Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Chemokines and Chemokine Receptors in Diabetic Nephropathy

Kidney function decline is one of the complications of diabetes mellitus and may be indicated as diabetic nephropathy (DN). DN is a chronic inflammatory disease featuring proteinuria and a decreasing glomerular filtration rate. Despite several therapeutic options being currently available, DN is still the major cause of end-stage renal disease. Accordingly, widespread innovation is needed to improve outcomes in patients with DN. Chemokines and their receptors are critically involved in the inflammatory progression in the development of DN. Although recent studies have shown multiple pathways related to the chemokine system, the specific and direct effects of chemokines and their receptors remain unclear. In this review, we provide an overview of the potential role and mechanism of chemokine systems in DN proposed in recent years. Chemokine system-related mechanisms may provide potential therapeutic targets in DN.
Prevalence of accessory septations of sphenoid sinus in pediatric population: Applications to endoscopic sinus surgery

Sphenoid sinus accessory septations and their possible insertion on internal carotid artery (ICA) may represent a risk for endoscopic sinus surgical procedures. However, scarce data on this variant for children are available so far. This retrospective study included 220 maxillofacial CT‐scans equally divided among males (13.4 ± 2.1 years) and females (13.9 ± 2.2 years). On each CT‐scan, prevalence of accessory septations, number of septations in sphenoid sinuses, and their possible insertion onto ICA bone walls were recorded. Significant differences in protrusion and insertion of septations onto the ICA bone walls according to sex were assessed through Chi‐square test (p < .05). Possible correlations between the prevalence of accessory septations, ICA insertion, and number of accessory septations and age were assessed by means of Pearson's regression (p < .05). On average, 66% of males and 71% of females had at least one accessory septation, without significant differences according to sex or age (p > .05): septal insertion on ICA was found in 13% of subjects, without any significant difference for sex or age (p > .05). The number of septations was significantly increased with age (p < .05). The present study showed that the prevalence of accessory septations and insertion onto the ICA are independent of age and these results are similar to those reported in adults. Results will be useful for the management of endoscopic sinus surgery.
Image-Based Food Classification and Volume Estimation for Dietary Assessment: A Review

A daily dietary assessment method named 24-hour dietary recall has commonly been used in nutritional epidemiology studies to capture detailed information of the food eaten by the participants to help understand their dietary behaviour. However, in this self-reporting technique, the food types and the portion size reported highly depends on users’ subjective judgement which may lead to a biased and inaccurate dietary analysis result. As a result, a variety of visual-based dietary assessment approaches have been proposed recently. While these methods show promises in tackling issues in nutritional epidemiology studies, several challenges and forthcoming opportunities, as detailed in this study, still exist. This study provides an overview of computing algorithms, mathematical models and methodologies used in the field of image-based dietary assessment. It also provides a comprehensive comparison of the state of the art approaches in food recognition and volume/weight estimation in terms of their processing speed, model accuracy, efficiency and constraints. It will be followed by a discussion on deep learning method and its efficacy in dietary assessment. After a comprehensive exploration, we found that integrated dietary assessment systems combining with different approaches could be the potential solution to tackling the challenges in accurate dietary intake assessment.
Massive-scale RNA-Seq experiments in human genetic diseases

