Miracle-dz/UniFAR-FTUs huggingface dataset:
GATA-type transcriptional factor Gat1 regulates nitrogen uptake and polymalic acid biosynthesis in polyextremotolerant fungus Aureobasidium pullulans.

Polymalic acid (PMA) is a novel biopolymer produced by the polyextremotolerant fungus Aureobasidium pullulans. In this study, a GATA-family transcriptional factor, Gat1, which regulates nitrogen uptake and PMA biosynthesis, was investigated. PMA production increased to 11.2% in the mutant overexpressing gat1, but decreased to 49.1% of the PMA titer when gat1 was knocked out from the genome of A. pullulans. Comparative transcriptome analysis of wide-type and mutant strains (∆gat1 and OE::gat1) revealed that 23 common differentially expressed genes were related to oxidative phosphorylation, ribosome biogenesis, and nitrogen metabolism. Under nitrogen-limited stress, regardless of the preferred nitrogen (glutamine, Gln) or non-preferred nitrogen (proline, Pro), 70% of Gat1 in the cells was located in the nucleus-cytoplasm, which resulted in an increase in nitrogen uptake and PMA biosynthesis regulation. Quantitative RT-PCR revealed that glucosekinase (GLK) in the glycolytic pathway and malate synthase (MLS) in the glyoxylate shunt pathway may be cross-regulated by Gat1 and nitrogen concentration (Gln or Pro), Therefore, glk was overexpressed in mutant strain (OE::gat1), which resulted in an increased PMA titer and yield of 12.6% and 13.0%, respectively. These findings indicate that Gat1 may play an important role in the dual-regulation of the nitrogen and carbon metabolisms in PMA biosynthesis. This article is protected by copyright. All rights reserved.
Conjugate eye movements guide jumping locomotion in an avian species

ABSTRACT Many animals rely on vision to successfully locomote through their environments. However, our understanding of the interaction between vision and locomotion is surprisingly limited. This study therefore examined the visual mechanisms guiding jumping locomotion in an avian species. It recorded the eye movements of captive Indian peafowl (Pavo cristatus) as they jumped up onto and down from a perch. Peafowl shifted their eyes forward as they were jumping, increasing the degree of binocular overlap. Their eye movements were highly conjugate as they were jumping but were otherwise loosely conjugate. Finally, the peafowl rarely directed their gaze toward landing spots. These results suggest that eye movements play a central role in avian locomotion and they can vary depending on the specific locomotor task. Summary: During jumping locomotion, female peafowl rarely gaze at their landing spots and their eye movements are highly conjugate while shifting forward, suggesting that vision plays a critical role in locomotion that varies depending on the locomotor task.
Intraocular VEGF deprivation induces degeneration and fibrogenic response in retina

VEGF is a critical driver of ocular neovascularization under disease conditions. Current therapeutic strategies rely on intraocular delivery of VEGF‐antagonizing reagents, which results in sustained suppression of pathogenic vascularization. Although significant advancement has been achieved in VEGF antagonism, substantial adverse effects have been reported in retrospective clinical studies. To study mechanisms for VEGF antagonism‐associated adverse effects in visual system, we intravitreally delivered recombinant adeno‐associated virusmediated expression of soluble Fms‐related tyrosine kinase‐1 (rAAV.sFLT‐1), the extracellular domain of VEGF receptor, and analyzed the morphology and functions of retinal tissue. Here, we confirmed that intraocular VEGF antagonism induced retinal degeneration and gliosis. The functional deficit in retinal response to visual stimulation was also demonstrated in rAAV.sFLT‐1‐treated eyes by electroretinogram. Moreover, high‐throughput RNA sequencing analysis suggests that VEGF antagonism activates retinal degeneration, inflammation, and other adverse effects. Taken together, our findings have shed light on pathogenic mechanisms for VEGF antagonism‐associated adverse effects and potential therapeutic targets. —Xiao, M. , Liu, Y. , Wang L. , Liang, J., Wang T. , Zhai, Y. , Wang Y. , Liu S. Liu W. Luo X. Wang F. Sun X. Intraocular VEGF deprivation induces degeneration and fibrogenic response in retina. FASEB J. 33, 13920‐13934 (2019). www.fasebj. org
The critical role of respiratory sinus arrhythmia on temporal cardiac dynamics.

