Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Network Science: An Algorithmic Approach

The emerging field of network science represents a new style of research that can unify such traditionally-diverse fields as sociology, economics, physics, biology, and computer science. It is a powerful tool in analyzing both natural and man-made systems, using the relationships between players within these networks and between the networks themselves to gain insight into the nature of each field. Until now, studies in network science have been focused on particular relationships that require varied and sometimes-incompatible datasets, which has kept it from being a truly universal discipline. Computational Network Science seeks to unify the methods used to analyze these diverse fields. This book provides an introduction to the field of Network Science and provides the groundwork for a computational, algorithm-based approach to network and system analysis in a new and important way. This new approach would remove the need for tedious human-based analysis of different datasets and help researchers spend more time on the qualitative aspects of network science research.Demystifies media hype regarding Network Science and serves as a fast-paced introduction to state-of-the-art concepts and systems related to network scienceComprehensive coverage of Network Science algorithms, methodologies, and common problemsIncludes references to formative and updated developments in the fieldCoverage spans mathematical sociology, economics, political science, and biological networks
Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics

Foodborne pathogens such as L. monocytogenes can persist in food production environments for a long time, causing perennial outbreaks. Hence, bacterial pathogens are able to survive cleaning and disinfection procedures. Accordingly, they may be repeatedly exposed to sublethal concentrations of disinfectants, which might result in bacterial adaptation to these biocides. Furthermore, antibiotic coresistance and cross-resistance are known to evolve under biocide selection pressure in vitro. Hence, antimicrobial tolerance seems to play a crucial role in the resilience and persistence of foodborne pathogens in the food chain and might reduce therapeutic options in infectious diseases. ABSTRACT Contamination of food during processing is recognized as a main transmission route of Listeria monocytogenes. To prevent microbial contamination, biocides are widely applied as disinfectants in food processing plants. However, there are concerns about the development of antimicrobial resistance in foodborne pathogens due to widespread biocide usage. In our study, 93 L. monocytogenes isolates from German food production facilities were (i) tested for biocide and antibiotic susceptibility using broth microdilution assays, (ii) analyzed for links between reduced biocide susceptibility and antibiotic resistance, and (iii) characterized by whole-genome sequencing, including the detection of genes coding for biocide tolerance, antibiotic resistance, and other virulence factors. Fifteen L. monocytogenes isolates were tolerant to benzalkonium chloride (BAC), and genes conferring BAC tolerance were found in 13 of them. Antibiotic resistance was not associated with biocide tolerance. BAC-tolerant isolates were assigned to 6 multilocus sequence type (MLST) clonal complexes, and most of them harbored internalin A pseudogenes with premature stop codons or deletions (n = 9). Our study demonstrated a high genetic diversity among the investigated isolates including genotypes that are frequently involved in human infections. Although in vitro adaptation studies to biocides have raised concerns about increasing cross-resistance to antibiotics, our results do not provide evidence for this phenomenon in field isolates. IMPORTANCE Foodborne pathogens such as L. monocytogenes can persist in food production environments for a long time, causing perennial outbreaks. Hence, bacterial pathogens are able to survive cleaning and disinfection procedures. Accordingly, they may be repeatedly exposed to sublethal concentrations of disinfectants, which might result in bacterial adaptation to these biocides. Furthermore, antibiotic coresistance and cross-resistance are known to evolve under biocide selection pressure in vitro. Hence, antimicrobial tolerance seems to play a crucial role in the resilience and persistence of foodborne pathogens in the food chain and might reduce therapeutic options in infectious diseases.
Directed Nanoparticle Assembly via Polymer Crystallization.