Since 2008, our research group is actively working in the field of NGS, with particular attention to RNA-Seq as innovative approach to understand cells’ transcriptome in disease states (Costa et al., 2010a). In particular, combining molecular biology and computational expertise, we have recently analysed (Costa et al., 2011) by RNA-Seq for the first time in Down syndrome (DS) the global transcriptome of endothelial progenitor cells (EPCs), morphologically and functionally impaired in DS (Costa et al., 2010b). After rRNA depletion followed by strand specific sequencing we measured expression from (even) low expressed genes, we identified new regions of active transcription outside annotated loci, novel splice isoforms and extended untranslated regions for known genes, potentially new microRNA targets or regulatory sites. However, although RNA-Seq provided a huge amount of useful data for DS, showing a genome-wide alteration of gene expression (not limited to HSA21 genes), the experiment revealed only a fraction of the underlying complexity, giving no information about the reasons of such global deregulation. Therefore, in this ongoing project we aim to study: 1) by ChIP-Seq, the binding maps of some (preliminarily selected) transcription factors (TFs), key players in gene expression modulation, and 2) by RNA-Seq, the related gene expression changes in the same cells. ChIP-Seq, combining standard chromatin immunoprecipitation and massively parallel sequencing, allows to identify DNA sequences bound by TFs in vivo, helping to decipher gene regulatory networks (Park 2009). We believe that integrating RNAand ChIP-Seq data would provide much more biological insights into gene expression regulation in DS cells, helping us to better understand some blood-related pathological aspects of the syndrome. Our group is also participating to a large-scale collaborative industrial project aimed to develop a diagnostic kit for personalized therapeutic strategies in type 2 diabetic (T2D) patients resistant to conventional drug therapies. In particular, to elucidate some mechanisms of drug resistance, our group will perform massive-scale transcriptome analysis by RNA-Seq in a well-selected subset of individuals (~50), also collaborating with bioinformaticians to further data analysis. In the light of these considerations, and given the objectives of the COST Action BM1006, our group will contribute to the goals of the SEQAHEAD project by actively integrating in the newborn European network of NGS, providing its expertise in sequencing technologies with a particular contribution (protocols, experimental data and pipelines for data analysis) to the RNA-Seq.
[Effectiveness of antihypertensive conservative-free therapy with fixed combination of bimatoprost and timolol (intermediate results)].

INTRODUCTION The effects of antihypertensive therapy are often determined by patient compliance with the prescribed treatment plan. Acceptance of conservative-free forms of drugs leads to a decrease in the frequency and severity of side effects, reduces the need for the use of artificial tears, which lowers the cost of treatment for the patients. PURPOSE to evaluate the hypotensive effectiveness of a fixed combination of bimatoprost (0.03%) and timolol (0.5%), and its effect on the ocular surface in patients with newly diagnosed advanced glaucoma. MATERIAL AND METHODS The study was conducted during February-November 2018, and included 46 patients (76 eyes) with newly diagnosed POAG and healthy volunteers (control group). All patients underwent visometry, ICare rebound tonometry (Tiolat, Finland), elastometry with Maklakov tonometer (using 5 g, 10 g and 15 g loads), automated perimetry (AP) (Octopus-600, Haag-Streit diagnostics, Switzerland), optical coherence tomography (OCT) of the macular zone and optic nerve head, pachymetry (Spectralis OCT, Heidelberg Engineering, Germany). At the start of the study and one month after the start of treatment with the drug Ganfort (Allergan, USA), patients were examined to evaluate the state of their ocular surface: Norn's test, Schirmer's test, vital staining with lissamine green, and an OSDI questionnaire. RESULTS At the start of treatment, administration of a fixed combination of bimatoprost and timolol led to a decrease in intraocular pressure by 7.9 (37.7%) mm Hg (V=271, p=5.496e-05) after 2 weeks of the use of Ganfort (Allergan, USA). During this period, the observation group did not exhibit statistically significant changes in the state of the ocular surface, which was comparable to the control group according to the data of the Norn's test, Schirmer's test, vital staining with lissamine green and the OSDI questionnaire (p>0.05). CONCLUSION The use of a fixed combination of bimatoprost and timolol, while effectively reducing IOP, did not result in statistically significant changes in the ocular surface. Some improvement of both objective and subjective indicators of the state of ocular surface associated with the use of the Ganfort drug was noted in patients of the observation group.
Fullerenol increases effectiveness of foliar iron fertilization in iron-deficient cucumber