Temporal cardiac properties provide alternative information in analyzing heart rate variability (HRV) which may be disregarded by the standard HRV analyses. Patients with congestive heart failure (CHF) were known to have distinct temporal features from the healthy individuals. However, the underlying mechanism leading to the variation remains unclear. Whether or not these parameters can finely classify the severity for CHF patients is uncertain as well. In this work, electrocardiogram was monitored in advanced CHF patients using 24-hour Holter in 4 conditions including baseline, one and three months after atenolol therapy, and healthy individuals. Slope and area under curve (AUC) of multiscale entropy (MSE) curve over short (scale 1-5) and long (scales 6-20) scales, and detrended fluctuation analysis (DFA) scaling exponents at short (4-11 beats) and intermediate (>11 beats) window sizes were calculated. The results show that short-time scaled MSE derived parameters (slope: -0.08 ± 0.10, -0.03 ± 0.10, 0.02 ± 0.06, 0.08 ± 0.06; AUC: 4.03 ± 2.11, 4.69 ± 1.28, 4.73 ± 0.94, 6.17 ± 1.23) and short-time scaled DFA exponent (0.79±0.16, 0.95±0.22, 1.11±0.19, 1.35 ± 0.20) can hierarchically classify all four conditions. More importantly, simulated RR intervals with different fractions and amplitude of respiratory sinus arrhythmia (RSA) components were examined to validate our hypothesis regarding the essentiality of RSA in the improvement of cardiovascular function, and its tight association with unpredictability and fractal property of HRV, which in line with our hypothesis that RSA contributes significantly to the generation of the unpredictability and fractal behavior of HR dynamics.
Recommended hospital preparations for future cases and outbreaks of novel influenza viruses

ABSTRACT Introduction: Seasonal influenza epidemics and periodic pandemics are important causes of morbidity and mortality. Influenza transmits predominantly by respiratory droplets and fomites but opportunistic airborne transmission may occur in the hospital setting due to overcrowding, poor compliance with infection control measures, and performance of aerosol-generating procedures. Areas covered: This article reviews the risk factors of nosocomial influenza outbreaks and discusses clinical, diagnostic, and treatment aspects of seasonal and avian influenza to facilitate hospital preparations for future influenza outbreaks. Literature search was conducted through PubMed of relevant peer-reviewed full papers in English journals with inclusion of relevant publications by the WHO and US CDC. Expert opinion: Accurate and rapid identification of an influenza outbreak is important to facilitate patient care and prevent nosocomial transmission. Timely treatment with a neuraminidase inhibitor (NAI) for adults hospitalized with severe influenza is associated with lower mortality and better clinical outcomes. Baloxavir, a polymerase endonuclease inhibitor, offers a new treatment alternative and its role in combination with NAI for treatment of severe influenza is being investigated. High-dose systemic corticosteroids are associated with worse outcomes in patients with severe influenza. It is important to develop more effective antiviral and immuno-modulating therapies for the treatment of influenza infections.
Neonatal septic arthritis in the North of Jordan

Abstract We studied neonatal septic arthritis in the North of Jordan and investigated the pattern of causative microorganisms. In 27 neonates, 27 episodes of septic arthritis were identified between January 2003 and December 2004. The diagnosis of septic arthritis was made based on clinical and radiological findings plus the result of culture of the aspirated pus from the affected joint (s). The mean age of presentation was 20.1 ± 5.7 days. Male to female ratio was 1.25:1 and most of the neonates (85%) had been admitted and discharged previously to the same neonatal intensive care unit. Hip joints were involved in 70% of the cases. Elevated erythrocyte sedimentation rate and positive C-reactive protein were found in all cases. Microorganism was grown in blood or synovial fluid samples from 59% of the neonates. Klebsiella pneumoniae was the most frequent genus isolated (30%), followed by Staphylococcus aureus and Enterobacter (22% and 7%, respectively). Gram-negative organisms continues to be the most commonly encountered bacteria causing septic arthritis in the neonates of North of Jordan. The high incidence of primary septic arthritis makes the early diagnosis essential. Previous admission to neonatal intensive care unit was the main risk factor.
A novel transcriptomic based approach to the detection of recombinant human erythropoietin doping

