Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytoplankton accumulation in Langmuir cells1

We investigate the distribution of phytoplankton in Langmuir circulations, under various assumptions about the motion of the water and of phytoplankton through the water. The details of water movement appear to be relatively unimportant compared to the details of phytoplankton movement: Stommel’s analysis of a very simple model is easily extended to more realistic descriptions of Langmuir circulation, hut it break down if plankton velocities are not constant. We discuss some possible ecological consequences, especially concerning red tides.
Catechin-like antioxidative potential of selected tea products

The presented study was aimed to establish the levels of antioxidative potential of five types of tea (white, red, green, black and blue/turquoise) originating from different geographical regions. Furthermore, the content and qualitative composition of phenolics in aqueous infusions of the tested tea products was compared. The highest antioxidant activity against DPPH• free radical was found in extracts obtained from white teas, whereas the lowest in extracts from red teas. Moreover, the highest total phenolics content was shown in the extracts prepared from the white teas. In addition, the HPLC analysis allowed to identify the following catechin derivatives in the tea extracts: (+)-catechin, (-)-epicatechin, (-)-epigallocatechin and (-)-epicatechin gallate. Simultaneously, it was shown that the dominant compound in extracts from the all tested teas was (+)-catechin.
A longitudinal test of the theory of planned behaviour to explain physical activity level in children: exploration of the role of gender and age

Abstract Objective Most previous research based on the Theory of Planned Behaviour (TPB) to explain children's physical activity (PA) remains cross-sectional and the moderating role of demographic variables on the link between TPB variables is rarely explored. This study aims to (1) test a longitudinal cross-lagged panel model based on the TPB to explain PA in children, and (2) examine in what extent this model operates equivalently across age and gender. Design Children (N = 363, M = 8.6 years) completed measures of TPB constructs and PA at two measurement times (T1 and T2) within three months. Main Outcome Measures Self-reported PA. Results Path analyses revealed that the model tested accounted for 25% of the variance in PA at T2. Subgroups analyses revealed that age significantly moderated the links between subjective norms at T1 and T2, between PA at T1 and T2, and between PA at T1 and subjective norms at T2. Gender significantly moderated the links between intentions at T1 and T2, and between PA at T1 and perceived behavioural control at T2. Conclusion The temporal stability of the variables of the TPB and the link between initial PA and subsequent TPB variables may vary by children's gender and age.
Regulator combinations identify systemic sclerosis patients with more severe disease

Systemic sclerosis (SSc) is a heterogeneous autoimmune disorder that results in skin fibrosis, autoantibody production, and internal organ dysfunction. We previously identified 4 “intrinsic” subsets of SSc based upon skin gene expression that are found across organ systems. Gene expression regulators that underlie the SSc-intrinsic subsets, or are associated with clinical covariates, have not been systematically characterized. Here, we present a computational framework to calculate the activity scores of gene expression regulators and identify their associations with SSc clinical outcomes. We found that regulator activity scores can reproduce the intrinsic molecular subsets, with distinct sets of regulators identified for inflammatory, fibroproliferative, limited, and normal-like samples. Regulators most highly correlated with modified Rodnan skin score (MRSS) also varied by intrinsic subset. We identified subgroups of patients with fibroproliferative and inflammatory SSc with more severe pathophenotypes, such as higher MRSS and increased likelihood of interstitial lung disease (ILD). Using an independent cohort, we show that the group with more severe ILD was more likely to show forced vital capacity decline over a period of 36–54 months. Our results demonstrate an association among the activation of regulators, gene expression subsets, and clinical variables that can identify patients with SSc with more severe disease.
Pullet Rearing Affects Collisions and Perch Use in Enriched Colony Cage Layer Housing

