Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescent Conjugates : p H Stability , Dye-DNA Interaction and Biological Activity

* email: icre@ch.tuiasi. ro The quantitative analysis of nucleic acids is mandatory for molecular biology. Numerous strategies have been exploited to develop ligands which bind to and disrupt DNA functioning, DNA intercalators, and minor or major groove binding agents. Many organic dyes such as ethidium bromide [1], acridine orange [2], SYBR Green I [3], have been proved to be sensitive probes for DNA. Many analytical methods have been used in the study of DNA binding or quantification, such as voltametry [4], chromatography [5], capillary electrophoresis [6] or UVVIS, Raman spectroscopy, fluorescence [7,8]. Fluorescence analysis plays an important role in the study of DNA-binding [9,10]. In this paper, some recently synthesized indolizinylpyridinium derivatives [11] were used to investigate their interaction with DNA by spectral methods: UV-VIS spectrophotometry and fluorescence quenching technique. The electric transport of these compounds was already investigated, all compounds being found to behave as ptype semiconductors with polycrystalline structure [12]. The difference between these dyes concerns the substituents attached to heterocycles (scheme 1). (Roth, Germany). These solutions were diluted to the corresponding concentration with the same buffer (for fluorescence and binding assays the buffer was daily prepared using a Steriflip® Filter Unit, Millipore). A dye stock solution (2 mM) was prepared by dissolving an appropriate amount of compound a in 10 mL DMF and stored in the dark. This solution was diluted 1:100 (20 μM final concentration) with buffer as working solution. The water which was used was doubly distilled.
893-907 El-Aswad BEW.pmd

High-fat diet (HFD) can cause hyperlipidemia, fatty liver and cardiovascular disorders. Herein, we evaluated therapeutic effects and possible underlying mechanisms of actions of Schistosoma mansoni soluble egg antigen (SEA) against experimental HFD induced dyslipidemia, hepatic and cardiovascular pathology. Forty Swiss albino mice were divided into four groups (10 each); mice fed standard diet (SD), mice fed HFD, mice fed HFD for 8 weeks then infected by S. mansoni cercaria (HFD+I) and mice fed HFD for 8 weeks then treated with SEA (HFD+SEA), all mice were euthanized 16 weeks after starting the experiment. HFD+SEA mice showed significantly (p<0.001) reduced total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglycerides (TG), and significantly (p<0.05) increased high-density lipoprotein cholesterol (HDL-C) comparing to HFD mice with non-significant difference with HFD+I mice group. Doppler flowmetry showed significantly (p<0.01) lower arterial resistance and significantly (p<0.05) higher blood flow velocity in HFD+SEA and HFD+I mice groups than HFD mice. HFD+SEA mice revealed improving in liver and aortic pathology and these were better than HFD+I mice group. HFD+SEA and HFD+I mice groups had less myocardium lipid deposits, but still showing some congested blood vessels. HFD myocardium revealed strong CD34+ expression on immunohistochemistry study, while that of HFD+SEA showed weak and HFD+I mice had moderate expressions. HFD+SEA mice had significantly (p<0.01) lower serum IL-1β and vascular endothelial growth factor (VEGF) and significantly (p<0.001) higher serum transforming growth factor beta 1 (TGF-β1) and IL-10 than HFD mice with non-significant difference with HFD+I mice. In conclusion, SEA lowered serum lipids, improved aortic function, decreased liver and cardiovascular pathology in HFD mice, so, it is recommended to purify active molecules from SEA to develop anti-dyslipidemic treatment.
Lactate production is a prioritized feature of adipocyte metabolism

Adipose tissue is essential for whole-body glucose homeostasis, with a primary role in lipid storage. It has been previously observed that lactate production is also an important metabolic feature of adipocytes, but its relationship to adipose and whole-body glucose disposal remains unclear. Therefore, using a combination of metabolic labeling techniques, here we closely examined lactate production of cultured and primary mammalian adipocytes. Insulin treatment increased glucose uptake and conversion to lactate, with the latter responding more to insulin than did other metabolic fates of glucose. However, lactate production did not just serve as a mechanism to dispose of excess glucose, because we also observed that lactate production in adipocytes did not solely depend on glucose availability and even occurred independently of glucose metabolism. This suggests that lactate production is prioritized in adipocytes. Furthermore, knocking down lactate dehydrogenase specifically in the fat body of Drosophila flies lowered circulating lactate and improved whole-body glucose disposal. These results emphasize that lactate production is an additional metabolic role of adipose tissue beyond lipid storage and release.
Electronic and optoelectronic applications of solution-processed two-dimensional materials

