simultaneously accounting for both pathways as well as for their dynamics would one be able to provide a clear picture of both the process of health accumulation and the dynamics of SES formation. We estimate a structural model where a variety of causal paths between different health dimensions and SES measures as well as their dynamics are simultaneously accounted for. This allows distinction between significant causal paths and insignificant ones, while accounting for endogeneity as well as for cofounders. We use the SOCIOLD survey where the targeted population is that of the older workforce (50 and older) from six EU countries (Denmark, Finland, France, Greece, the Netherlands and the UK). Our results show that (i) reverse causality is indeed a crucial issue: one’s previous socio-economic status influences current health and previous health influences current socioeconomic status, (ii) there are cumulative effects in the sense that both health and socio-economic statuses depend on their past values and (iii) the results are sensitive to whether simultaneity is explicitly accounted for or not.
Cognitive mapping of public space: Causal assumptions and core values among Nordic city planners

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Identification of ocean oil spills in SAR imagery based on fuzzy logic algorithm

Ocean oil spills cause serious damage to the marine environment, especially around coastal waters. Synthetic aperture radar (SAR) has been proven to be a useful tool for oil spill detection under low to moderate wind conditions. SAR operates in the microwave band and the data is not affected by the cloud cover and day/night conditions. However, the operational application of SAR for oil spill detection in the ocean is limited by false alarm targets or lookalike phenomena such as low wind speed, natural films, etc. In this study, we develop analysis of variance (ANOVA) to extract the features based on their characteristic geometry, grey level and texture features in the SAR images. We further analysed a fuzzy logic algorithm to separate oil spills features from lookalikes. We trained this algorithm using 38 SAR images (11 ENVISAT-Advanced Synthetic Aperture Radar (ASAR) and 27 European Remote Sensing (ERS)-2 SAR images) with 120 known oil spills and 80 lookalikes to generate an oil spill probability of a dark pixel in a SAR image. An independent set of 26 SAR images were used to validate the algorithm and it was found that 80.9% of the oil spills were correctly classified, and 20.0% of the lookalikes were wrongly classified as oil spills. The complete algorithmic procedure was coded in Matlab7.0 using its Fuzzy Logic Toolbox.
Circadian Misalignment Leads to Changes in Cortisol Rhythms, Blood Biochemical Variables and Serum miRNA Pro�les

Background: Circadian clock plays a critical role in synchronizing the inner molecular, metabolic and physiological processes to the environmental cues which cycle with a period of 24 h. Misalignment in the circadian rhythms leads to decrease in adaptation, performance and increased risk of associated disorders. The non-24-h schedules and shift schedules are commonly used in maritime operations, both of which could result in disturbance in circadian rhythms. The comprehensive effects of these schedules remain to be further elucidated. Methods: In this study, we �rstly conducted an experiment in which the volunteers followed a 3-d rotary schedule with consecutive shift in sleep time (rotatory schedule), and analyzed the changes in salivary cortisol rhythms and blood variables. Next we conducted another experiment in which the volunteers followed an 8 h on and 4 h off schedule (non-24-h schedule) to compare the changes in blood/serum variables. Furthermore, the plasma miRNAs from the volunteers following the rotatory schedule were subject for miRNA sequencing. Results: The rotatory schedule led to elevated levels of serum cortisol during the early stage, and the phase became delayed during the early and stages. The results show both of the schedules caused comprehensive changes in blood/serum biochemical variable, and consistently, the increase in phosphate levels. In addition, a subset of serum miRNAs targeting genes involved in circadian rhythms, sleep homeostasis and multiple important physiological processes or pathways were identi�ed in the experiment with rotatory schedule. Conclusions: This study revealed an increased stress during the rotatory schedule. Circadian misalignment caused by either non-24-h or rotatory schedule lead to extensive changes in blood/serum variables. As to the rotatory schedule, altered expression of serum miRNAs may account for the consequences of circadian misalignment. These �ndings would help understand the deleterious effects of shift schedules and optimize to enhance performance and welfare of the personnel working with similar schedules.
Positron emission tomography using(18)F-fluoro-deoxyglucose and euglycaemic hyperinsulinaemic glucose clamp: optimal criteria for the prediction of recovery of post-ischaemic left ventricular dysfunction. Results from the European Community Concerted Action Multicenter study on use of(18)F-fluoro-de

