Miracle-dz/UniFAR-FTUs huggingface dataset:
A floristic analysis of the marine algae and seagrasses between Cape Mendocino, California and Cape Blanco, Oregon, USA

Abstract The biogeographic area between Cape Mendocino, California and Cape Blanco, Oregon in the USA spans over 320 km and is characterized by prominent coastal headlands. This study was a first attempt to produce a current intertidal macroalgal and seagrass species list for this understudied region with basic habitat attributes included. A total of 164 species of marine macroalgae (105 species within 16 orders in Rhodophyta, 32 species within six orders in Heterokontophyta, Phaeophyceae, and 27 species in six orders in Chlorophyta) and two species of seagrasses (Anthophyta) were identified. The optimal habitat for most species was the rocky intertidal in the mid zone (>50%), while some species were specialists in either tidepool and/or sandy habitats (∼20%). Furthermore, based on Akaike Information Criterion, our top ranking model suggests that species richness is dependent on zonation, functional grouping and site location. Based on the seven functional group classification, the leathery macrophytes and crusts were the most prevalent at the two capes exposed to higher wave action and upwelling. One near-endemic species (Cumathamnion sympodophyllum), one invasive species (Sargassum muticum), and seven new records for the region were identified.
Gas exchange and growth of three arctic tree-line tree species under different soil temperature and drought preconditioning regimes

Low soil temperatures and water availability are thought to be major factors determining the distribution of tree species at the arctic tree line. A comparative study examined the response of Betula papyrifera, Populus balsamifera, and Picea mariana seedlings to different soil temperatures and drought regimes in a growth chamber experiment. Morphological and ecophysiological responses (net assimilation rate, stomatal conductance to water vapour, and residual conductance) of these tree line tree species were measured and compared. Mean biomass accumulation of the deciduous species was greater than that of Picea mariana with increasing soil temperatures. Root biomass showed an increase of 30% in the three species between the soil temperatures of 3 and 15 °C. Response of ecophysiological variables to increased soil temperature was greater in B. papyrifera and Populus balsamifera than in Picea mariana. In a second experiment, drought-preconditioned B. papyrifera and Populus balsamifera seedlings were subjecte.
Engineered anti-inflammatory peptides inspired by mapping an evasin–chemokine interaction

Chemokines mediate leukocyte migration and homeostasis and are key targets in inflammatory diseases including atherosclerosis, cytokine storm, and chronic autoimmune disease. Chemokine redundancy and ensuing network robustness has frustrated therapeutic development. Salivary evasins from ticks bind multiple chemokines to overcome redundancy and are effective in several preclinical disease models. Their clinical development has not progressed because of concerns regarding potential immunogenicity, parenteral delivery, and cost. Peptides mimicking protein activity can overcome the perceived limitations of therapeutic proteins. Here we show that peptides possessing multiple chemokine-binding and anti-inflammatory activities can be developed from the chemokine-binding site of an evasin. We used hydrogen–deuterium exchange MS to map the binding interface of the evasin P672 that physically interacts with C–C motif chemokine ligand (CCL) 8 and synthesized a 16-mer peptide (BK1.1) based on this interface region in evasin P672. Fluorescent polarization and native MS approaches showed that BK1.1 binds CCL8, CCL7, and CCL18 and disrupts CCL8 homodimerization. We show that a BK1.1 derivative, BK1.3, has substantially improved ability to disrupt P672 binding to CCL8, CCL2, and CCL3 in an AlphaScreen assay. Using isothermal titration calorimetry, we show that BK1.3 directly binds CCL8. BK1.3 also has substantially improved ability to inhibit CCL8, CCL7, CCL2, and CCL3 chemotactic function in vitro. We show that local as well as systemic administration of BK1.3 potently blocks inflammation in vivo. Identification and characterization of the chemokine-binding interface of evasins could thus inspire the development of novel anti-inflammatory peptides that therapeutically target the chemokine network in inflammatory diseases.
Prognostic value of LAT-1 status in solid cancer: A systematic review and meta-analysis

