Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription factors: building hubs in the 3D space

ABSTRACT The hierarchical three-dimensional folding of the mammalian genome constitutes an important regulatory layer of gene expression and cell fate control during processes such as development and tumorigenesis. Accumulating evidence supports the existence of complex topological assemblies in which multiple genes and regulatory elements are frequently interacting with each other in the 3D nucleus. Here, we will discuss the nature, organizational principles, and potential function of such assemblies, including the recently reported enhancer “hubs,” “cliques,” and FIREs (frequently interacting regions) as well as multi-contact hubs. We will also review recent studies that investigate the role of transcription factors (TFs) in driving the topological genome reorganization and hub formation in the context of cell fate transitions and cancer. Finally, we will highlight technological advances that enabled these studies, current limitations, and future directions necessary to advance our understating in the field.
Silica Nanoparticles in Transmucosal Drug Delivery

Transmucosal drug delivery includes the administration of drugs via various mucous membranes, such as gastrointestinal, nasal, ocular, and vaginal mucosa. The use of nanoparticles in transmucosal drug delivery has several advantages, including the protection of drugs against the harsh environment of the mucosal lumens and surfaces, increased drug residence time, and enhanced drug absorption. Due to their relatively simple synthetic methods for preparation, safety profile, and possibilities of surface functionalisation, silica nanoparticles are highly promising for transmucosal drug delivery. This review provides a description of silica nanoparticles and outlines the preparation methods for various core and surface-functionalised silica nanoparticles. The relationship between the functionalities of silica nanoparticles and their interactions with various mucous membranes are critically analysed. Applications of silica nanoparticles in transmucosal drug delivery are also discussed.
Critical Control Points of Street-Vended Foods in the Dominican Republic.

Hazard analyses were conducted at four street-vending stands in the Dominican Republic. Temperatures of foods were measured during cooking, display (holding), and reheating (when done). Samples were taken at each step of the operation and at 5 to 6-h intervals during display. Foods usually attained temperatures that exceeded 90°C at the geometric center during cooking and reheating. At three of the stands, foods (e.g., fish, chickens, pork pieces) were fried and held until sold. Leftovers were held overnight at ambient temperatures in the home of the vendor or in a locked compartment of the stand. They were usually reheated early in the morning and displayed until sold. During the interval of holding, aerobic mesophilic counts progressively increased with time from about 103 after cooking to between 105 to 109/g. The higher counts were usually associated with holding overnight. Escherichia coli (in water, milk and cheese samples), Bacillus cereus (in bean and rice samples), and Clostridium perfringens (in meat, chicken and bean samples) were isolated, but usually in numbers less than 103/g. At the other stand, foods (e.g. beans, rice, meat and chicken) were cooked just before serving as complete meals. There were no leftovers. This operation was less hazardous, although there were many sanitary deficiencies. Recommendations for prevention and control of microbial hazards (mainly reducing holding time, periodic reheating and requesting reheating just before purchasing) are given. The need and suggestions for implementing educational activities to alert and inform those concerned about hazards and preventive measures are presented.
Increased Intestinal Permeability is Associated with Later Development of Crohn's Disease.

BACKGROUND & AIMS Increased intestinal permeability have been associated with Crohn's disease (CD), but it is not clear whether these are a cause or result of the disease. We performed a prospective study to determine whether increased intestinal permeability is associated with future development of CD. METHODS We assessed the intestinal permeability, measured by the urinary fractional excretion of lactulose to mannitol ratio (LMR) at recruitment in 1420 asymptomatic first-degree relatives (6-35 years old) of patients with CD (collected from 2008 through 2015). Participants were then followed for a diagnosis of CD from 2008 to 2017, with a median follow up time of 7.8 years. We analyzed data from 50 participants who developed CD after a median of 2.7 years during the study period, along with 1370 individuals who remained asymptomatic until October 2017. We used the Cox proportional hazards model to evaluate time-related risk of CD based on the baseline LMR. RESULTS An abnormal LMR (> 0.03) was associated with diagnosis of CD during the follow-up period (hazard ratio, 3.03; 95% CI, 1.64-5.63; P=3.97×10-4). This association remained significant even when the test was performed more than 3 years before the diagnosis of CD (hazard ratio, 1.62, 95% CI, 1.051-2.50; P=.029). CONCLUSIONS Increased intestinal permeability is associated with later development of CD; these findings support a model in which altered intestinal barrier function contributes to pathogenesis. Abnormal gut barrier function might serve as a biomarker for risk of CD onset.
A Comparison of Intermittent and Continuous Exercise Bouts at Different Intensities on Appetite and Postprandial Metabolic Responses in Healthy Men