The water-soluble fullerenols are novel carbon-based nanomaterials with unique properties, which afford them with wide agricultural applications. Iron (Fe) deficiency is the most common and widespread nutrition disorder affecting plants. Foliar Fe treatments of plants have been carried out with solutions devoid of fullerenol. In this study, the role of fullerenol [C60(OH)22–24] in alleviation of Fe deficiency in Cucumis sativus (a Strategy I plant) via foliar fertilization was investigated. Cucumber plants were grown hydroponically, either with (Fe) or in Fe-free (−Fe) nutrient solution. The following foliar spray treatments were applied: fullerenol at final concentrations of 1 (F1) and 10 (F10) mg L-1; Fe(II)SO4·7H2O; Fe(II)-EDTA (ethylenediaminetetraacetic acid); and Fe(II)-F1 and Fe(II)-F10. The best used compound was a combination of Fe(II)-sulfate with fullerenol, especially Fe-F1. The addition of fullerenol to Fe(II)-sulfate solutions significantly increased leaf-active Fe (extracted by an Fe(II) chelator) and re-greening at the site of application. The fullerenol-induced mutual influences did not appear when fullerenol was sprayed alone, suggesting a beneficial role of Fe(II)–fullerenol interactions in the penetration of Fe(II) in the leaves and re-greening under Fe-limited conditions. The results are of importance to enhancing the potential of foliar Fe fertilization as the commonly used strategy for ameliorating Fe deficiency and improving crop yield and quality.
Toward standardization of echocardiography for the evaluation of left ventricular function in adult rodents: a position paper of the ESC Working Group on Myocardial Function.

Echocardiography is a reliable and reproducible method to assess non-invasively cardiac function in clinical and experimental research. Significant progress in the development of echocardiographic equipment and transducers has led to the successful translation of this methodology from humans to rodents, allowing for the scoring of disease severity and progression, testing of new drugs, and monitoring cardiac function in genetically modified or pharmacologically treated animals. However, as yet, there is no standardization in the procedure to acquire echocardiographic measurements in small animals. This position paper focuses on the appropriate acquisition and analysis of echocardiographic parameters in adult mice and rats, and provides reference values, representative images and videos for the accurate and reproducible quantification of left ventricular function in healthy and pathological conditions.
EFFECT OF NITROGEN SOURCE ON PLATYMONAS (CHLOROPHYTA) CELL COMPOSITION AND AMINO ACID UPTAKE RATES 1

The effect of nitrogen source (nitrate, ammonia and/or amino acids) on cell composition and amino acid uptake rates was examined. Substantial levels of free amino acids accumulated intracellularly with all nitrogen sources used. Ammonia accumulated only when provided in the medium. The presence of ammonia in the medium decreased the intracellular accumulation of free amino acids, especially arginine. Amino acid uptake rates were suppressed by the presence of excess nitrogen, especially ammonia. However, the suppression of uptake did not show any particular relation to the nitrogenous cell composition.
The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer

In search of new biomarkers suitable for the diagnosis and treatment of prostate cancer, genome-wide transcriptome sequencing was carried out with tissue specimens from 40 prostate cancer (PCa) and 8 benign prostate hyperplasia patients. We identified two intergenic long non-coding transcripts, located in close genomic proximity, which are highly expressed in PCa. Microarray studies on a larger cohort comprising 155 patients showed a profound diagnostic potential of these transcripts (AUC~0.94), which we designated as tumor associated prostate cancer increased lncRNA (TAPIR-1 and -2). To test their therapeutic potential, knockdown experiments with siRNA were carried out. The knockdown caused an increase in the p53/TP53 tumor suppressor protein level followed by downregulation of a large number of cell cycle- and DNA-damage repair key regulators. Furthermore, in radiation therapy resistant tumor cells, the knockdown leads to a renewed sensitization of these cells to radiation treatment. Accordingly, in a preclinical PCa xenograft model in mice, the systemic application of nanoparticles loaded with siRNA targeting TAPIR-1 significantly reduced tumor growth. These findings point to a crucial role of TAPIR-1 and -2 in PCa.
From the Kinetic Theory of Gases to the Kinetics of Rate Processes: On the Verge of the Thermodynamic and Kinetic Limits