Background The expression of the L-type amino acid transporter 1 (LAT1) plays a significant role in tumor progression. However, it remains unclear whether high LAT1 expression correlates with poor prognosis of solid tumor patients. Here, we conducted a meta-analysis to assess the potential of LAT1 in predicting the prognosis of tumor patients. Methods and findings A total of 4,579 cases were analyzed from 35 qualified studies. In patients with solid tumors, elevated expression of LAT1 is associated with poor prognosis (overall survival [OS]: pooled hazard ratio (HR) = 1.848, 95% confidence interval (CI) = 1.620–2.108, P < 0.001; disease free survival [DFS]: pooled HR = 1.923, 95% CI = 1.585–2.333, P < 0.001; progression free survival [PFS]: pooled HR = 1.345, 95% CI = 1.133–1.597, P = 0.001). Furthermore, in subgroup analysis, we found an association between high LAT1 expression and poor OS in non-small cell lung cancer (HR = 1.554, 95% CI = 1.345–1.794, P < 0.001), pancreatic cancer (HR = 2.052, 95% CI = 1.613–2.724, P < 0.001) and biliary tract cancer (HR = 2.253, 95% CI = 1.562–3.227, P < 0.001). Conclusion The results of this meta-analysis indicate the reliability and potential of using LAT1 expression as a predictive biomarker in solid cancers prior to treatment. However, further studies with larger sample sizes would be beneficial for fully evaluating the predictive value of LAT1 expression for clinical applications.
Gradual positive and negative affect induction: The effect of verbalizing affective content

In this paper, we study the effect of verbalizing affective pictures on affective state and language production. Individuals describe (Study I: Spoken Descriptions of Pictures) or passively view (Study II: Passively Viewing Pictures) 40 pictures for the International Affective Picture System (IAPS) that gradually increase from neutral to either positive or negative content. We expected that both methods would result in successful affect induction, and that the effect would be stronger for verbally describing pictures than for passively viewing them. Results indicate that speakers indeed felt more negative after describing negative pictures, but that describing positive (compared to neutral) pictures did not result in a more positive state. Contrary to our hypothesis, no differences were found between describing and passively viewing the pictures. Furthermore, we analysed the verbal picture descriptions produced by participants on various dimensions. Results indicate that positive and negative pictures were indeed described with increasingly more affective language in the expected directions. In addition to informing our understanding of the relationship between (spoken) language production and affect, these results also potentially pave the way for a new method of affect induction that uses free expression.
Urinary MicroRNAs as Potential Markers for Non-Invasive Diagnosis of Bladder Cancer

Currently, voided urine cytology (VUC) serves as the gold standard for the detection of bladder cancer (BCa) in urine. Despite its high specificity, VUC has shortcomings in terms of sensitivity. Therefore, alternative biomarkers are being searched, which might overcome these disadvantages as a useful adjunct to VUC. The aim of this study was to evaluate the diagnostic potential of the urinary levels of selected microRNAs (miRs), which might represent such alternative biomarkers due to their BCa-specific expression. Expression levels of nine BCa-associated microRNAs (miR-21, -96, -125b, -126, -145, -183, -205, -210, -221) were assessed by quantitative PCR in urine sediments from 104 patients with primary BCa and 46 control subjects. Receiver operating characteristic (ROC) curve analyses revealed a diagnostic potential for miR-96, -125b, -126, -145, -183, and -221 with area under the curve (AUC) values between 0.605 and 0.772. The combination of the four best candidates resulted in sensitivity, specificity, positive and negative predictive values (NPV), and accuracy of 73.1%, 95.7%, 97.4%, 61.1%, and 80.0%, respectively. Combined with VUC, sensitivity and NPV could be increased by nearly 8%, each surpassing the performance of VUC alone. The present findings suggested a diagnostic potential of miR-125b, -145, -183, and -221 in combination with VUC for non-invasive detection of BCa in urine.
SIMULTANEOUS DETECTION OF LISTERIA MONOCYTOGENES, STAPHYLOCOCCUS AUREUS, SALMONELLA ENTERICA AND ESCHERICHIA COLI O157:H7 IN FOOD SAMPLES USING MULTIPLEX PCR METHOD