Nanoparticles can be assembled into complex structures and architectures using a variety of methods. In this review, we discuss recent progress of using polymer crystallization (particularly polymer single crystals, PSCs) to direct nanoparticle assembly. PSCs have been extensively studied since 1957. Mainly appearing as quasi-two-dimensional (2D) lamellae, PSCs are typically used as model systems to determine polymer crystalline structures, or as markers to investigate the crystallization process. Recent research has demonstrated that they can also be used as nanoscale functional materials. Herein, we show that nanoparticles can be directed to assemble into complex shapes using in-situ or ex-situ polymer crystal growth. End-functionalized polymers can crystallize into 2D nanosheet PSCs, which are used to conjugate with complementary nanoparticles, leading to a nanosandwich structure. These nanosandwiches can find interesting applications for catalysis, surface enhanced Raman spectroscopy, and nanomotors. Dissolution of the nanosandwich leads to the formation of Janus nanoparticles, providing a unique method for asymmetric nanoparticle synthesis.
Structural and functional analysis of parameters governing tankyrase-1 interaction with telomeric repeat-binding factor 1 and GDP-mannose 4,6-dehydratase

Human tankyrase-1 (TNKS) is a member of the poly(ADP-ribose) polymerase (PARP) superfamily of proteins that posttranslationally modify themselves and target proteins with ADP-ribose (termed PARylation). The TNKS ankyrin repeat domain mediates interactions with a growing number of structurally and functionally diverse binding partners, linking TNKS activity to multiple critical cell processes, including Wnt signaling, Golgi trafficking, and telomere maintenance. However, some binding partners can engage TNKS without being modified, suggesting that separate parameters influence TNKS interaction and PARylation. Here, we present an analysis of the sequence and structural features governing TNKS interactions with two model binding partners: the PARylated partner telomeric repeat-binding factor 1 (TRF1) and the non-PARylated partner GDP-mannose 4,6-dehydratase (GMD). Using a combination of TNKS-binding assays, PARP activity assays, and analytical ultracentrifugation sedimentation analysis, we found that both the specific sequence of a given TNKS-binding peptide motif and the quaternary structure of individual binding partners play important roles in TNKS interactions. We demonstrate that GMD forms stable 1:1 complexes with the TNKS ankyrin repeat domain; yet, consistent with results from previous studies, we were unable to detect GMD modification. We also report in vitro evidence that TNKS primarily directs PAR modification to glutamate/aspartate residues. Our results suggest that TNKS-binding partners possess unique sequence and structural features that control binding and PARylation. Ultimately, our findings highlight the binding partner:ankyrin repeat domain interface as a viable target for inhibition of TNKS activity.
Varied Effects of Tending Ant Species on the Development of Facultatively Myrmecophilous Lycaenid Butterfly Larvae

Ants often tend and protect the larvae of various myrmecophilous lycaenid species, which influences the fitness of butterflies by altering their growth and developmental time. Tending produces diverse effects depending on lycaenid sex and the lycaenid/ant species combination. Effects are widely variable, especially in facultatively myrmecophilous lycaenids such as Plebejus argyrognomon praeterinsularis, because they are associated with several ant species and can survive without any ant tending. We studied the effects of ant tending on the adult body mass and larval developmental time of P. argyrognomon praeterinsularis. Female larvae grew significantly heavier as adults when tended by Camponotus japonicus rather than by either Lasius japonicus or no ant species. Ant tending did not affect the body mass of adult males or the developmental time of either male or female larvae. Thus, tending by C. japonicus could increase the fitness of P. argyrognomon praeterinsularis by increasing the mass of females without prolonging the duration of vulnerable immature stages, because larger females generally lay more eggs. This means that even facultatively myrmecophilous lycaenids might gain fitness benefits from particular ant species, which could be important in the conservation and management of at-risk species of facultatively myrmecophilous lycaenids.
Tolerant GPS receiver circuit for electronics errors

There is continual motivation to scale down transistors size and to reduce the supply voltage of the circuits. However, by approaching the limits of transistor scaling and operating at a minimal supply voltage, circuit reliability has emerged as a critical concern. Circuits become more and more susceptible to errors due to Process, Voltage and Temperature (PVT) variations. Occurrence of errors can affect the behavior of circuits and generate a permanent system failure. Therefore, it is increasingly important to deal with errors effects in order to keep future devices working properly. The objective of the thesis is to address the reliability in digital systems and introduce new fault tolerant techniques to perform reliable signal processing applications on unreliable hardware. An example of application has been considered in the thesis: the tracking process of GPS receivers. It contains a very interesting set of different signal processing problem with different requirements of reliability: Correlation process, tracking loops (recursive operations), state machine, Gold and carrier generators. Starting from a noiseless GPS receiver, redundant mechanisms have been proposed and added to design a more resilient GPS receiver tolerant to errors. An Application-Specific Integrated Circuit (ASIC) will be designed, based on thesis results, using the 28 nm technology to validate the performances of the proposed techniques performances. During the thesis, an emulation platform was designed to prepare the experimental environment for the ASIC.
Association of genetic polymorphisms of CYP2E1, NAT2, GST and SLCO1B1 with the risk of anti-tuberculosis drug-induced liver injury: a systematic review and meta-analysis

