Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulated night shift work induces circadian misalignment of the human peripheral blood mononuclear cell transcriptome

Significance Night shift work is associated with adverse health effects, including diabetes, cardiovascular disease, and cancer. Understanding the molecular mechanisms that underlie this association is instrumental in advancing the diagnosis, prevention, and treatment of shift work-related health concerns. We characterized the effect on genome-wide gene expression levels of a 4-day protocol simulating night shifts in healthy human subjects under highly controlled laboratory conditions. We demonstrate that this night shift protocol leads to a dampening of gene expression rhythms and a desynchrony between rhythmic transcripts and the shifted sleep/wake cycle. Moreover, we uncovered key biological processes and regulatory molecules that are altered during this night shift protocol and that may contribute to the development of health problems on the long term. Misalignment of the endogenous circadian timing system leads to disruption of physiological rhythms and may contribute to the development of the deleterious health effects associated with night shift work. However, the molecular underpinnings remain to be elucidated. Here, we investigated the effect of a 4-day simulated night shift work protocol on the circadian regulation of the human transcriptome. Repeated blood samples were collected over two 24-hour measurement periods from eight healthy subjects under highly controlled laboratory conditions before and 4 days after a 10-hour delay of their habitual sleep period. RNA was extracted from peripheral blood mononuclear cells to obtain transcriptomic data. Cosinor analysis revealed a marked reduction of significantly rhythmic transcripts in the night shift condition compared with baseline at group and individual levels. Subsequent analysis using a mixed-effects model selection approach indicated that this decrease is mainly due to dampened rhythms rather than to a complete loss of rhythmicity: 73% of transcripts rhythmically expressed at baseline remained rhythmic during the night shift condition with a similar phase relative to habitual bedtimes, but with lower amplitudes. Functional analysis revealed that key biological processes are affected by the night shift protocol, most notably the natural killer cell-mediated immune response and Jun/AP1 and STAT pathways. These results show that 4 days of simulated night shifts leads to a loss in temporal coordination between the human circadian transcriptome and the external environment and impacts biological processes related to the adverse health effects associated to night shift work.
Incremental dialysis for preserving residual kidney function—Does one size fit all when initiating dialysis?

While many patients have substantial residual kidney function (RKF) when initiating hemodialysis (HD), most patients with end stage renal disease in the United States are initiated on 3‐times per week conventional HD regimen, with little regard to RKF or patient preference. RKF is associated with many benefits including survival, volume control, solute clearance, and reduced inflammation. Several strategies have been recommended to preserve RKF after HD initiation, including an incremental approach to HD initiation. Incremental HD prescriptions are personalized to achieve adequate volume control and solute clearance with consideration to a patient's endogenous renal function. This allows the initial use of less frequent and/or shorter HD treatment sessions. Regular measurement of RKF is important because HD frequency needs to be increased as RKF inevitably declines. We narratively review the results of 12 observational cohort studies of twice‐weekly compared to thrice‐weekly HD. Incremental HD is associated with several benefits including preservation of RKF as well as extending the event‐free life of arteriovenous fistulas and grafts. Patient survival and quality of life, however, has been variably associated with incremental HD. Serious risks must also be considered, including increased hospitalization and mortality perhaps related to fluid and electrolyte shifts after a long interdialytic interval. On the basis of the above literature review, and our clinical experience, we suggest patient characteristics which may predict favorable outcomes with an incremental approach to HD. These include substantial RKF, adequate volume control, lack of significant anemia/electrolyte imbalance, satisfactory health‐related quality of life, low comorbid disease burden, and good nutritional status without evidence of hypercatabolism. Clinicians should engage patients in on‐going conversations to prepare for incremental HD initiation and to ensure a smooth transition to thrice‐weekly HD when needed.
Similarity evaluation between query and retrieved masses using a content-based image retrieval (CBIR) CADx system for characterization of breast masses on ultrasound images: an observer study