Simple Summary Early-life experiences for laying hens occur in the pullet rearing environment. Hens reared in aviaries use vertical space more than hens reared in non-enriched cages, but this effect has only been studied up to 23 weeks of age. Additionally, hens reared in aviaries sustain fewer keel bone fractures than those reared in non-enriched cages through the age of 73 weeks. Fractures are associated with hens having collisions with structures in their environment, but the long-term effect of rearing on collisions is not known. Lohmann LSL-Lite hens were reared in either aviaries or non-enriched cages until 19 weeks of age, then moved into enriched colony cages. Video recordings at 21, 35, and 49 weeks of age were used to identify behaviors associated with acceleration events for hens fitted with tri-axial accelerometers, as well as the proportion of birds utilizing elevated perches at two different heights. Our results indicate that hens reared in non-enriched cages experience more collisions than aviary-reared hens. Aviary-reared hens also prefer to utilize a higher perch than the cage-reared hens. These results suggest that rearing has long-term effects on space use and the ease with which hens transition among vertical spaces. Abstract Hens reared in aviaries (AVI) as pullets have improved spatial abilities compared to hens reared in non-enriched cages (CON). However, this effect on behavior has been shown only to 23 weeks of age. Lohmann LSL-Lite hens were reared in either CON or AVI until 19 weeks of age and then moved into enriched colony cages (ECC) containing two elevated perches of different heights (n = 6 ECC/treatment). Focal hens (3 per ECC) were fitted with tri-axial accelerometers to record acceleration events at 21, 35, and 49 weeks of age. Video recordings from each age were used to identify behaviors associated with acceleration events as well as the proportion of hens utilizing perches. CON hens experienced more acceleration events (p = 0.008) and more collisions (p = 0.04) than AVI hens during the day at 21 and 35 weeks of age. The total proportion of hens perching at night was similar between treatments across most time points, but fewer CON hens used the high perch compared to AVI hens throughout the study (p = < 0.001). Rearing in aviaries influences hen behavior out to peak lay for collisions and out to mid-lay for perch height preference in ECC.
Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers

In this paper, we perform computer simulation of two lysine-based dendrimers with Lys-2Lys and Lys-2Gly repeating units. These dendrimers were recently studied experimentally by NMR (Sci. Reports, 2018, 8, 8916) and tested as carriers for gene delivery (Bioorg. Chem., 2020, 95, 103504). Simulation was performed by molecular dynamics method in a wide range of temperatures. We have shown that the Lys-2Lys dendrimer has a larger size but smaller fluctuations as well as lower internal density in comparison with the Lys-2Gly dendrimer. The Lys-2Lys dendrimer has larger charge but counterions form more ion pairs with its NH3+ groups and reduce the bare charge and zeta potential of the first dendrimer more strongly. It was demonstrated that these differences between dendrimers are due to the lower flexibility and the larger charge (+2) of each 2Lys spacers in comparison with 2Gly ones. The terminal CH2 groups in both dendrimers move faster than the inner CH2 groups. The calculated temperature dependencies of the spin-lattice relaxation times of these groups for both dendrimers are in a good agreement with the experimental results obtained by NMR.
Non-invasive detection and differentiation of cardiac amyloidosis using 99mTc-pyrophosphate scintigraphy and 11C-Pittsburgh compound B PET imaging

Abstract Purpose To investigate the utility of the combined use of 11C-Pittsburgh compound B (11C-PiB) positron emission tomography (PET) imaging and 99mTc-pyrophosphate (99mTc-PYP) scintigraphy for detection and differentiation of three major types of cardiac amyloidosis, i.e. immunoglobulin light chain (AL), hereditary transthyretin (ATTRv), and wild-type transthyretin (ATTRwt) amyloidosis. Methods Whole-body 11C-PiB PET and 99mTc-PYP scintigraphy were performed in 17 patients with AL amyloidosis, 22 patients with ATTRv, and eight patients with ATTRwt amyloidosis. The correlations between organ involvement and the uptake of 11C-PiB and 99mTc-PYP were analyzed in each patient. Results Cardiac amyloidosis was detectable by 99mTc-PYP scintigraphy or 11C-PiB PET in all systemic amyloidosis patients with cardiac involvement. 99mTc-PYP scintigraphy and 11C-PiB PET showed an interesting complementary relation. Strict combination of positive 11C-PiB and negative 99mTc-PYP uptake (PiB pattern) was observed in all AL amyloidosis patients with cardiac involvement. In contrast, strict combination of positive 99mTc-PYP and negative 11C-PiB uptake (PYP pattern) was observed in all ATTRwt amyloidosis patients with cardiac involvement. ATTRv amyloidosis patients with cardiac involvement were divided into two groups: PiB pattern or PYP pattern. All of the early-onset V30M (p.V50M) ATTRv patients showed the PiB pattern, whereas all of the late-onset V30M and non-V30M ATTRv patients showed the PYP pattern. Conclusions All three major types of cardiac amyloidosis can be detected and differentiated non-invasively by combined use of the two amyloid imaging methods and TTR gene testing.
Discovering the signature of a lupus-related microRNA profile in the Gene Expression Omnibus repository