Exercise intensity affects many potential postprandial responses, but there is limited information on the influence of exercise modality. Therefore, the aim of this study was to investigate if the nature of exercise at two different intensities would affect gastric emptying rate (GER), appetite and metabolic responses following ingestion of a semi-solid meal. Twelve healthy men completed, in a random order, four 60-min cycles at 60% VO2peak (MOD), 40% VO2peak (LOW) and in a continuous (CON) or intermittent (INT) manner. INT consisted of 20 × 1-min exercise bouts with 2-min rest breaks. INT and CON were matched for total work output at each intensity. GER of the post-exercise meal was measured for 2 h using the 13C-breath method. Blood glucose, substrate utilisation and appetite ratings were measured at regular intervals throughout all trials and 24-h energy intake (EI) post-trials was assessed. GER-Delta over Baseline (DOB) was lower (p < 0.05) on MOD-INT vs. MOD-CON from 30–120 min post-meal. Blood glucose was higher mid-exercise (p < 0.05) on MOD-INT vs. MOD-CON. Although post-exercise LOW-CON was significantly higher than LOW-INT (p < 0.05), blood glucose was also higher 30-min post-meal ingestion on both CON trials compared to INT (p < 0.001). No interaction effect was observed for perceived appetite responses 2 h after meal ingestion (all p > 0.05). 24-h post-trial EI was similar between LOW-CON vs. LOW-INT (p > 0.05), although MOD-INT vs. MOD-CON 3500 ± 1419 vs. 2556 ± 989 kCal: p < 0.001 was elevated. In summary, MOD-INT exercise delays GER without stimulating perceived appetite in the 2 h period after meal ingestion, although EI was greater in the 24-h post-trial.
Analyses of the Root-Knot Nematode (Meloidogyne graminicola) Transcriptome during Host Infection Highlight Specific Gene Expression Profiling in Resistant Rice Plants

The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa infection were previously characterized but no information is available about the molecular dialogue established with a resistant plant. We compared the M. graminicola transcriptomes of stage-two juveniles (J2s) before and during infection of susceptible or resistant rice. Among 36,121 M. graminicola genes surveyed, 367 were differentially expressed during infection of resistant or susceptible plants. Genes encoding cell wall-degrading enzymes, peptidases and neuropeptides were expressed for a longer time in resistant plants compared to susceptible plants. Conversely, genes related to nematode development were not activated in the resistant host. The majority of M. graminicola effector genes had similar expression patterns, whatever the host genotype. However, two venom allergen-like protein (VAP)-encoding genes were specifically induced in resistant plants and Mg-VAP1 silencing in J2s reduced their ability to colonize roots. This study highlighted that M. graminicola adapts its gene expression to the host susceptibility. Further investigation is required to assess the role of Mg-VAPs in the rice–nematode interaction.
The long-term sand crab study: phenology, geographic size variation, and a rare new colour morph in Lepidopa benedicti (Decapoda: Albuneidae)