The purpose of this study is to evaluate the similarity between the query and retrieved masses by a Content-Based Image Retrieval (CBIR) computer-aided diagnosis (CADx) system for characterization of breast masses on ultrasound (US) images based on radiologists' visual similarity assessment. We are developing a CADx system to assist radiologists in characterizing masses on US images. The CADx system retrieves masses that are similar to a query mass from a reference library based on automatically extracted image features. An observer study was performed to compare the retrieval performance of four similarity measures: Euclidean distance (ED), Cosine (Cos), Linear Discriminant Analysis (LDA), and Bayesian Neural Network (BNN). For ED and Cos, a k-nearest neighbor (k-NN) algorithm was used for retrieval. For LDA and BNN, the features of a query mass were combined first into a malignancy score and then masses with similar scores were retrieved. For a query mass, three most similar masses were retrieved with each method and were presented to the radiologists in random order. Three MQSA radiologists rated the similarity between the query mass and the computer-retrieved masses using a nine-point similarity scale (1=very dissimilar, 9=very similar). The average similarity ratings of all radiologists for LDA, BNN, Cos, and ED were 4.71, 4.95, 5.18 and 5.32. The ED measures retrieved masses of significantly higher similarity (p<0.008) than LDA and BNN. Although the BNN measure had the best classification performance (Az: 0.90±0.03) in the CBIR scheme, ED exhibited higher image retrieval performance than others based on radiologists' assessment.
A peripheral blood transcriptome biomarker test to diagnose functional recovery potential in advanced heart failure

Heart failure (HF) is a complex clinical syndrome that causes systemic hypoperfusion and failure to meet the body’s metabolic demands. In an attempt to compensate, chronic upregulation of the sympathetic nervous system and renin-angiotensin-aldosterone leads to further myocardial injury, HF progression and reduced O2 delivery. This triggers progressive organ dysfunction, immune system activation and profound metabolic derangements, creating a milieu similar to other chronic systemic diseases and presenting as advanced HF with severely limited prognosis. We hypothesize that 1-year survival in advanced HF is linked to functional recovery potential (FRP), a novel clinical composite parameter that includes HF severity, secondary organ dysfunction, co-morbidities, frailty, disabilities as well as chronological age and that can be diagnosed by a molecular biomarker.
Expression of T-type calcium channels cav 3 . 1 and cav 3 . 2 in different segments and different gestational ages of mouse uterus

Objective: To explore the expression of T-type calcium channels Cav3.1 and Cav3.2 in different segments of mouse uterus as well as different gestational ages during pregnancy. Study design: Uterus samples were collected from C57BL/6 mice at 0, 7, 14, 19 days of pregnancy and one day postpartum. The mRNA expression levels of T-type calcium channel were detected by quantitative RT-PCR. Protei n expression levels of Cav3.1 and Cav3.2 at different gestational ages and different segments [upper segment (US) and lower segment (LS)] were determined by immunohistochemistry and western blot, respectively. Results: We only observed the expression of Cav3.1 and Cav3.2 in mouse uterus but not Cav3.3. The expression levels of Cav3.1 and Cav3.2 increased during pregnancy and declined rapidly after labor. Besides, Cav3.1 and Cav3.2 were significantly higher expressed in US compared to LS during late pregnancy (P < 0.05). Conclusion: Our results provide a comprehensive analysis of expression of T-type calcium channel subunit in US and LS of non-pregnant, pregnant and postpartum mouse myometrial cells.
Personal Space of Autonomous Car’s Passengers Sitting in the Driver’s Seat