Lupus is one of the most prevalent systemic autoimmune diseases. It is a multifactorial disease in which genetic, epigenetic and environmental factors play significant roles. The pathogenesis of lupus is not yet well understood. However, deregulation of microRNAs (miRNAs) – one of the post-transcriptional regulators of genes – can contribute to the development of autoimmune diseases. Over the last two decades, advances in the profiling of miRNA using microarray have received much attention, and it has been demonstrated that miRNAs play a regulatory role in the pathogenesis of lupus. Therefore, dysregulated miRNAs can be considered as promising diagnostic biomarkers for lupus. This article is an overview of lupus-related miRNA profiling studies and arrays in the Gene Expression Omnibus (GEO) database. The aims of our study were to widen current knowledge of known dysregulated miRNAs as potential biomarkers of SLE and to introduce a bioinformatics approach to using microarray data and finding novel miRNA and gene candidates for further study. We identified hsa-miR-4709-5p, hsa-miR-140, hsa-miR-145, hsa-miR-659, hsa-miR-134, hsa-miR-150, hsa-miR-584, hsa-miR-409 and hsa-miR-152 as potential biomarkers by integrated bioinformatics analysis.
Nothofagus (Fagaceae) forest on Mt Giluwe, New Guinea

Abstract Populations of Nothofagus spp. (Fagaceae) were studied on Mt Giluwe, New Guinea (6°S, 144°E, 2300–2800 m alt.). Nothofagus spp. formed monospecific stands transitional with a taxonomically diverse forest, replaced abruptly by gymnosperm forest above 2800 m altitude. Extensive stands of N. pullei had a single dominant size class and, at 30–79 cm d.b. h. , many cohorts were subject to dieback associated with pathogenic Phytophthora spp. and pinhole borers. Regeneration in dieback patches was dominated by N. pullei suckers, forming a new cohort. In the absence of dieback, all Nothofagus species reached a maximum d.b. h of 100–150 cm and regenerated, especially in canopy gaps, forming a mixed size structure. A variety of canopy tree taxa were established in stands containing large N. grandis trees, forming a transition or succession to the taxonomically diverse forest. Regular growth rings of parenchyma and, less clearly, vessels were apparently annual. Dieback typically occurred in trees with 100–180 r.
Analysis of Physiological and Metabolite Response of Celosia argentea to Copper Stress.

Copper-tolerant (Cu) plants with high ornamental value play an important role in the ecological landscape restoration of the copper tail mining area. We first discovered Celosia argentea adaptability in copper mine area in China. However, its copper resistance and mechanism are not clear. In this study, C. argentea was selected for pot culture experiments, and its heavy metal accumulation and translocation, physiological and metabolic products were analyzed under different concentrations of Cu (0-2400 mg • kg-1) stress. Our results indicated that the root with strong copper accumulation. The oxidative stress defense mechanisms were activated under Cu treatment of C. argentea leaves. Higher Cu concentration triggered higher electrolyte leakage (EL), Malondialdehyde (MDA), superoxide dismutase (SOD) and peroxidase (POD) activities, and consequently a higher capacity of scavenging oxygen radical and maintaining cellular membranes integrity. Results showed that the citrate cycle, some amino acids and sugars related biological pathways were alterted of C. argentea under Cu stress. Metabolomics data revealed that C. argentea elevated sugars content as an antioxidant to regulate ROS. Some organic acids and amino acids level were up-regulated compared with the control, indicating that they may act on chelating Cu in cells to detoxify excess Cu2+ . The up-regulation of polyamines (ethanolamine) and some organic acids may mitigate oxidative stress and enhance tolerance. These results indicate that C. argentea can be used as a copper-tolerant plant in copper mine restoration, and its copper tolerance mechanism also provides a basis for plant improvement or breeding in future mine restoration.
Design and Characterization of Bioactive Bilayer Films: Release Kinetics of Isopropyl Palmitate