A variety of current experiments and molecular dynamics computations are expanding our understanding of rate processes occurring in extreme environments, especially at low temperatures, where deviations from linearity of Arrhenius plots are revealed. The thermodynamic behavior of molecular systems is determined at a specific temperature within conditions on large volume and number of particles at a given density (the thermodynamic limit): on the other side, kinetic features are intuitively perceived as defined in a range between the extreme temperatures, which limit the existence of each specific phase. In this paper, extending the statistical mechanics approach due to Fowler and collaborators, ensembles and partition functions are defined to evaluate initial state averages and activation energies involved in the kinetics of rate processes. A key step is delayed access to the thermodynamic limit when conditions on a large volume and number of particles are not fulfilled: the involved mathematical analysis requires consideration of the role of the succession for the exponential function due to Euler, precursor to the Poisson and Boltzmann classical distributions, recently discussed. Arguments are presented to demonstrate that a universal feature emerges: Convex Arrhenius plots (super-Arrhenius behavior) as temperature decreases are amply documented in progressively wider contexts, such as viscosity and glass transitions, biological processes, enzymatic catalysis, plasma catalysis, geochemical fluidity, and chemical reactions involving collective phenomena. The treatment expands the classical Tolman’s theorem formulated quantally by Fowler and Guggenheim: the activation energy of processes is related to the averages of microscopic energies. We previously introduced the concept of “transitivity”, a function that compactly accounts for the development of heuristic formulas and suggests the search for universal behavior. The velocity distribution function far from the thermodynamic limit is illustrated; the fraction of molecules with energy in excess of a certain threshold for the description of the kinetics of low-temperature transitions and of non-equilibrium reaction rates is derived. Uniform extension beyond the classical case to include quantum tunneling (leading to the concavity of plots, sub-Arrhenius behavior) and to Fermi and Bose statistics has been considered elsewhere. A companion paper presents a computational code permitting applications to a variety of phenomena and provides further examples.
Season Affects Yield and Metabolic Profiles of Rice (Oryza sativa) under High Night Temperature Stress in the Field

Rice (Oryza sativa) is the main food source for more than 3.5 billion people in the world. Global climate change is having a strong negative effect on rice production. One of the climatic factors impacting rice yield is asymmetric warming, i.e., the stronger increase in nighttime as compared to daytime temperatures. Little is known of the metabolic responses of rice to high night temperature (HNT) in the field. Eight rice cultivars with contrasting HNT sensitivity were grown in the field during the wet (WS) and dry season (DS) in the Philippines. Plant height, 1000-grain weight and harvest index were influenced by HNT in both seasons, while total grain yield was only consistently reduced in the WS. Metabolite composition was analysed by gas chromatography-mass spectrometry (GC-MS). HNT effects were more pronounced in panicles than in flag leaves. A decreased abundance of sugar phosphates and sucrose, and a higher abundance of monosaccharides in panicles indicated impaired glycolysis and higher respiration-driven carbon losses in response to HNT in the WS. Higher amounts of alanine and cyano-alanine in panicles grown in the DS compared to in those grown in the WS point to an improved N-assimilation and more effective detoxification of cyanide, contributing to the smaller impact of HNT on grain yield in the DS.
Mechanism of water extraction from gypsum rock by desert colonizing microorganisms

Significance This research provides an in-depth analysis of how microorganisms are able to survive in the world’s driest non-polar place, the Atacama Desert, Chile. We show that these organisms extract water from gypsum rocks in this desert, enabling these colonizing microorganisms to sustain life in this extreme environment. We believe the results in this work could not only shed light on how microorganisms can obtain water under severe xeric conditions, but also provide insights into potential life in even more extreme environments, such as Mars, as well as offer strategies for advanced water storage methods. Microorganisms, in the most hyperarid deserts around the world, inhabit the inside of rocks as a survival strategy. Water is essential for life, and the ability of a rock substrate to retain water is essential for its habitability. Here we report the mechanism by which gypsum rocks from the Atacama Desert, Chile, provide water for its colonizing microorganisms. We show that the microorganisms can extract water of crystallization (i.e., structurally ordered) from the rock, inducing a phase transformation from gypsum (CaSO4·2H2O) to anhydrite (CaSO4). To investigate and validate the water extraction and phase transformation mechanisms found in the natural geological environment, we cultivated a cyanobacterium isolate on gypsum rock samples under controlled conditions. We found that the cyanobacteria attached onto high surface energy crystal planes ({011}) of gypsum samples generate a thin biofilm that induced mineral dissolution accompanied by water extraction. This process led to a phase transformation to an anhydrous calcium sulfate, anhydrite, which was formed via reprecipitation and subsequent attachment and alignment of nanocrystals. Results in this work not only shed light on how microorganisms can obtain water under severe xeric conditions but also provide insights into potential life in even more extreme environments, such as Mars, as well as offering strategies for advanced water storage methods.
Rescue oxygenation success by cannula or scalpel-bougie emergency front-of-neck access in an anaesthetised porcine model