This article deals with the specific context of an autonomous car navigating in an urban center within a shared space between pedestrians and cars. The driver delegates the control to the autonomous system while remaining seated in the driver’s seat. The proposed study aims at giving a first insight into the definition of human perception of space applied to vehicles by testing the existence of a personal space around the car. It aims at measuring proxemic information about the driver’s comfort zone in such conditions. Proxemics, or human perception of space, has been largely explored when applied to humans or to robots, leading to the concept of personal space, but poorly when applied to vehicles. In this article, we highlight the existence and the characteristics of a zone of comfort around the car which is not correlated to the risk of a collision between the car and other road users. Our experiment includes 19 volunteers using a virtual reality headset to look at 30 scenarios filmed in 360° from the point of view of a passenger sitting in the driver’s seat of an autonomous car. They were asked to say “stop” when they felt discomfort visualizing the scenarios. As said, the scenarios voluntarily avoid collision effect as we do not want to measure fear but discomfort. The scenarios involve one or three pedestrians walking past the car at different distances from the wings of the car, relative to the direction of motion of the car, on both sides. The car is either static or moving straight forward at different speeds. The results indicate the existence of a comfort zone around the car in which intrusion causes discomfort. The size of the comfort zone is sensitive neither to the side of the car where the pedestrian passes nor to the number of pedestrians. In contrast, the feeling of discomfort is relative to the car’s motion (static or moving). Another outcome from this study is an illustration of the usage of first person 360° video and a virtual reality headset to evaluate feelings of a passenger within an autonomous car.
A System to Recommend Open Educational Resources during an Online Course

Recently, personalization in Technology Enhanced Learning (TEL) has been researched extensively. With the spreading of online learning environments (OLE) as MOOCs and LMSs, a large number of learners with different characteristics and backgrounds can follow online courses. To support personalization, recommender systems can be used to provide each learner with learning objects helping him to reach his learning objectives. These recommendations are more specific to compute than usual recommendations (like consumer products). Furthermore, if they are included in a course, they depend not only on the learner’s profile but also on the content of the course, because they need to fit with the course format at any point. At the same time, there is a growing number of open educational resources (OER) available to usefully enrich the content of online courses. To facilitate their reuse some of these OERs are described with metadata schemas following Linked Open Data principles (LOD). In this paper, we introduce a MOOC-based OER recommender system (MORS) that can be plugged in an OLE to provide recommendations of OERs to learners based on their profiles, the course profile and a process for calculating recommendations based on OERs metadata. This paper presents our approach that has been implemented in a MOOC platform: Open edX. However the proposed approach could be implemented in any OLE by using the same process to calculate recommendations, as long as the learner and the course profiles can be extracted.
Intracellular cavity of sensor domain controls allosteric gating of TRPA1 channel

A cavity in the ion channel TRPA1 coordinates electrophilic, voltage, and calcium sensitivity and might be targeted to treat pain and other disorders. Regulatory cavity in TRPA1 The ion- and voltage-gated channel TRPA1 contributes to acute and chronic pain and itch, as well as vascular function. The channel is sensitive to temperature, pressure, various environmental irritants, and other molecules generated by injury or inflammation in an allosteric manner, meaning that the channel’s response to one stimulus alters its response to another. Zimova et al. investigated the structure of TRPA1 and found an intracellular region within the sensor domain that coordinates this complex allostery. For example, mutations in this cavity prevented stabilization of the channel by interacting intracellular phospholipids, resulting in dysregulated sensitivity to calcium ions. These findings suggest that alterations to the cavity may underlie chronic pain or itch in patients. Transient receptor potential ankyrin 1 (TRPA1) is a temperature-sensitive ion channel activated by various pungent and irritant compounds that can produce pain in humans. Its activation involves an allosteric mechanism whereby electrophilic agonists evoke interactions within cytosolic domains and open the channel pore through an integrated nexus formed by intracellular membrane proximal regions that are densely packed beneath the lower segment of the S1–S4 sensor domain. Studies indicate that this part of the channel may contain residues that form a water-accessible cavity that undergoes changes in solvation during channel gating. We identified conserved polar residues facing the putative lower crevice of the sensor domain that were crucial determinants of the electrophilic, voltage, and calcium sensitivity of the TRPA1 channel. This part of the sensor may also comprise a domain capable of binding to membrane phosphoinositides through which gating of the channel is regulated in a state-dependent manner.
Dietary Pattern and Macronutrients Profile on the Variation of Inflammatory Biomarkers: Scientific Update