Active packaging incorporating antioxidants and antimicrobials is creating a niche in the market and becoming increasingly important. The main goal of this work was the design of bioactive bilayer films (zein/pullulan) incorporating licorice essential oil. The bilayer films were fully characterized in terms of their chemical, physical, barrier, antioxidant, and antimicrobial properties. Furthermore, the release kinetics of isopropyl palmitate, the major compound of the licorice essential oil, was evaluated by HPLC-DAD (high-performance liquid chromatography coupled to diode-array detector). Scanning Electron Microscopy (SEM) micrographs of cross-sections of the bilayer films clearly show the two layers of the films. Besides presenting the capacity to scavenge free radicals and to inhibit the lipid peroxidation, the developed bilayer films were also able to inhibit the growth of known foodborne pathogens (Enterococcus faecalis and Listeria monocytogenes). The release kinetics profile of isopropyl palmitate from bilayer films incorporating licorice essential oil demonstrated that in 50% ethanol at room temperature, the release was more effective, suggesting that the bilayer films will be more efficient if applied to package semi-fatty food.
CHARACTERISTICS AND PROGNOSIS OF TRIPLE-NEGATIVE BREAST CANCER PATIENTS: A CROATIAN SINGLE INstitution RETROSPECTIVE COHORT STUDY

SUMMARY Triple-negative breast cancer (TNBC) occurs in around one-sixth of all breast cancer (BC) patients, with the most aggressive behavior and worst prognosis of all BC subtypes. It is a heterogeneous disease, with specific molecular characteristics and natural dynamics of early recurrence and fast progression. Due to the lack of biomarkers or any valid treatment targets, it can only be treated with classic cytotoxic chemotherapy. We analyzed a cohort of 152 patients, median age 58 years, diagnosed with and treated for early stage TNBC at the University Hospital for Tumors, Sestre milosrdnice University Hospital Centre, Zagreb, Croatia, during the 2009-2012 period. Patients were treated with primary surgical approach, adjuvant chemotherapy and adjuvant irradiation. We observed a relatively large proportion of locally advanced TNBC at diagnosis, with large tumor size and nodal involvement, with high grade and high proliferation index Ki67. Patient age, tumor size and lymph node involvement, as expected, were significant and clinically most important prognostic factors for 5-year disease-free survival (67%; 95% CI 60%-75%) and overall absolute survival rate (74%; 95% CI 66%-81%).
Exosome-Mediated Transfer of Long Noncoding RNA HOTAIR Regulates Temozolomide Resistance by miR-519a-3p/RRM1 Axis in Glioblastoma.

Background: Chemoresistance obstructs the treatment of glioblastoma (GB). Exosome-mediated transfer of long noncoding RNAs (lncRNAs) was reported to regulate chemoresistance in diverse cancers. The authors aimed to investigate the underlying mechanism of lncRNA HOX transcript antisense intergenic RNA (HOTAIR) in regulating temozolomide (TMZ) resistance in GB. Materials and Methods: 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was utilized to check TMZ resistance and cell proliferation. The abilities of cell migration and invasion were evaluated by transwell assay. The protein levels of E-cadherin, N-cadherin, Vimentin, CD63, CD81, and ribonucleoside-diphosphate reductase subunit M1 (RRM1) were measured by western blot. Quantitative real-time polymerase chain reaction was conducted to detect the levels of HOTAIR, microRNA (miR)-519a-3p, and RRM1. The starBase was hired to predict the target sites between miR-519a-3p and HOTAIR or RRM1 and the dual-luciferase reporter assay was performed to verify the interaction. Xenograft tumor model was established to investigate the biological role of HOTAIR in vivo. Results: The high abilities of cell viability and metastasis were observed in TMZ-resistant GB cells. LncRNA HOTAIR was significantly upregulated in TMZ-resistant GB cells and its downregulation inhibited proliferation, migration, invasion, and epithelial/mesenchymal transition in TMZ-resistant GB cells. Further analysis indicated that exosomal lncRNA HOTAIR induced TMZ resistance and modulated TMZ resistance through miR-519a-3p/RRM1 axis. Besides, serum exosomal lncRNA HOTAIR was stable and had diagnostic value. Moreover, knockdown of lncRNA HOTAIR reduced TMZ resistance in vivo. Conclusions: Exosomal lncRNA HOTAIR mediated TMZ resistance through miR-519a-3p/RRM1 axis in GB.
Ecological Interface Design, the Proximity Compatibility Principle, and Automation Reliability in Road Traffic Management