In this study, one multiplex polymerase chain reaction (MPCR) assay was developed for simultaneous detection of four foodborne pathogens, i.e., Listeria monocytogenes, Staphylococcus aureus, Salmonella enterica and Escherichia coli O157:H7. Five specific primer pairs were designed based on the nucleotide sequences of hemolysin gene (hly) of Listeria monocytogenes, thermostable nuclease gene (nuc) of Staphylococcus aureus, invasion gene (invA) of Salmonella enterica, shiga-like toxin gene (stx) and intimin gene (eae) of Escherichia coli O157:H7 in this assay. The specificity and sensitivity of the MPCR method were validated, and the limit of detection (LOD) of this method was about 10 copies. One cfu/mL each of these foodborne pathogens spiked in practical food samples, i.e., ground meat, beef, pork, fish, shrimp, cheese, canola leaf and cabbage, could be detected simultaneously after 24 h enrichment at a rate of 87.5%, indicating that the established MPCR detection method was effective and suitable for practical use. PRACTICAL APPLICATIONS This study presents a quick and effective identification method to simultaneous monitor four foodborne pathogens in food samples. The specificity and sensitivity of this method can be used to unambiguously identify these four foodborne pathogens in practical food samples based on the species-specific genes. Therefore, this detection method is applicable for surveillance measures of these four foodborne pathogens in the food production chain.
Assisted reproductive technologies induce temporally specific placental defects and the preeclampsia risk marker sFLT1 in mouse

ABSTRACT Although widely used, assisted reproductive technologies (ARTs) are associated with adverse perinatal outcomes. To elucidate their underlying causes, we have conducted a longitudinal analysis of placental development and fetal growth using a mouse model to investigate the effects of individual ART procedures: hormone stimulation, in vitro fertilization (IVF), embryo culture and embryo transfer. We demonstrate that transfer of blastocysts naturally conceived without hormone stimulation and developed in vivo prior to transfer can impair early placentation and fetal growth, but this effect normalizes by term. In contrast, embryos cultured in vitro before transfer do not exhibit this compensation but rather display placental overgrowth, reduced fetal weight, reduced placental DNA methylation and increased levels of sFLT1, an anti-angiogenic protein implicated in causing the maternal symptoms of preeclampsia in humans. Increases in sFLT1 observed in this study suggest that IVF procedures could increase the risk for preeclampsia. Moreover, our results indicate that embryo culture is the major factor contributing to most placental abnormalities and should therefore be targeted for optimization. Highlighted Article: Pregnancies conceived using assisted reproductive technologies are at higher risk for abnormal placentation. Using a mouse model, we investigate how individual procedures contribute to placental defects across development.
Development of Fortified Citrus Olive Oils: From Their Production to Their Nutraceutical Properties on the Cardiovascular System

Recently the use of food by-products as natural sources of biologically active substances has been extensively investigated especially for the development of functional foods fortified with natural antioxidants. Due to their content of bioactive compounds, such as carotenoids, flavonoids and limonoids, citrus peels could be suitable to formulate enriched olive oils able to boost healthy nutrition. The aim of this study was: (i) to determine the compositional and sensory profiles of citrus olive oil; and (ii) to evaluate its nutraceutical properties in rats with high fat diet-induced metabolic syndrome and oxidative stress. The results obtained show the potential of using citrus peels as a source of bioactive compounds to improve the sensory profile as well as the phytochemical composition of olive oil. We demonstrated that the production system of Citrus x aurantium olive oil and Citrus limon olive oil improves its organoleptic properties without altering its beneficial effects, which, like control extra virgin olive oil, showed protective effects relating to glucose and serum lipid levels, metabolic activity of adipocytes, myocardial tissue functionality, oxidative stress markers and endothelial function at blood vessel level.
The epidermis-specific cyclin CYCP3;1 is involved in the excess BR signaling-inhibited root meristem cell division.