Objectives The objective of this study was to investigate the association between genetic polymorphisms of N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1), glutathione S-transferase (GST) and solute carrier organic anion transporter family member 1B1 (SLCO1B1) and the risk of anti-tuberculosis drug-induced liver injury (ATDILI). Design Systematic review and meta-analysis. Data sources PubMed, Embase, Web of Science and Cochrane Reviews databases were searched through April 2019. Eligibility criteria We included case-control or cohort studies investigating an association between NAT2, CYP2E1, GST or SLCO1B1 polymorphisms and the ATDILI risk in patients with tuberculosis. Data extraction and synthesis Three authors screened articles, extracted data and assessed study quality. The strength of association was evaluated for each gene using the pooled OR with a 95% CI based on the fixed-effects or random-effects model. Sensitivity analysis was performed to confirm the reliability and robustness of the results. Results Fifty-four studies were included in this analysis (n=26 for CYP2E1, n=35 for NAT2, n=19 for GST, n=4 for SLCO1B1). The risk of ATDILI was significantly increased with the following genotypes: CYP2E1 RsaI/PstI c1/c1 (OR=1.39, 95% CI 1.06 to 1.83), NAT2 slow acetylator (OR=3.30, 95% CI 2.65 to 4.11) and GSTM1 null (OR=1.30, 95% CI 1.12 to 1.52). No significant association with ATDILI was found for the genetic polymorphisms of CYP2E1 DraI, GSTT1, GSTM1/GSTT1, SLCO1B1 388A>G and SLCO1B1 521T>C (p>0.05). Conclusions ATDILI is more likely to occur in patients with NAT2 slow acetylator genotype, CYP2E1 RsaI/PstI c1/c1 genotype and GSTM1 null genotype. Close monitoring may be warranted for patients with these genotypes.
Adhesion of Two New Glass Fiber Post Systems Cemented with Self-Adhesive Resin Cements

The aim of this in vitro study was to evaluate the adhesion strength of two new fiber post systems (FiberSite™ Post and Cytec™ Blanco Post) cemented with two different adhesive resin cements (Panavia™ SA and Maxcem™ Elite). Root canals of sixty extracted human mandibular premolars were prepared using ProTaper Universal™ rotary files (Dentsply Sirona Endodontics, York, PA, USA). The root canals were irrigated with 5.25% sodium hypochlorite (NaOCl) during instrumentation. After root canal preparation, the canals were irrigated with 2 mL of 17% EDTA (1 min), followed by 2 mL of 5.25% (5 min) NaOCI, and 2 mL saline. The root canals were dried with paper points and divided randomly into two study groups (n = 30) according to the type of post system: Group 1, FiberSite™ Post (MegaDental, Partanna, Italy); and group 2, Cytec™ Blanco Post (Hahnenkratt, Königsbach-Stein, Germany), with one of the two adhesive resin cements: Subgroup A, Panavia™ SA Cement Plus Automix (Kuraray, Osaka, Japan); subgroup B, Maxcem™ Elite (Kerr, Orange, CA, USA). Following thermocycling, the adhesion strength was evaluated using the push-out adhesion (bond) strength test. Fractographic analysis was performed using stereomicroscope. The data were analyzed using two-way analysis of variance (p = 0.05). The adhesion strength values of both the posts were significantly higher when cemented with subgroup B (Maxcem™ Elite). The highest adhesion strength value was demonstrated by group 1B (FiberSite™ post cemented with Maxcem™ Elite cement). The type of post did not have a significant impact on the bond strength values for either cement material.
Vitamin D Status and Indices of Mineral Homeostasis in the Population: Differences Between 25-Hydroxyvitamin D and 1,25-Dihydroxyvitamin D