It is known that the dietary pattern and macronutrients profile may influence the expression and secretion of inflammatory biomarkers, and the low-grade inflammation is associated with the manifestation of noncommunicable chronic diseases. Therefore, this review aimed to present and discuss the role of dietary patterns and macronutrients on the variation of inflammatory markers related to NCD risk. Scientific evidences within the last five years based on clinical trials, case-controls, cohorts, and cross-sectional studies indicate that normocaloric, carbohydrate-moderated, low-glycemic index, protein-moderated, monounsaturated and polyunsaturated fatty acid-rich, omega-3, and low-saturated fat diets display positive effects on the inflammatory state, both in healthy individuals and in those with cardiovascular risk, although the second group seems to benefit more from changes in the dietary profile.
Contribution of Somesthetic Information to the Perception of Body Orientation in the Pitch Dimension

This study investigated the contribution of otolithic and somesthetic inputs in the perception of body orientation when pitching at very slow velocities. In Experiment 1, the subjects’ task was to indicate their subjective postural vertical, in two different conditions of body restriction, starting from different angles of body tilt. In the “strapped” condition, subjects were attached onto a platform by means of large straps. In the “body cast” condition, subjects were completely immobilized in a depressurized system, which attenuates gravity-based somesthetic cues. Results showed that the condition of body restriction and the initial tilt largely influenced the subjective postural vertical. In Experiment 2, subjects were displaced from a vertical position and had to detect the direction of body tilts. Results showed that the threshold for the perception of body tilt was higher when subjects were immobilized in the body cast and when they were tilted backward. Experiment 3 replicated the same protocol from a supine starting position. Compared to results of Experiment 2, the threshold for the perception of body tilt decreased significantly. Overall, these data suggested that gravity-based somesthetic cues are more informative than otolithic cues for the perception of a quasi-static body orientation.
Effect of atmospheric nutrients on the autotrophic communities in a low nutrient, low chlorophyll system

The effect of atmospheric inputs on phytoplanktonic dynamics was investigated in the Mediterranean Sea during the season characterized by a stratified water column, low primary productivity, and low concentrations of nutrients ([nitrate] < 50 nmol L−1; [phosphate] = 20 nmol L−1; [silicate] = 0.7 µmol L−1). We report here data obtained during microcosm enrichment experiments performed on the natural assemblage using different combinations of realistic additions (Saharan dust, Fe, Fe + phosphate, and anthropogenic particles). Saharan dust and Fe + phosphate treatments significantly stimulated primary production. Anthropogenic particles and Fe + phosphate treatments increased the chlorophyll a concentrations, enhancing mainly the small cells (pico‐ and nanophytoplankton). The autotrophic community structure was significantly altered; for example, Fe and Fe + phosphate additions benefited prokaryotic populations, indicating possible nitrogen fixation. The colimitation of both phosphate and Fe was removed by these additions. Results emphasized the effect of Fe, although the ambient concentration was close to 1 nmol L−1. The addition of dust benefited eukaryotic populations, which indicates that the dust was a possible source of nitrogen. An abiotic dissolution experiment of macronutrients attached to dust confirmed this hypothesis. The dissolution of Fe attached to the dust (0.23–0.61%) and to the anthropogenic particles (0.86–1.85%) was consistent with previous studies conducted under abiotic conditions. This result suggests that the possible enhancement of the dissolution processes caused by biological activity might have been balanced by Fe consumption by the biota and its adsorption on both mineral and organic particles.
Alcance de la creación de valor en las Empresas Responsables