In the obese, the evidence for the choice of the optimal emergency front-of-neck access technique is very limited and conflicting. We compared cannula and scalpel-bougie emergency front-of-neck access techniques in an anaesthetised porcine model with thick pretracheal tissue. Cannula and scalpel-bougie cricothyroidotomy techniques were performed in 11 and 12 anaesthetised pigs, respectively. Following successful tracheal access, oxygenation was commenced and continued for 5 min using Rapid-O2 device for cannula and circle breathing system for scalpel-bougie study groups. The primary outcome was a successful rescue oxygenation determined by maintenance of arterial oxygen saturation >90% 5 min after the beginning of oxygenation. Secondary outcomes included success rate of airway device placement, time to successful airway device placement, and trauma to the neck and airway. The success rate of rescue oxygenation was 18% after cannula, and 83% after scalpel-bougie technique (P = 0.003). The success rate of airway device placement was 73% with cannula and 92% with scalpel-bougie technique (P = 0.317). Median (inter-quartile-range) times to successful airway device placement were 108 (30–256) and 90 (63–188) seconds (P = 0.762) for cannula and scalpel-bougie emergency front-of-neck access, respectively. Proportion of animals with iatrogenic trauma additional to the procedure itself was 27% for cannula and 75% for scalpel-bougie technique (P = 0.039). Thus, in the porcine model of obesity, the scalpel-bougie technique was more successful in establishing and maintaining rescue oxygenation than cannula-based technique; however, it was associated with a higher risk of severe trauma.
Temperature‐Related Responses of an Invasive Mussel and 2 Unionid Mussels to Elevated Carbon Dioxide

Zebra mussels (Dreissena polymorpha) have exacerbated the decline of native freshwater mussels (order Unionida) in North America since their arrival in the 1980s. Options for controlling invasive mussels, particularly in unionid mussel habitats, are limited. Previously, carbon dioxide (CO2) showed selective toxicity for zebra mussels, relative to unionids, when applied in cool water (12 °C). We first determined 96‐h lethal concentrations of CO2 at 5 and 20 °C to zebra mussels and responses of juvenile plain pocketbook (Lampsilis cardium). Next, we compared the time to lethality for zebra mussels at 5, 12, and 20 °C during exposure to partial pressure of CO2 (PCO2) values of 110 to 120 atm (1 atm = 101.325 kPa) and responses of juvenile plain pocketbook and fragile papershell (Leptodea fragilis). We found efficacious CO2 treatment regimens at each temperature that were minimally lethal to unionids. At 5 °C, plain pocketbook survived 96‐h exposure to the highest PCO2 treatment (139 atm). At 20 °C, the 96‐h lethal concentration to 10% of animals (LC10) for plain pocketbook (173 atm PCO2, 95% CI 147–198 atm) was higher than the LC99 for zebra mussels (118 atm PCO2, 95% CI 109–127 atm). Lethal time to 99% mortality (LT99) of zebra mussels in 110 to 120 atm PCO2 ranged from 100 h at 20 °C to 300 h at 5 °C. Mean survival of both plain pocketbook and fragile papershell juveniles exceeded 85% in LT99 CO2 treatments at all temperatures. Short‐term infusion of 100 to 200 atm PCO2 at a range of water temperatures could reduce biofouling by zebra mussels with limited adverse effects on unionid mussels. Environ Toxicol Chem 2020;39:1546–1557. Published 2020. This article is a U.S. Government work and is in the public domain in the USA. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.