Opinions are conflicting about the epidemiology of vitamin D deficiency. This population-based study investigated cross-sectionally the associations of 25-hydroxyvitamin D (calcidiol) and 1,25-dihydroxyvitamin D (calcitriol) with indices of mineral homeostasis. Study cohort consisted of 979 persons of the Moli-Sani study, both sexes, ages ≥35 years. Data collection included serum calcidiol by different assays, serum calcitriol, serum parathyroid hormone, serum and urine calcium, and phosphorus. Prevalence of mild-to-moderate calcidiol deficiency (10–19 ng/mL) was 36.4% and did not associate with hypocalcemia or hyperparathyroidism. Prevalence of severe calcidiol deficiency (<10 ng/mL) was 16.8% and associated with hyperparathyroidism only (odds ratio = 8.81, 95% confidence interval = 2.4/32.9). Prevalence of calcitriol deficiency (<18 pg/mL) was 3.1% and associated with hypocalcemia (29.1, 7.4/114.5) but not hyperparathyroidism. In ANOVA along concentration strata, lower calcidiol associated with higher parathyroid hormone only (p < 0.001). Lower calcitriol associated with lower serum and urine calcium (p < 0.001) but not with parathyroid hormone. Calcidiol findings were consistent with different calcidiol assays. In the population, mild-to-moderate calcidiol deficiency did not associate with abnormal mineral homeostasis. Severe calcidiol deficiency and calcitriol deficiency associated with different disorders: lower calcidiol associated with hyperparathyroidism whereas lower calcitriol associated with hypocalcemia and low urine calcium.
Characterization and In Silico Analysis of The Structural Features of G-CSF Derived from Lysates of Escherichia coli

Objective Granulocyte colony-stimulating factor (G-CSF) has a wide variety of functions including stimulation of hematopoiesis and proliferation of granulocyte progenitor cells. Recombinant human G-CSF (rh-G-CSF) is used for treatment of neutropenia in patients receiving chemotherapy. The mature bloodstream neutrophils express G-CSF receptor (G-CSFR), presenting a significant and specific mechanism for circulating G-CSF clearance. Computational studies are essential bioinformatics methods used for characterization of proteins with regard to their physicochemical properties and 3D configuration, as well as protein–ligand interactions for recombinant drugs. We formerly produced rh-G-CSF in E. coli and showed that the isolated protein had unacceptable biological activity in mice. In the present paper, we aimed to characterize the purified rh-G-CSF by analytical tests and developed an in vivo model by computational modelling of G-CSF. Materials and Methods In this experimental study, we analyzed the purified G-CSF using the analytical experiments. Then, the crystalline structure was extracted from Protein Data Bank (PDB) and molecular dynamics (MD) simulation was performed using Gromacs 5.1 package under an Amber force field. The importance of amino acid contents of G-CSF, to bind the respective receptor was also detected; moreover, the effect of dithiothreitol (DTT) used in G-CSF purification was studied. Results The results revealed that characteristics of the produced recombinant G-CSF were comparable with those of the standard G-CSF and the recombinant G-CSF with the residual amino acid was stable. Also, purification conditions (DTT and existence of extra cysteine) had a significant effect on the stability and functionality of the produced G-CSF. Conclusion Experimental and in silico analyses provided good information regarding the function and characteristics of our recombinant G-CSF which could be useful for industrial researches.
Named-Entity-Recognition-Based Automated System for Diagnosing Cybersecurity Situations in IoT Networks