Administration of recombinant human erythropoietin (rHuEpo) improves endurance performance. Hence rHuEpo is, allegedly, frequently subject to abuse by athletes, although rHuEpo is prohibited by the World Anti-Doping Agency. A transcriptomic-based longitudinal screening approach has the potential to improve further the performance of current detection methods. AIM: To assess the effects of rHuEpo on blood gene expression profiles in order to identify a “molecular signature” of rHuEpo doping. METHODS: 19 Caucasian trained males at sea-level (Scotland – SCO) and 20 Kenyan endurance runners at moderate altitude (~2,150 m, Kenya – KEN) received rHuEpo injections of 50 IU∙kg-1 body mass every two days for 4 weeks. Blood was obtained 2 weeks before, during and 4 weeks after administration. 3,000 m time trial performance was measured pre, post administration and at the end of the study. RNA was extracted from blood stabilized in Tempus RNA tubes, amplified, labelled and hybridized to Illumina HumanHT-12v4 Expression BeadChips. Expression data was analyzed using Rank Products with a 5% false discovery rate and an additional 1.5 fold-change threshold. A subset of target and housekeeping genes was further validated using QuantiGene Plex assay. RESULTS: Despite markedly different baseline values between SCO and KEN, as exemplified by the haematocrit (41.9 ± 1.8% vs. 45.3 ± 2.6, p 0.188). These results confirmed that the perturbation involving rHuEpo worked effectively. Relative to baseline, the expression of hundreds of genes were found to be altered by rHuEpo. In particular, 30 transcripts were already differentially expressed two days after the first injection while 15 transcripts were profoundly up-regulated during and subsequently down-regulated up to 4 weeks post administration in both groups. Importantly, the same pattern was observed in all subjects. The functions of the discovered genes were mainly related to either the functional or structural properties of the erythrocyte or to the cell cycle and its regulation. CONCLUSION: This research successfully identified the blood “molecular signature” of rHuEpo administration and provides the strongest evidence to date that gene biomarkers have the potential to substantially improve the performance of current anti-doping methods such as the Athlete Biological Passport for rHuEpo detection.
Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy Dovepress

php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License (http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms (https://www.dovepress.com/terms.php). Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy 2017:10 1–11 Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy Dovepress
Agatha BW.indd

Agatha van der Klaauw werd geboren op 14 maart 1980 te Leiderdorp. Zij behaalde in 1998 het eindexamen aan het Stedelijk Gymnasium te Leiden. In 1999 haalde zij cum laude het propaedeutisch examen Geneeskunde. In 2002 deed zij onderzoek op de afdeling Nucleaire Geneeskunde te Leiden waarna zij in 2002 cum laude het doctoraal examen Geneeskunde behaaldde. Het artsexamen werd cum laude behaald in 2004. Direct aansluitend werd met dit promotie-onderzoek begonnen op de afdeling Endocrinologie onder leiding van Professor Romijn en Professor Smit.
Can Greenbergian universals be induced from language networks?

Language networks have been proposed to be the underlying representation for syntactic knowledge (Roelofs, 1992; Pickering and Branigan, 1998). Such networks are known to explain various word order related priming effects in psycholinguistics. Under the assumption that word order information is encoded in these networks, we explore if Greenbergian word order universals (Greenberg, 1963) can be induced from such networks. Language networks for 34 languages were constructed from the Universal Dependencies Treebank (Nivre et al., 2016) based on the assumptions in Roelofs (1992); Pickering and Branigan (1998). We conducted a series of experiments to investigate if certain network parameters can be used to cluster various languages based on the word order typology proposed by Greenberg. Our results show that some network parameters robustly cluster the languages correctly, thereby providing some support for language network as a valid representation for such linguistic generalizations.
Thuja occidentalis and Duranta repens as indicators of urban air pollution in industrialized areas of southwest Nigeria