Cell division is precisely regulated and highly tissue specific; studies have suggested that diverse signals in the epidermis, especially the epidermal brassinosteroids (BRs), can regulate root growth. However, the underlying molecular mechanisms that integrate hormonal cues such as BR signaling with other endogenous, tissue-specific developmental programs to regulate epidermal cell proliferation remain unclear. In this study, we used molecular and biochemical approaches, microscopic imaging and genetic analysis to investigate the function and mechanisms of a P-type Cyclin in the root growth regulation. We found that CYCP3;1, specifically expressed in the root meristem epidermis and lateral root cap, can regulate meristem cell division. Mitotic analyses and biochemical studies demonstrated that CYCP3;1 promotes cell division at the G2-M duration by associating and activating cyclin-dependent kinase B2-1 (CDKB2;1). Furthermore, we found that CYCP3;1 expression was inhibited by BR signaling through BRI1-EMS-SUPPRESSOR1 (BES1), a positive downstream transcription factor in the BR signaling pathway. These findings not only provide a mechanism of how root epidermal-specific regulators modulate root growth, but also reveal why the excess of BRs or the enhanced BR signaling inhibits cell division in meristem to negatively regulate root growth. This article is protected by copyright. All rights reserved.
A New Instrument for Measuring Dietary Knowledge in Patients With Diabetes: Psychometric Testing of the CoNOCidiet-Diabetes.

PURPOSE To determine the psychometric properties of the CoNOCidiet-Diabetes, a new instrument based on nursing outcome "Knowledge: prescribed diet. " METHODS Methodological design. The participant were 359 patients diagnosed with diabetes visiting 27 primary healthcare centers in Spain. Reliability (internal consistency and test-retest), validity (convergent criterion validity, concurrent content validity and known-groups validity), and sensitivity to change was tested. FINDINGS CoNOCidiet-Diabetes has shown evidence of acceptable psychometric properties as instrument but some items should be revised. CONCLUSIONS This research provides a new instrument developed to specifically measure dietary knowledge in individuals with diabetes. IMPLICATIONS For nursing practice: The literalness of the CoNOCidiet-Diabetes with the nursing outcome "Knowledge: prescribed diet" facilitate its measurement using the patient's statements.
Calliobothrium schneiderae n. sp. (Cestoda: Tetraphyllidea) from the Spotted Estuary Smooth-Hound Shark, Mustelus lenticulatus, from New Zealand

Abstract New collections of tapeworms from the spiral intestine of the spotted estuary smooth-hound shark, Mustelus lenticulatus, in New Zealand led to the discovery of a species that appeared to be conspecific with specimens identified by Alexander (1963) as Calliobothrium eschrichti. Study of these newly collected specimens and some of Alexander's voucher material indicated that the species is new to science. Of the 15 described species in this genus, Calliobothrium schneiderae n. sp. differs from all but Calliobothrium barbarae, C. eschrichti, Calliobothrium leuckarti, and Calliobothrium hayhowi in that it is a small-bodied species that is nonlaciniate and lacks an accessory piece between the bases of its axial hooks. It differs from C. barbarae in testis number, total length, number of proglottids, and ovary shape, and differs from C. eschrichti in total length and vitelline follicle distribution. The new species also differs from C. leuckarti in total length and number of testes. It most closely resembles C. hayhowi, but differs in hook size and oncosphere packaging. The criterion suggested by Caira (1985) to distinguish axial from abaxial hooks is modified to include axial hooks being posterior in position, to accommodate species, such as C. schneiderae n. sp. , in which the abaxial hooks in a pair articulate with one another along the longitudinal axis of the bothridium, rather than with their respective axial hooks. Examination of a specimen Alexander identified as Calliobothrium verticillatum suggests that this identification may also be in error, and that this large lacinate specimen of Calliobothrium also represents a new species.
Multifaceted regulation of Notch signaling by glycosylation.