ABSTRACT The isolation of graphene in 2004 has initiated much interest in two-dimensional (2D) materials. With decades of development, solution processing of 2D materials has becoming very promising due to its large-scale production capability, and it is therefore necessary to examine progress on solution-processed 2D materials and their applications. In this review, we highlight recent advances in the assembly of solution-processed 2D materials into thin films and the use of them for electronics and optoelectronics. We first present an overview about typical approaches to assemble solution-processed 2D materials into desired structures, including layer-by-layer assembly, Langmuir–Blodgett assembly, spin coating, electrophoretic deposition, inkjet printing, and vacuum filtration. Then, electronic and optoelectronic applications of such assembly films are presented, such as thin-film transistors, transparent conductive films, mechanical and chemical sensors, photodetectors and optoelectronic devices, as well as flexible and printed electronics. Finally, our perspectives on challenges and future opportunities in this important field are proposed. Graphical Abstract
Heparanase and chemotherapy synergize to drive macrophage activation and enhance tumor growth.

The emerging role of heparanase in tumor initiation, growth, metastasis, and chemoresistance is well recognized, encouraging the development of heparanase inhibitors as anticancer drugs. Unlike the function of heparanase in cancer cells, little attention has been given to heparanase contributed by cells composing the tumor microenvironment. Here, we focused on the cross-talk between macrophages, chemotherapy, and heparanase and the combined effect on tumor progression. Macrophages were markedly activated by chemotherapeutics paclitaxel (PCT) and cisplatin, evidenced by increased expression of pro-inflammatory cytokines, supporting recent studies indicating that chemotherapy may promote rather than suppress tumor re-growth and spread. Strikingly, cytokine induction by chemotherapy was not observed in macrophages isolated from heparanase-knockout mice, suggesting macrophage activation by chemotherapy is heparanase-dependent. PCT-treated macrophages enhanced the growth of lewis lung carcinoma tumors which was attenuated by a CXCR2 inhibitor. Mechanistically, PCT and cisplatin activated methylation of histone H3 on lysine 4 (H3K4) in wild-type but not heparanase-knockout macrophages. Furthermore, the H3K4 presenter WDR5 functioned as a molecular determinant that mediated cytokine induction by PCT. This epigenetic, heparanase-dependent host-response mechanism adds a new perspective to the tumor-promoting functions of chemotherapy, and offers new treatment modalities to optimize chemotherapeutics.
Fluid flow through nanopore space: discussion and proposition of a model for Polish shales

Two main models of fluids flow through nanopore space were considered. Single tube capillary model (and its improvements) and net model of nanopore space. Flexibility, efficiency and reliability of each was taken into account. Among others the Javadpour model seems to be relatively reliable and easy to apply for Polish shale gas reservoirs. Additionally it is possible to improved it, by introducing results of new investigations, such as Klinkenberg permeability obtained by Pulse Decay measurements.
The secretome of Pichia pastoris in fed‐batch cultivations is largely independent of the carbon source but changes quantitatively over cultivation time