La inclusion de elementos basicos inherentes a la Responsabilidad Social Corporativa (RSC) en el mundo empresarial y en la vida de las empresas ha presentado desde el primer momento dificultades al considerarse antiteticos los conceptos de responsabilidad social y de creacion de valor: contraponiendo shareholders y stakeholders. Ante estas dificultades, las motivaciones que justifican la adopcion de los conceptos de la RSC son diversas pero cada vez hay un mayor consenso en que la RSC integra de manera esencial la estrategia corporativa. Asi, la RSC hace que las empresas esten en continua interactuacion con su entorno, reconcibiendo productos y mercados, redefiniendo una mejora constante en su cadena de valor y cooperando al desarrollo local. Este trabajo quiere aportar luz sobre la posible existencia de correlacion entre la aplicacion de la RSC y la capacidad de las empresas para crear valor, principalmente sobre la cuenta de resultados. El analisis se ha realizado con 122 empresas cotizadas espanolas durante el periodo 2000-2009.
Suppressing viscous fingering in structured porous media

Significance Viscous fingering commonly takes place during injection of one fluid that displaces a resident fluid in a porous medium. Fingering normally is promoted where the injected fluid is less viscous than the resident fluid being displaced. We propose a design of a porous medium in the form of an ordered structure to suppress or trigger (depending on the application) viscous fingering in porous media without modifying fluid properties or wettability. We utilize pore-scale direct numerical simulations, state-of-art experiments and analysis to derive predictive tools to evaluate effects of various parameters on controlling viscous fingering in porous media. Moreover, we propose generalized analytical solutions and a phase diagram for the parameter space affecting viscous fingering patterns. Finger-like protrusions that form along fluid−fluid displacement fronts in porous media are often excited by hydrodynamic instability when low-viscosity fluids displace high-viscosity resident fluids. Such interfacial instabilities are undesirable in many natural and engineered displacement processes. We report a phenomenon whereby gradual and monotonic variation of pore sizes along the front path suppresses viscous fingering during immiscible displacement, that seemingly contradicts conventional expectation of enhanced instability with pore size variability. Experiments and pore-scale numerical simulations were combined with an analytical model for the characteristics of displacement front morphology as a function of the pore size gradient. Our results suggest that the gradual reduction of pore sizes act to restrain viscous fingering for a predictable range of flow conditions (as anticipated by gradient percolation theory). The study provides insights into ways for suppressing unwanted interfacial instabilities in porous media, and provides design principles for new engineered porous media such as exchange columns, fabric, paper, and membranes with respect to their desired immiscible displacement behavior.
HEART RATE VARIABILITY ANALYSIS THROUGH MULTIRESOLUTION ORTHOGONAL WAVELET TRANSFORM

Heart rate fluctuations contain important diagnostic information about a number of biological control and feedback subsystems. In the present study we show that the multiresolution decomposition through orthogonal wavelet transform is able to reveal short-time as well as long-term heart rhythm variations. We demonstrate that return maps and autocorrelation of the low/high frequency regions of the heart rate variability can be very useful for understanding the underlying chaotic and deterministic control patterns.
The Bethe ansatz for the six-vertex and XXZ models: An exposition

In this paper, we review a few known facts on the coordinate Bethe ansatz. We present a detailed construction of the Bethe ansatz vector (psi) and energy (Lambda), which satisfy (V psi = Lambda psi), where (V) is the transfer matrix of the six-vertex model on a finite square lattice with periodic boundary conditions for weights (a= b=1) and (c > 0). We also show that the same vector (psi) satisfies (H psi = E psi), where (H) is the Hamiltonian of the XXZ model (which is the model for which the Bethe ansatz was first developed), with a value (E) computed explicitly. Variants of this approach have become central techniques for the study of exactly solvable statistical mechanics models in both the physics and mathematics communities. Our aim in this paper is to provide a pedagogically-minded exposition of this construction, aimed at a mathematical audience. It also provides the opportunity to introduce the notation and framework which will be used in a subsequent paper by the authors [5] that amounts to proving that the random-cluster model on (mathbb{Z}^{2}) with cluster weight (q >4) exhibits a first-order phase transition.