To build a complex body composed of various cell types and tissues and to maintain tissue homeostasis in the post-embryonic period, animals use a small number of highly conserved intercellular communication pathways. Among these is the Notch signaling pathway, which is mediated via the interaction of transmembrane Notch receptors and ligands usually expressed by neighboring cells. Maintaining optimal Notch pathway activity is essential for normal development, as evidenced by various human diseases caused by decreased and increased Notch signaling. It is therefore not surprising that multiple mechanisms are used to control the activation of this pathway in time and space. Over the last 20 years, protein glycosylation has been recognized as a major regulatory mechanism for Notch signaling. In this review, we will provide a summary of the various types of glycan that have been shown to modulate Notch signaling. Building on recent advances in the biochemistry, structural biology, cell biology and genetics of Notch receptors and the glycosyltransferases that modify them, we will provide a detailed discussion on how various steps during Notch activation are regulated by glycans. Our hope is that the current review article will stimulate additional research in the field of Notch glycobiology and will potentially be of benefit to investigators examining the contribution of glycosylation to other developmental processes.
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method

Solute-solvent systems are an important topic of study, as the effects of the solvent on the solute can drastically change its properties. Theoretical studies of these systems are done with ab initio methods, molecular simulations or a combination of both. The simulations of molecular systems are usually performed with either molecular dynamics (MD) or Monte Carlo (MC) methods. Classical MD has evolved much in the last decades, both in algorithms and implementations, having several stable and efficient codes developed and available. Similarly, MC methods have also evolved, focusing mainly in creating and improving methods and implementations in available codes. In this paper, we provide some enhancements to a Configurational Bias Monte Carlo (CBMC) methodology to simulate flexible molecules using the molecular fragments concept. In our implementation the acceptance criterion of the CBMC method was simplified and a generalization was proposed to allow the simulation of molecules with any kind of fragments. We also introduce the new version of DICE, a MC code for molecular simulation (available at https://portal.if.usp.br/dice). This code was mainly developed to simulate solute-solvent systems in liquid and gas phases and in interfaces (gas-liquid and solid-liquid) that has been mostly used to generate configurations for a sequential quantum mechanics/molecular mechanics method (S-QM/MM). This new version introduces several improvements over the previous ones, with the ability of simulating flexible molecules with CBMC as one of them. Simulations of well known molecules, such as n-octane and 1,2-dichloroethane in vacuum and in solution, are presented to validate the new implementations comparing with MD simulations, experimental data and other theoretical results. The efficiency of the conformational sampling was analyzed using the acceptance rates of different alkanes: n-octane, neopentane and 4-ethylheptane. Furthermore, a very complex molecule, the boron subphtalocyanine, was simulated in vacuum and in aqueous solution showing the versatility of the new implementation. We show that the CBMC is a very good method to perform conformation sampling of complex moderate sized molecules (up to 150 atoms) in solution following the Boltzmann thermodynamic equilibrium distribution.
The Effect of Bioactive Glass-Enhanced Orthodontic Bonding Resins on Prevention of Demineralization: A Systematic Review

At present, bioactive glasses (BAGs) are demonstrating promising results in the remineralization of hard tissues. Their bioactive properties can potentially overcome the demineralization effect accompanying orthodontic treatment. This review aimed to evaluate the effectiveness of bioactive glass enhanced orthodontic bonding resins on enamel remineralization, in addition to their antibacterial, ion release and acid neutralization effect. Four databases (PubMed, MEDLINE, Web of Science and Scopus) were searched. Two hundred and fifty-one full-text articles were screened independently, out of which seven studies satisfied the inclusion criteria. Quality appraisal was performed by two independent reviewers. Methodologies used to assess the anti-demineralization effect included Micro-Computed Tomography, Polarized Light Microscopy and Hardness Testing (Knoop and Berkovich). All seven articles confirmed the superior remineralization effect of BAG orthodontic bonding resins compared to their non-BAG counterparts. A proportional relationship was proved between BAG concentrations and increased anti-demineralization effect. The addition of antibacterial agents to BAG does not necessarily improve its anti-demineralization effect. Although studies have confirmed the effectiveness of BAG orthodontic bonding resins on enamel remineralization, there was a degree of heterogeneity across studies due to the lack of an in vitro studies standardized protocol.