AIMS To assess the accuracy of positron emission tomography to predict recovery of global cardiac function after revascularization in patients with coronary artery disease. METHODS AND RESULTS One hundred and seventy-eight patients (157 male, 58+/-10 years) with coronary artery disease and left ventricular dysfunction (mean ejection fraction 39+/-14%) were enrolled in six European centres. They underwent a common protocol for the assessment of viability using(18)F-fluoro-2-deoxyglucose (FDG) positron emission tomography during a standardized euglycaemic hyperinsulinaemic glucose clamp before revascularization by either surgery (n=140) or angioplasty (n=38). Seven patients were excluded because of incomplete revascularization of a dysfunctional region. Based on the recovery of global ejection fraction 2-6 months after revascularization, patients were classified into two groups: 82 patients who had a >5% improvement in ejection fraction postoperatively, and 89 patients without postoperative ejection fraction improvement. Optimal cut-off points for postoperative improvement of global cardiac function were computed, using receiver operating curve analysis. The highest sensitivity (79%) and specificity (55%) for predicting postoperative ejection fraction improvement by positron emission tomography was found when three or more dysfunctional segments had a relative FDG uptake >45% of normal remote myocardium (overall accuracy 67%). CONCLUSIONS In a large cohort of coronary patients with impaired ejection fraction, FDG positron emission tomography demonstrated high sensitivity and moderate specificity to predict improvement of cardiac function after coronary revascularization.
Assessment of Intestinal Availability (F G ) of Substrate Drugs of Cytochrome P450s by Analyzing Changes in Pharmacokinetic Properties Caused by Drug – Drug Interactions s

In this study, we developed the drug – drug interaction (DDI) method as a new assessment technique of intestinal availability (F G , the fraction of drug transferred from the intestinal enterocytes into the liver, escaping from intestinal metabolism) based on the clearance theory. This method evaluates F G from changes caused by DDIs in the area under the blood concentration-time curve and in the elimination half-life of victim drugs. Application of the DDI method to data from the literature revealed that the mean and S.D. of F G values for 20 substrate drugs of CYP3A was 0.56 6 0.29, whereas that for 8 substrate drugs of CYP2C9, CYP2C19, and CYP2D6 was 0.86 6 0.11. These results were consistent with the fact that intestinal metabolism is mediated predominantly by CYP3A. The DDI method showed reasonable correlations with the conventional i.v. /p.o. method and the grape fruit juice (GFJ) method (coefficients of determination of 0.41 and 0.81, respectively). The i.v. /p.o. method was more susceptible to fluctuations in the hepatic blood flow rate compared with the DDI and GFJ methods. The DDI method evaluates F G separating from the absorption ratio (F A ) although it requires approximation of F A . Since preciseness of approximation of F A does not greatly affect the evaluation of F G by the DDI method, we proposed a reasonable approximation method of F A for the evaluation of F G in the DDI method. The DDI method would be applicable to a broad range of situations in which various DDI data are utilizable.
Self-reported needs and experiences of people with dementia living in nursing homes: a scoping revie

Self-reported needs and experiences of people with dementia living in nursing homes: a scoping review Kate Shiells, Lara Pivodic, Iva Holmerová & Lieve Van den Block To cite this article: Kate Shiells, Lara Pivodic, Iva Holmerová & Lieve Van den Block (2020) Selfreported needs and experiences of people with dementia living in nursing homes: a scoping review, Aging & Mental Health, 24:10, 1553-1568, DOI: 10.1080/13607863.2019. 1625303 To link to this article: https://doi.org/10.1080/13607863.2019. 1625303
Increased sucrose accumulation regulates iron-deficiency responses by 12 promoting auxin signaling in Arabidopsis plants

Previous studies have identified that auxins acts upstream of nitric oxide in 49 regulating iron-deficiency responses in roots, but the upstream signaling 50 molecule of auxins remains unknown.In this study, we showed that Fe-deficiency 51 increased sucrose level in roots of Arabidopsis . Exogenous application of sucrose 52 further stimulated Fe-deficiency-induced ferric-chelate-reductase (FCR) activity 53 and expression of Fe-acquisition-related genes FRO2 , IRT1 , and FIT in roots. 54 The opposite patterns were observed in the dark treatment. In addition, FCR 55 activity and expression of Fe-acquisition-related genes were higher in the 56 sucrose-high-accumulating transgenic plant 35S::SUC2 , but were lower in the 57 sucrose-low-accumulating mutant suc2-5 , compared to wild-type plants under 58 Fe-deficient conditions. Consequently, Fe-deficiency tolerance was enhanced in 59 35S::SUC2 , but was compromised in suc2-5 . Exogenous sucrose also increased 60 root GUS activity in auxin-inducible reporter DR5-GUS transgenic plants under 61 Fe-deficiency. However, exogenous sucrose failed to increase FCR activity and 62 expression of Fe-acquisition-related genes in the auxin transport-impaired 63 mutants aux1 - 7 and pin1-1 , as well as in the wild type plants treated with an 64 auxin transport inhibitor, under Fe-deficiency. In summary, we found that 65 increased sucrose accumulation is required for regulating Fe-deficiency 66 responses in plants, with auxins acting downstream in transmitting the 67 Fe-deficiency signal.
Pairwise graphical model for brain-state identification : application to decoding of spatial representations from hippocampal CA 1 and CA 3 recordings