The quantitative changes of the secretome of recombinant Pichia pastoris (Komagataella phaffii) CBS7435 over the time‐course of methanol‐ or glucose‐limited fed‐batch cultures were investigated by LC‐ESI‐MS/MS to define the carbon source‐specific secretomes under controlled bioreactor conditions. In both set‐ups, no indication for elevated cell lysis was found. The quantitative data revealed that intact and viable P. pastoris cells secrete only a low number of endogenous proteins (in total 51), even during high cell density cultivation. Interestingly, no marked differences in the functional composition of the P. pastoris secretome between methanol‐ and glucose‐grown cultures were observed with only few proteins being specifically affected by the carbon source. The ‘core secretome’ of 22 proteins present in all analysed carbon sources (glycerol, glucose and methanol) consists mainly of cell wall proteins. The quantitative analysis additionally revealed that most secretome proteins were already present after the batch phase, and depletion rather than accumulation occurred during the fed‐batch processes. Among the changes over cultivation time, the depletion of both the extracellularly detected chaperones and the only two identified proteases (Pep4 and Yps1‐1) during the methanol‐ or glucose‐feed phase appear as most prominent.
A 3’ UTR SNP rs885863, a cis-eQTL for the circadian gene VIPR2 and lincRNA 689, is associated with opioid addiction

There is a reciprocal relationship between the circadian and the reward systems. Polymorphisms in several circadian rhythm-related (clock) genes were associated with drug addiction. This study aims to search for associations between 895 variants in 39 circadian rhythm-related genes and opioid addiction (OUD). Genotyping was performed with the Smokescreen® array. Ancestry was verified by principal/MDS component analysis and the sample was limited to European Americans (EA) (OUD; n = 435, controls; n = 138). Nominally significant associations (p < 0.01) were detected for several variants in genes encoding vasoactive intestinal peptide receptor 2 (VIPR2), period circadian regulator 2 (PER2), casein kinase 1 epsilon (CSNK1E), and activator of transcription and developmental regulator (AUTS2), but no signal survived correction for multiple testing. There was intriguing association signal for the untranslated region (3’ UTR) variant rs885863 in VIPR2, (p = .0065; OR = 0.51; 95% CI 0.31–0.51). The result was corroborated in an independent EA OUD sample (n = 398, p = 0.0036; for the combined samples). Notably, this SNP is an expression quantitative trait locus (cis-eQTL) for VIPR2 and a long intergenic non-coding RNA, lincRNA 689, in a tissue-specific manner, based on the Genotype-Tissue Expression (GTEx) project. Vasoactive intestinal peptide (VIP) is an important peptide of light-activated suprachiasmatic nucleus cells. It regulates diverse physiological processes including circadian rhythms, learning and memory, and stress response. This is the first report of an association of a VIPR2 variant and OUD. Additionally, analysis of combinations of single nucleotide polymorphisms (SNPs) genotypes revealed an association of PER2 SNP rs80136044, and SNP rs4128839, located 41.6 kb downstream of neuropeptide Y receptor type 1 gene, NPY1R (p = 3.4 × 10−6, OR = 11.4, 95% CI 2.7–48.2). The study provides preliminary insight into the relationship between genetic variants in circadian rhythm genes and long non-coding RNA (lncRNAs) in their vicinity, and opioid addiction.
CHARACTERISATION OF THE EU-HOM-DAMPED NORMAL CONDUCTING 500 MHz CAVITY FROM THE BEAM POWER SPECTRUM AT DELTA ∗

A HOM-dampedprototypecavity (EU-cavity) [1] developed in the framework of an EC collaboration has been installed into the Dortmundsynchrotronlight source DELTA. This paper reports on beam studies performed at beam energies of 1.5 GeV and 542 MeV in an attempt to get information on coupled bunch instability (CBI) thresholds. In addition an evaluation of the longitudinalcavity impedance is presented, based on beam power spectra up to 3 GHz for differentfilling patterns of the storage ring by analysing the RF signal from the HOM-dampers.
Signatures of altered DNA methylation gene expression after central and peripheral nerve injury

Nerve damage can lead to movement and sensory dysfunction, with high morbidity and disability rates causing severe burdens on patients, families, and society. DNA methylation is a kind of epigenetics, and a great number of previous studies have demonstrated that DNA methylation plays an important role in the process of nerve regeneration and remodeling. However, compared with the central nervous system, the peripheral nervous system shows stronger recovery after injury, which is related to the complex microenvironment and epigenetic changes occurring at the site of injury. Therefore, what common epigenetic changes between the central and peripheral nervous systems remain to be elucidated. We first screened differential methylation genes after spinal cord injury and sciatic nerve injury using whole‐genome bisulfite sequencing and methylated DNA immunoprecipitation sequencing, respectively. Subsequently, a total of 16 genes had the same epigenetic changes after spinal cord injury and sciatic nerve injury. The Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed to identify the critical biological processes and pathways. Furthermore, a protein−protein interaction network analysis indicated that Dnm3, Ntrk3, Smurf1, Dpysl2, Kalrn, Shank1, Dlg2, Arsb, Reln, Bmp5, Numbl, Prickle2, Map6, and Htr7 were the core genes. These outcomes may provide novel insights into the molecular mechanism of the subacute phase of nerve injury. These verified genes can offer potential diagnostic and therapeutic targets for nerve injury.
Visually Grounded Paraphrase Extraction