This paper assessed biochemical parameters in leaves of selected ornamental species growing in urban areas of southwest Nigeria to obtain the air pollution tolerance index (APTI) and anticipated performance index (API) for classification into tolerant and sensitive species against air pollution. Four sites and three ornamental species (Polyalthia longifolia, Thuja occidentalis and Duranta repens) common to the sites were used for this study. Results showed significant variations in biochemical variables, hence biochemical parameters cannot be used solely to categorize the species. APTI values obtained suggested that P. longifolia is tolerant species to air pollutants while T. occidentalis and D. repens are sensitive species that can be used as bioindicators of air pollutants. The API value revealed P. longifolia and T. occidentalis to be poor performer and very poor performer respectively while D. repens cannot be recommended for greenbelt development. Therefore, T. occidentalis and D. repens, can be recommended as bioindicators of poor urban air quality.
Undecidability of Satisfiability of Expansions of FO[

We provide two new characterizations of FO[<,mod]-definable sets, i.e. sets of integers definable in first-order logic with the order relation and modular relations, and use these characterizations to prove that satisfiability of first-order logic over words with an order relation and a semilinear set (i.e. a set definable in first-order logic with addition) that is not FO[<,mod]definable is undecidable.
Spins , Moments and Radii of Cd Isotopes

The complex nature of the nucleon-nucleon interaction and the wide range of systems covered by the roughly 3000 known nuclides leads to a multitude of effects observed in nuclear structure. Among the most prominent ones is the occurence of shell closures at so-called ”magic numbers”, which are explained by the nuclear shell model. Although the shell model already is on duty for several decades, it is still constantly extended and improved. For this process of extension, fine adjustment and verification, it is important to have experimental data of nuclear properties, especially at crucial points like in the vicinity of shell closures. This is the motivation for the work performed in this thesis: the measurement and analysis of nuclear ground state properties of the isotopic chain of 100−130Cd by collinear laser spectroscopy . The experiment was conducted at ISOLDE/CERN using the collinear laser spectroscopy apparatus COLLAPS. This experiment is the continuation of a run on neutral atomic cadmium from A = 106 to A = 126 and extends the measured isotopes to even more exotic species. The required gain in sensitivity is mainly achieved by using a radiofrequency cooler and buncher for background reduction and by using the strong 5s S1/2 → 5p P3/2 transition in singly ionized Cd. The latter requires a continuous wave laser system with a wavelength of 214.6 nm, which has been developed during this thesis. Fourth harmonic generation of an infrared titanium sapphire laser is achieved by two subsequent cavity-enhanced second harmonic generations, leading to the production of deep-UV laser light up to about 100mW. The acquired data of the Z = 48 Cd isotopes, having one proton pair less than the Z = 50 shell closure at tin, covers the isotopes from N = 52 up to N = 82 and therefore almost the complete region between the neutron shell closures N = 50 and N = 82. The isotope shifts and the hyperfine structures of these isotopes have been recorded and the magnetic dipole moments, the electric quadrupole moments, spins and changes in mean square charge radii are extracted. The obtained data reveal among other features an extremely linear behaviour of the quadrupole moments of the I = 11/2− isomeric states and a parabolic development in differences in mean square nuclear charge radii between ground and isomeric state. The development of charge radii between the shell closures is smooth, exposes a regular odd-even staggering and can be described and interpreted in the model of Zamick and Thalmi.
Hydrophobic ion pairing: encapsulating small molecules, peptides, and proteins into nanocarriers