The aim of this paper was to enhance the process of diagnosing and detecting possible vulnerabilities within an Internet of Things (IoT) system by using a named entity recognition (NER)-based solution. In both research and practice, security system management experts rely on a large variety of heterogeneous security data sources, which are usually available in the form of natural language. This is challenging as the process is very time consuming and it is difficult to stay up to date with the constant findings in the areas of security threats, vulnerabilities, attacks, countermeasures, and risks. The proposed system is conceived as a semantic indexing solution of existing vulnerabilities and serves as an information tool for security management experts. By integrating the proposed system, the users can easily discover the potential vulnerabilities of their IoT devices. The proposed solution integrates ontologies and NER techniques in order to obtain a high rate of automation with the scope of reaching a self-maintained and up-to-date system in terms of vulnerabilities and common exposures knowledge. To achieve this, a total of 312 CVEs (common vulnerabilities and exposures) specific to the IoT field were identified. CVEs are arguably one of the most important cybersecurity resources nowadays, containing information about the latest discovered vulnerabilities. This set is further used as data corpus for an NER model designed to identify the main entities and relations that are relevant to IoT security. The goal is to automatically monitor cybersecurity information relevant to IoT, and filter and present it in an organized and structured framework based on users’ needs. The taxonomies specific to IoT security are implemented via a domain ontology, which is later used to process natural language. Relevant tokens are marked as entities and the relations between them identified. The text analysis solution is connected to a gateway which scans the environment and identifies the main IoT devices and communication technologies. The strength of the approach proposed within this research is that the designed semantic gateway is using context-aware searches in the modeled IoT security database and can identify possible vulnerabilities before they can be exploited.
Fish communities diverge in species but converge in traits over three decades of warming

Describing the spatial and temporal dynamics of communities is essential for understanding the impacts of global environmental change on biodiversity and ecosystem functioning. Trait‐based approaches can provide better insight than species‐based (i.e. taxonomic) approaches into community assembly and ecosystem functioning, but comparing species and trait dynamics may reveal important patterns for understanding community responses to environmental change. Here, we used a 33‐year database of fish monitoring to compare the spatio‐temporal dynamics of taxonomic and trait structure in North Sea fish communities. We found that the majority of variation in both taxonomic and trait structure was explained by a pronounced spatial gradient, with distinct communities in the southern and northern North Sea related to depth, sea surface temperature, salinity and bed shear stress. Both taxonomic and trait structure changed significantly over time; however taxonomically, communities in the south and north diverged towards different species, becoming more dissimilar over time, yet they converged towards the same traits regardless of species differences. In particular, communities shifted towards smaller, faster growing species with higher thermal preferences and pelagic water column position. Although taxonomic structure changed over time, its spatial distribution remained relatively stable, whereas in trait structure, the southern zone of the North Sea shifted northward and expanded, leading to homogenization. Our findings suggest that global environmental change, notably climate warming, will lead to convergence towards traits more adapted for novel environments regardless of species composition.
Targeting Degradation of EGFR through the Allosteric Site Leads to Cancer Cell Detachment-Promoted Death

Targeting epidermal growth factor receptor (EGFR) with tyrosine kinase inhibitors (TKI) has been widely exploited to disrupt aberrant phosphorylation flux in cancer. However, a bottleneck of potent TKIs is the acquisition of drug resistance mutations, secondary effects, and low ability to attenuate tumor progression. We have developed an alternative means of targeting EGFR that relies on protein degradation through two consecutive routes, ultimately leading to cancer cell detachment-related death. We describe furfuryl derivatives of 4-allyl-5-[2-(4-alkoxyphenyl)-quinolin-4-yl]-4H-1,2,4-triazole-3-thiol that bind to and weakly inhibit EGFR tyrosine phosphorylation and induce strong endocytic degradation of the receptor in cancer cells. The compound-promoted depletion of EGFR resulted in the sequestration of non-phosphorylated Bim, which no longer ensured the integrity of the cytoskeleton machinery, as shown by the detachment of cancer cells from the extracellular matrix (ECM). Of particular note, the longer CH3(CH2)n chains in the terminal moiety of the anti-EGFR molecules confer higher hydrophobicity in the allosteric site located in the immediate vicinity of the catalytic pocket. Small compounds accelerated and enhanced EGFR and associated proteins degradation during EGF and/or glutamine starvation of cultures, thereby demonstrating high potency in killing cancer cells by simultaneously modulating signaling and metabolic pathways. We propose a plausible mechanism of anti-cancer action by small degraders through the allosteric site of EGFR. Our data represent a rational and promising perspective in the treatment of aggressive tumors.