Little is known about the basic ecology of albuneid sand crabs because they conceal themselves by digging in sand, and are typically found at low densities. I sampled sand crabs, Lepidopa benedicti were sampled at South Padre Island, Texas, regularly for more than five years. Density is high in the summer, and low in the winter. The sex ratio is slightly, but consistently, female skewed. Ovigerous females, carrying about one thousand eggs, are found in mid-summer, with most of the young of the year settling in autumn. The average size of individuals in the South Texas population is smaller than individuals in the Atlantic Ocean, but the population density appear to be higher in Texas. I also describe a new orange colour morph. The results are not consistent with an earlier suggestion that South Texas acts as a population sink for L. benedicti.
Preterm Brain Injury, Antenatal Triggers, and Therapeutics: Timing Is Key

With a worldwide incidence of 15 million cases, preterm birth is a major contributor to neonatal mortality and morbidity, and concomitant social and economic burden Preterm infants are predisposed to life-long neurological disorders due to the immaturity of the brain. The risks are inversely proportional to maturity at birth. In the majority of extremely preterm infants (<28 weeks’ gestation), perinatal brain injury is associated with exposure to multiple inflammatory perinatal triggers that include antenatal infection (i.e., chorioamnionitis), hypoxia-ischemia, and various postnatal injurious triggers (i.e., oxidative stress, sepsis, mechanical ventilation, hemodynamic instability). These perinatal insults cause a self-perpetuating cascade of peripheral and cerebral inflammation that plays a critical role in the etiology of diffuse white and grey matter injuries that underlies a spectrum of connectivity deficits in survivors from extremely preterm birth. This review focuses on chorioamnionitis and hypoxia-ischemia, which are two important antenatal risk factors for preterm brain injury, and highlights the latest insights on its pathophysiology, potential treatment, and future perspectives to narrow the translational gap between preclinical research and clinical applications.
The RNAi Pathway Is Important to Control Mayaro Virus Infection in Aedes aegypti but not for Wolbachia-Mediated Protection

Mayaro virus (MAYV), a sylvatic arbovirus belonging to the Togaviridae family and Alphavirus genus, is responsible for an increasing number of outbreaks in several countries of Central and South America. Despite Haemagogus janthinomys being identified as the main vector of MAYV, laboratory studies have already demonstrated the competence of Aedes aegypti to transmit MAYV. It has also been demonstrated that the Wolbachia wMel strain is able to impair the replication and transmission of MAYV in Ae. aegypti. In Ae. aegypti, the small interfering RNA (siRNA) pathway is an important antiviral mechanism; however, it remains unclear whether siRNA pathway acts against MAYV infection in Ae. aegypti. The main objective of this study was to determine the contribution of the siRNA pathway in the control of MAYV infection. Thus, we silenced the expression of AGO2, an essential component of the siRNA pathway, by injecting dsRNA-targeting AGO2 (dsAGO2). Our results showed that AGO2 is required to control MAYV replication upon oral infection in Wolbachia-free Ae. aegypti. On the other hand, we found that Wolbachia-induced resistance to MAYV in Ae. aegypti is independent of the siRNA pathway. Our study brought new information regarding the mechanism of viral protection, as well as on Wolbachia mediated interference.
In Vivo Confocal Microscopy of Stromal Lenticule Addition Keratoplasty for Advanced Keratoconus.

PURPOSE To investigate the in vivo corneal microscopic changes after femtosecond laser-assisted stromal lenticule addition keratoplasty in keratoconus by means of in vivo confocal microscopy. METHODS Patients affected by advanced keratoconus were included in the study. Negative meniscus-shaped stromal lenticules, produced with a femtosecond laser (VisuMax; Carl Zeiss Meditec) from eye bank corneas were transplanted into a stromal pocket dissected in the recipient cornea at a depth of 120 µm. In vivo confocal microscopy was performed during the 12-month follow-up to investigate changes of the corneal and lenticule structure. RESULTS Ten patients were enrolled in the study. No changes of the dendritic cell population were documented during the follow-up period. Mild edema and stromal keratocyte activation gradually decreased during the first month. Subbasal nerve density returned to preoperative values after 6 months. Donor-recipient interfaces appeared hyperreflective but gradually improved over time with significantly reduced reflectivity after 3 months. No evidence of stromal inflammatory cell migration or matrix opacification was observed. Endothelial and keratocyte density remained stable over time. A variable degree of stromal radially distributed folds, not visible on biomicroscopy, was observed in the lenticule and in the posterior recipient stroma. CONCLUSIONS Stromal lenticule addition keratoplasty produces transitory nerve plexus density reduction and minor inflammatory reaction that rapidly decreases during the first month. Donor-recipient interface reflectivity is comparable to a femtosecond laser refractive procedure with no sign of stromal opacification or stromal rejection in 1 year of follow-up. [J Refract Surg. 2020;36(8):544-550. ].
QUANTITATIVE GENETIC ANALYSIS OF HYDROXYCINNAMIC ACIDS IN MAIZE (Zea mays L.) FOR PLANT IMPROVEMENT AND PRODUCTION OF HEALTH-PROMOTING COMPOUNDS.