In this paper, two user interfaces (UIs) are compared for supporting decision making in a road traffic management activity. Both UIs provide the information needed to make critical decisions related to traffic management and are designed according to ecological interface design (EID) concepts. One user interface design also incorporates concepts from the proximity compatibility principle (PCP). In addition to comparing the two UI designs, this paper considers the impact of the reliability of automation on user decision time and accuracy. It is shown that the UI designed with a combined of EID and PCP leads to significantly faster total task time, due to faster performance on the information gathering phase of the task. Contrary to expectations, time to gather information is not affected by automation reliability. Participants adapted their decisions according to automation reliability, even without explicit feedback to indicate reliability. Implications for UI design and decision making are discussed.
O Banco de sementes de um trecho de uma floresta Atlântica montana (São Paulo - Brasil)

Soil seed bank of tropical forests is involved in the establishment of ecological groups and in woody species richness restoration during forest regeneration, after natural or antropic disturbances. In order to analyze the seed bank composition in a tropical montane forest, Southeastern Brazil, 57 soil samples were collected, inside a 2-hectare forest plot, representing 28,500 cm3 of collected soil. Along 17 months, 497 seeds germinated, 65% between 0 and 2.5 cm depth. They represented a density of 872 seeds/m2. The seed bank analyzed is characterized as having two components: one composed by 66 herbaceous taxa, belonging to families with high richness of pioneer species; and another composed by 19 pioneer shrub and tree species, most of them with diaspores shorter than 1 mm length. The results found in the study site suggest that in the Atlantic montane forest soil seed bank can be important for the establishment of woody species, which form ecological groups involved in forest regeneration, following slash-and-burn. After treefall gaps, seed bank is probably responsible for the establishment of Melastomataceae species, the richest and more abundant group of pioneer species sampled in gaps.
Bats and humans during the SARS-CoV-2 outbreak: the case of bat-coronavirus from Mexico.

The novel SARS-CoV-2 coronavirus has attracted attention due to the high number of human cases around the world. It has been proposed that this virus originated in bats, possibly transmitted to humans by an intermediate host, making bats a group of great interest during this outbreak. Almost 10% of the world's bat species inhabit Mexico, and 14 previous novel CoVs have been recorded in Mexican bats. However, the phylogenetic relationships between these viruses and the novel coronavirus are unknown. The aim of this communication was therefore to describe the phylogenetic relationships between Mexican bat-CoVs and SARS-CoV-2. We showed that Mexican bat-CoVs sequences are grouped into two genera, Alphacoronavirus and Betacoronavirus, and the new coronavirus is an independent clade within Betacoronavirus. Due to the diversity of CoVs in Mexican bats, the propensity of CoVs to shift hosts, the invasion mechanisms described for this new virus, and previous reports of animals infected by SARS-CoV-2, the risk of a possible infection from humans to Mexican bats should not be discarded and warrants further analyses. To avoid future zoonotic infectious diseases and to limit persecution of bats, we urge researchers and the general population to take extreme precautions and avoid manipulation of bats during the current and future similar outbreaks.
Advances in Fungal Peptide Vaccines

Vaccination is one of the greatest public health achievements in the past century, protecting and improving the quality of life of the population worldwide. However, a safe and effective vaccine for therapeutic or prophylactic treatment of fungal infections is not yet available. The lack of a vaccine for fungi is a problem of increasing importance as the incidence of diverse species, including Paracoccidioides, Aspergillus, Candida, Sporothrix, and Coccidioides, has increased in recent decades and new drug-resistant pathogenic fungi are emerging. In fact, our antifungal armamentarium too frequently fails to effectively control or cure mycoses, leading to high rates of mortality and morbidity. With this in mind, many groups are working towards identifying effective and safe vaccines for fungal pathogens, with a particular focus of generating vaccines that will work in individuals with compromised immunity who bear the major burden of infections from these microbes. In this review, we detail advances in the development of vaccines for pathogenic fungi, and highlight new methodologies using immunoproteomic techniques and bioinformatic tools that have led to new vaccine formulations, like peptide-based vaccines.