Hippocampus can store spatial representations, or “maps”, which are recalled each time a subject is placed in the corresponding environment. We consider the problem of decoding the recalled maps as a function of time from multi-cellular recordings. We introduce a graphical model-based decoder, which accounts for the pairwise correlations between the spiking activities of neurons and does not require any positional information, i.e. any knowledge about place fields. We first show, on recordings of hippocampal activity in constant environmental conditions, that our decoder efficiently decodes maps in CA3 and outperfoms existing methods in CA1, where maps are much less orthogonal. Our decoder is then applied to data from teleportation experiments, in which instantaneous switches between environmental conditions trigger the recall of the corresponding maps. We test the sensitivity of our approach on the transition dynamics between the respective memory states (maps). We find that the rate of spontaneous state shifts (flickering) after a teleportation event is increased not only within the first few seconds as already reported, but the network also shows a higher instability level for on much longer (> 1 min) intervals, both in CA3 and in CA1. In addition, we introduce an efficient Bayesian decoder of the rat full trajectory over time, and find that the animal location can be accurately predicted at all times, even during flickering events. Precise information about the animal position is thus always present in the neural activity, irrespectively of the dynamical shifts in the recalled maps.
Visual Odometry for Quantitative Bronchoscopy Using Optical Flow

Optical Flow, the extraction of motion from a sequence of images or a video stream, has been extensively researched since the late 1970s, but has been applied to the solution of few practical problems. To date, the main applications have been within fields such as robotics, motion compensation in video, and 3D reconstruction. In this paper we present the initial stages of a project to extract valuable information on the size and structure of the lungs using only the visual information provided by a bronchoscope during a typical procedure. The initial implementation provides a realtime estimation of the motion of the bronchoscope through the patients airway, as well as a simple means for the estimation of the cross sectional area of the airway.
Kinetic parameters related to sources and sinks of vibrationally excited OH in the nightglow

Kinetic parameters related to vibrational deactivation and chemical removal of vibrationally excited OH radicals in the mesosphere are deduced from ground-based measurements of the mean vibrational distribution of the OH Meinel bands in the nightglow. The derived parameters, which rely on a laboratory measured rate coefficient for the removal of OH(v = 9) by O{sub 2} and a set of relative Meinel band transition probabilities, have been obtained for two limiting Meinel band excitation models that differ in the extent to which single-quantum vibrational deactivation and sudden death' collisional removal processes determine the OH vibrational distribution. It is shown that the OH Meinel band emission can be adequately explained with the deduced parameters and the H + O{sub 3} {yields} OH + O{sub 2} reaction as the only chemical source of vibrationally excited OH. Evidence is presented which suggests that the reaction HO{sub 2} + O {leftrightarrow} HO + O{sub 2} may perhaps be involved as a sink of vibrationally excited OH rather than as a potential source. The deduced kinetic parameters should be particularly useful in future Meinel band studies as they have been obtained from an analysis for which there is no assumption about the very uncertain OHmore » radiative lifetimes. « less
Deformation of a layered Earth by an axially symmetric surface mass distribution

Series expressions are developed for the surface displacements of a spherical earth model, deformed by both surface tractions and body forces arising from an axially symmetric distribution of mass over its surface. The model consist of m - 1 homogeneous elastic spherical shells, plus an inner core which is treated either as elastic or as a liquid.
Erythrocyte sodium/lithium countertransport is associated with thrombotic and fibrinolytic factors in 58-year-old men

Summary The metabolic syndrome, in which insulin resistance is the core feature, is associated both with dysregulation of thrombosis/ fibrinolysis and erythrocyte sodium/lithium countertransport (SLC). To investigate this further we designed a cross-sectional study to examine whether factors involved in coagulationand fibrinolysis systems were associated with SLC independently of insulin resistance in 93 58-year-old men. SLC was in univariate analysis positively correlated with PAI-1 activity (r = 0.35, p <0.01), tPA antigen (r = 0.38, p <0.01), von Willebrand factor (r = 0.25, p <0.05), protein S (r = 0.26, p <0.05), and C (r = 0.30, p <0.01), and negatively associated with tPA activity(r = −0.28, p <0.01). Since these correlations could be influenced by the components of the metabolic syndrome itself, a separate analysis with adjustment for glucose infusion rate (GIR), plasma insulin, body fat, sagittal diameter of the abdomen (SD) and log serum triglyceride concentration (TG) was conducted. Then SLC was associated with tPA antigen independent of GIR, plasma insulin, body fat, SD and TG. SLC was also associated with protein C independent of GIR, insulin, body fat and SD but not TG. In conclusion, we found a relationship between SLC and the fibrinolytic system that was not related to the metabolic syndrome.