Hydroxycinnamic acids, including ferulic acid and p-coumaric acid, have been tied to multiple positive health and agronomic benefits. However, little work has been done to improve the concentration of hydroxycinnamic acids in maize. We evaluated a set of twelve commercially important maize (Zea mays L.) inbred lines and 66 hybrids derived from their crosses for hydroxycinnamic acid concentration in the grain, grain yield, and test weight. The grain was obtained from replicated field experiments, which were conducted for three years. Both ferulic acid and p-coumaric acid were found to be highly heritable, and most of the genetic variation was additive. Grain yield and test weight were not correlated with hydroxycinnamic acid concentration. These findings suggest that breeding maize for improved hydroxycinnamic acid concentration is feasible. Maize hybrids with high hydroxycinnamic acid concentrations in the grain could be useful for the production of dietary supplements or all-natural food additives, while imparting enhanced resistance to biotic and abiotic stresses during the growing season and grain storage.
Bacterial products in donor airways prevent the induction of lung transplant tolerance

Although postoperative bacterial infections can trigger rejection of pulmonary allografts, the impact of bacterial colonization of donor grafts on alloimmune responses to transplanted lungs remains unknown. Here, we tested the hypothesis that bacterial products present within donor grafts at the time of implantation promote lung allograft rejection. Administration of the toll‐like receptor 2 (TLR2) agonist Pam3Cys4 to Balb/c wild‐type grafts triggered acute cellular rejection after transplantation into B6 wild‐type recipients that received perioperative costimulatory blockade. Pam3Cys4‐triggered rejection was associated with an expansion of CD8+ T lymphocytes and CD11c+CD11bhiMHC (major histocompatibility complex) class II+ antigen‐presenting cells within the transplanted lungs. Rejection was prevented when lungs were transplanted into TLR2‐deficient recipients but not when MyD88‐deficient donors were used. Adoptive transfer of B6 wild‐type monocytes, but not T cells, following transplantation into B6 TLR2‐deficient recipients restored the ability of Pam3Cys4 to trigger acute cellular rejection. Thus, we have demonstrated that activation of TLR2 by a bacterial lipopeptide within the donor airways prevents the induction of lung allograft tolerance through a process mediated by recipient‐derived monocytes. Our work suggests that donor lungs harboring bacteria may precipitate an inflammatory response that can facilitate allograft rejection.
Accurate Long-Term Multiple People Tracking Using Video and Body-Worn IMUs

Most modern approaches for video-based multiple people tracking rely on human appearance to exploit similarities between person detections. Consequently, tracking accuracy degrades if this kind of information is not discriminative or if people change apparel. In contrast, we present a method to fuse video information with additional motion signals from body-worn inertial measurement units (IMUs). In particular, we propose a neural network to relate person detections with IMU orientations, and formulate a graph labeling problem to obtain a tracking solution that is globally consistent with the video and inertial recordings. The fusion of visual and inertial cues provides several advantages. The association of detection boxes in the video and IMU devices is based on motion, which is independent of a person’s outward appearance. Furthermore, inertial sensors provide motion information irrespective of visual occlusions. Hence, once detections in the video are associated with an IMU device, intermediate positions can be reconstructed from corresponding inertial sensor data, which would be unstable using video only. Since no dataset exists for this new setting, we release a dataset of challenging tracking sequences, containing video and IMU recordings together with ground-truth annotations. We evaluate our approach on our new dataset, achieving an average IDF1 score of 91.2%. The proposed method is applicable to any situation that allows one to equip people with inertial sensors.
Innovative Characterization of Particulate Matter Deposited on Urban Vegetation Leaves through the Application of a Chemical Fractionation Procedure