A paraphrase is a restatement of the meaning of a word, phrase, or sentence within the context of a specific language (e.g., “a red jersey” and “a red uniform shirt” in Figure 1 are paraphrases). Paraphrases have been exploited for natural language understanding, and shown to be very effective for various natural language processing (NLP) tasks, including question answering, summarization, machine translation, text normalization , textual entailment recognition, and semantic parsing (Ganitkevitch and Callison-Burch, 2014). In this paper, we propose a novel task to extract visually grounded paraphrases (VGPs). We define VGPs as different phrasal expressions that describe the same visual concept in an image. Nowadays, with the spread of the web and social media, it is easy to collect large amounts of images with their describing text. For example, different news sites release news with the same topic using the same image; photos with many comments are posted to social networking sites and blogs. As these describing texts are written by different people but about the same image, there are potentially large amounts of VGPs in the describing text (Figure 1). We aim to accurately extract these paraphrases using the image as a pivot to associate different phrases. The extracted VGPs can be applied to various computer vision (CV) and NLP tasks, such as image captioning (Vinyals et al., 2015) and visual question answering (VQA) (Wu et al., 2017), for the better understanding of both images and languages. For example, a VQA system must understand queries of different expressions about the same visual concept (e.g., “a male” and “the pitcher” in Figure 1) in order to answer a question properly. VGPs can also be applied to the evaluation of image captioning systems in the similar Caption 1: a baseball player in a
Phosphorylation of TIP3 Aquaporins during Phaseolus vulgaris Embryo Development

The membrane phosphoproteome in plant seed changes dynamically during embryo development. We examined the patterns of Phaseolus vulgaris (common bean) seed membrane protein phosphorylation from the mid-maturation stage until two days after germination. Serine and threonine phosphorylation declined during seed maturation while tyrosine phosphorylation remained relatively constant. We discovered that the aquaporin PvTIP3;1 is the primary seed membrane phosphoprotein, and PvTIP3;2 shows a very low level of expression. The level of phosphorylated Ser7 in PvTIP3;1 increased four-fold after seed maturation. Since phosphorylation increases water channel activity, we infer that water transport by PvTIP3;1 is highest in dry and germinating seeds, which would be optimal for seed imbibition. By the use of isoform-specific, polyclonal peptide antibodies, we found that PvTIP3;2 is expressed in a developmental pattern similar to PvTIP3;1. Unexpectedly, PvTIP3;2 is tyrosine phosphorylated following seed maturation, which may suggest a mechanism for the regulation of PvTIP3;2 following seed germination. Analysis of protein secondary structure by circular dichroism spectroscopy indicated that the amino-terminal domain of PvTIP3;1 is generally unstructured, and phosphorylation increases polyproline II (PPII) helical structure. The carboxy-terminal domain also gains PPII character, but in a pH-dependent manner. These structural changes are a first step to understand TIP3 aquaporin regulation.
Quarto as a Reinforcement Learning problem

Reinforcement Learning has proven itself through a recent history of superhuman level performances in various tasks. Board games are of particular interest because they can be simulated completely, as the rules are pre-determined. Reinforcement Learning is a machine learning method, wherein the problem space is explored such that actions leading toward beneficial situations reward an Agent and situations that lead to unfavourable positions are punished. The aim of this thesis is to implement different learning methods and compare how well they play the game of Quarto. Training is done through self-play, where neural networks approximate the value-functions that are used to estimate how good a given position or action is. The results of my experiments indicate that differences in hyper-parameter settings lead to different performances. While the choice of learning algorithm did not change much in the way of overall performances, some differences in behaviour throughout training could be measured.
Cloud computing for disaster response management stemming from terrorism in Iraq