Hydrophobic ion pairing has emerged as a method to modulate the solubility of charged hydrophilic molecules ranging in class from small molecules to large enzymes. Charged hydrophilic molecules are ionically paired with oppositely-charged molecules that include hydrophobic moieties; the resulting uncharged complex is water-insoluble and will precipitate in aqueous media. Here we review one of the most prominent applications of hydrophobic ion pairing: efficient encapsulation of charged hydrophilic molecules into nano-scale delivery vehicles – nanoparticles or nanocarriers. Hydrophobic complexes are formed and then encapsulated using techniques developed for poorly-water-soluble therapeutics. With this approach, researchers have reported encapsulation efficiencies up to 100% and drug loadings up to 30%. This review covers the fundamentals of hydrophobic ion pairing, including nomenclature, drug eligibility for the technique, commonly-used counterions, and drug release of encapsulated ion paired complexes. We then focus on nanoformulation techniques used in concert with hydrophobic ion pairing and note strengths and weaknesses specific to each. The penultimate section bridges hydrophobic ion pairing with the related fields of polyelectrolyte coacervation and polyelectrolyte-surfactant complexation. We then discuss the state of the art and anticipated future challenges. The review ends with comprehensive tables of reported hydrophobic ion pairing and encapsulation from the literature.
8-OH-DPAT-induced hypothermia in 5-HT receptor knockout mice

To test for adaptive compensatory changes that may have occurred in the functional activity of somatodendritic 5-HT receptors 1A Ž . during the development of constitutive AknockoutB mice lacking the 5-HT receptor subtype 5-HT yry KO , we assayed for 1B 1B Ž decrease in body temperature induced by an acute subcutaneous injection of the 5-HT receptor agonist, 8-hydroxy 2 di-n1A Ž . Ž . w Ž . propyl amino tetralin 8-OH-DPAT , either alone or in the presence of a selective 5-HT receptor antagonist, N42-methoxyphenyl 1A x Ž . Ž . 1-piperazinyl -N2-pyridinyl cyclo-hexanecarboxamide WAY 100635 . We compared dose–response curves, time course study, Ž . Ž . calculated ED values potency , maximal response to 8-OH-DPAT efficacy as well as measurements of the dose-dependent blockade 50 of this response by WAY 100635 between wild-type controls and mutant mice. We found a higher efficacy of 8-OH-DPAT-induced hypothermia in 5-HT yry KO compared to wild-type mice suggesting that an adaptive thermoregulatory process involving the 1B functional activity of somatodendritic 5-HT receptors is altered in mutant mice lacking 5-HT receptors. q 2001 Elsevier Science B.V. 1A 1B All rights reserved.
Updating Ontology Alignments in Life Sciences based on New Concepts and their Context

Ontologies and their associated mappings in life sciences play a central role in several semantic-enabled tasks. However, the continuous evolution of these ontologies requires updating existing concept alignments. Whereas mapping maintenance techniques have mostly handled revision and removal type of ontology changes, the addition of concepts demands further studies. This article proposes a technique to refine a set of established mappings based on the evolution of biomedical ontologies. We investigate ways of suggesting correspondences with the new version of the ontology without applying a matching operation to the whole set of ontology entities. Obtained results explore the neighbourhood of concepts in the alignment process to update mapping sets. Our experimental evaluation with several versions of aligned biomedical ontologies shows the effectiveness in considering the context of new concepts.
Cellular Uplink Bandwidth Prediction Based on Radio Measurements

In 4G networks, the emergence of machine communications such as connected vehicles increases the high demand of uplink transmissions, thus, degrading the quality of service per user equipment. Enforcing quality-of-service in such cellular network is challenging, as radio phenomenon, as well as user (and their devices) mobility and dynamics, are uncontrolled. To solve this issue, estimating what the quality of transmissions will be in a short future for a connected user is essential. For that purpose, we argue that radio metrics are key features whose evolutions can help predicting the bandwidth that the considered connections can take advantage of in the following hundreds of milliseconds. The paper then describes how a 4G testbed has been deployed in order to study the correlation between radio noise and throughput in uplink transmissions. Based on radio measurements, the main supervised machine learning algorithms are used, such as Random Forest and Support Vector Machine to predict the uplink received bandwidth. For a specific user service, we are able to predict the end-to-end received bandwidth, i.e. the amount of received data on the server side during a specific period at a very low scale of 100 ms. Results also prove that uplink bandwidth predictions are less accurate compared to bandwidth prediction for downlink based on radio measurements.