In this study, we have evaluated the efficiency of a chemical fractionation procedure for the characterization of both the water-soluble and the insoluble fraction of the main elemental components of particulate matter (PM) deposited on urban leaves. The proposed analytical approach is based on the chemical analysis of leaf washing solutions and membrane filters used for their filtration. The ionic concentration of leaf washing solutions was compared with their electrical conductivity, making it a valuable proxy for the quantification of the water-soluble and ionic fraction of leaf deposited PM. The chemical composition of both the water-soluble and the insoluble fraction of PM, resulting from this fractionation procedure, was compared with results obtained by scanning electron microscopy coupled with energy-dispersed X-Rays spectroscopy (SEM/EDX) and processed through chemometrics. Results obtained proved that the proposed approach is able to provide an estimation of total leaf deposited PM and it is highly reliable for the evaluation of the emission impact of different PM sources, being able to increase the selectivity of PM elemental components as specific source tracers; consequently providing useful information also for the assessment of human health risks.
Metabolic incorporation of H218O into specific glucose‐6‐phosphate oxygens by red‐blood‐cell lysates as observed by 13C isotope‐shifted NMR signals

Water enriched with oxygen‐18 (H218O) is a potential tracer for evaluating the sources of glucose and glycogen synthesis since it is incorporated into specific sites of glucose‐6‐phosphate via specific enzyme‐mediated exchange/addition mechanisms. Unlike 2H, 18O does not experience significant isotope effects for any of these processes. Therefore, H218O might provide more precise estimates of endogenous carbohydrate synthesis compared with deuterated water provided that positional 18O enrichments of glucose can be measured. As a proof of concept, H218O was incorporated into a well characterized hemolysate model of sugar phosphate metabolism and 13C NMR was applied to quantify positional 18O enrichment of glucose‐6‐phosphate oxygens.
Mediating role of disordered eating in the relationship between screen time and BMI in adolescents: longitudinal findings from the Research on Eating and Adolescent Lifestyles (REAL) study

Abstract Objective: This study investigated whether the duration and type of screen time (ST) (TV viewing, recreational computer use, video gaming) is longitudinally associated with z-BMI and if these relationships are mediated by disordered eating (emotional, restrained). Design: At baseline, participants were n 1197 (T1; 60 % female) adolescents (mean age = 13·51 years) who completed surveys over 2 years. ST was assessed by a self-reported measure created by the investigative team, while emotional and restrained eating was measured by the Dutch Eating Behaviour Questionnaire (DEB-Q). Height and weight were objectively measured to quantify z-BMI. Setting: Thirty-one public and two private schools from the region of Ottawa, Canada. Participants: Students in grades 7–12. Results: Parallel multiple mediation analyses revealed that more time spent watching TV at baseline is associated with higher z-BMI at T3 (total effect; B = 0·19, se = 0·07, P = 0·01, 95 % CI 0·05, 0·34), but no relationships were observed for total ST exposure or other types of ST and z-BMI. Disordered eating did not mediate the positive association between baseline TV viewing and z-BMI at T3. Conclusions: TV viewing was longitudinally associated with higher z-BMI in a community-based sample of adolescents, but disordered eating behaviours did not mediate this relationship. However, other non-pathological eating behaviours may mediate the association between ST and obesity and warrant further investigation. Finding suggests that targeting reduction in youth’s TV viewing may be an effective component in the prevention of childhood obesity.