Abstract: Effective response to disasters requires assessing information prior to, during, and after potentially catastrophic events, as well as initiating activities that will lessen their impact upon society. The post-war transitions in Iraq have affected the institutional capacities of the state to respond in an efficient manner. Although the draft National Disaster Risk Reduction Law acknowledges the importance of information and knowledge management, it fails to provide a framework for establishing a dedicated information system. Due to the importance of an effective and efficient disaster management information system, this should be linked to local authorities, local early warning systems, and the media, to ensure effective use of disaster risk information for public awareness. The fact that disaster management data is often complex, large, and from different organisations, this requires a fast, scalable and accessible system to manage the complexity of the collected data. As cloud computing is considered a technology for providing synchronous, on-line information management with accessibility of data regardless of the storage resources’ location, this paper highlights the advantages of using cloud computing in managing information and communication in disaster response management, with particular reference to terrorism in the context of Iraq. The paper contributes to the existing knowledge on disaster response management, a field of study that is still largely under explored in the context of the Middle East, and in the context of terrorism more specifically, by reviewing its literature, through a systematic review methodology. This paper will focus, therefore, on the use of cloud computing as a solution to information sharing and communication, during the immediate response to a terrorist attack, due to the advantages of cloud computing in this context, in terms of data availability, reliability, IT and cost reduction.
Molecular model of the ferroportin intracellular gate and implications for the human iron transport cycle and hemochromatosis type 4A

Ferroportin 1 (FPN1) is a major facilitator superfamily transporter that is essential for proper maintenance of human iron homeostasis at the systemic and cellular level. FPN1 dysfunction leads to the progressive accumulation of iron in reticuloendothelial cells, causing hemochromatosis type 4A (or ferroportin disease), an autosomal dominant disorder that displays large phenotypic heterogeneity. Although crystal structures have unveiled the outward‐ and inward‐facing conformations of the bacterial homolog Bdellovibrio bacteriovorus Fpn (or Bd2019) and calcium has recently been identified as an essential cofactor, our molecular understanding of the iron transport mechanism remains incomplete. Here, we used a combination of molecular modeling, molecular dynamics simulations, and Ala site‐directed mutagenesis, followed by complementary in vitro functional analyses, to explore the structural architecture of the human FPN1 intracellular gate. We reveal an interdomain network that involves 5 key amino acids and is likely very important for stability of the iron exporter facing the extracellular milieu. We also identify inter‐ and intradomain interactions that rely on the 2 Asp84 and Asn174 critical residues and do not exist in the bacterial homolog. These interactions are thought to play an important role in the modulation of conformational changes during the transport cycle. We interpret these results in the context of hemochromatosis type 4A, reinforcing the idea that different categories of loss‐of‐function mutations exist. Our findings provide an unprecedented view of the human FPN1 outward‐facing structure and the particular function of the so‐called “gating residues” in the mechanism of iron export. —Guellec, J., Elbahnsi, A. , Le Tertre, M. , Uguen, K. , Gourlaouen, I. , Férec, C. , Ka, C. , Callebaut, I. , Le Gac, G. Molecular model of the ferroportin intracellular gate and implications for the human iron transport cycle and hemochromatosis type 4A. FASEB J. 33, 14625‐14635 (2019). www.fasebj. org
An Integrated Model for Discontinuous Preference Change and Satiation

We develop a structural model of horizontal and temporal variety seeking using a dynamic factor model that relates attribute satiation to brand preferences. The factor model employs a threshold specification that triggers preference changes when customer satiation exceeds an admissible level but does not change otherwise. The factor model is developed for high dimensional switching data encountered when multiple brands are purchased across multiple time periods. The model is applied to two scanner-panel datasets where we find distinct shifts in consumer preferences over time where consumers are found to value variety much more than indicated by traditional models. Insights into brand preference are provided by a dynamic joint space map that displays brand positions and temporal changes in consumer preferences over time.