bluuebunny/crossref_metadata_2025 huggingface dataset:
Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics
Authors: Erenpreisa Jekaterina , Giuliani Alessandro
Published: December 2019

The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful ‘tumour-reversion’ therapeutic strategies.
ORESARA15 Acts Synergistically with ANGUSTIFOLIA3 and Separately from AINTEGUMENTA to Promote Cell Proliferation during Leaf Growth
Authors: Jun Sang Eun , Kim Jin Hee , Hwang Ji Young , Huynh Le Thien Tu , Kim Gyung-Tae
Published: December 2019

Developing leaves undergo sequential coordinated cell proliferation and cell expansion to determine their final size and shape. Although several important regulators of cell proliferation have been reported, the gene network regulating leaf developmental processes remains unclear. Previously, we showed that ORESARA15 (ORE15) positively regulates the rate and duration of cell proliferation by promoting the expression of direct targets, GROWTH-REGULATING FACTOR (GRF) transcription factors, during leaf growth. In the current study, we examined the spatiotemporal patterns of ORE15 expression and determined that ORE15 expression partially overlapped with AN3/GIF1 and ANT expression along the midvein in the proximal region of the leaf blade in young leaves. Genetic analysis revealed that ORE15 may function synergistically with AN3 to control leaf growth as a positive regulator of cell proliferation. Our molecular and genetic studies are the first to suggest the importance of functional redundancies between ORE15 and AN3, and between AN3 and ANT in cell proliferation regulatory pathway during leaf growth.
Expression of Retinoid Acid Receptor-Responsive Genes in Rodent Models of Placental Pathology
Authors: Mocker Alexander , Schmidt Marius , Huebner Hanna , Wachtveitl Rainer , Cordasic Nada , Menendez-Castro Carlos , Hartner Andrea , Fahlbusch Fabian B.
Published: December 2019

In humans, retinoic acid receptor responders (RARRES) have been shown to be altered in third trimester placentas complicated by the pathologies preeclampsia (PE) and PE with intrauterine growth restriction (IUGR). Currently, little is known about the role of placental Rarres in rodents. Therefore, we examined the localization and expression of Rarres1 and 2 in placentas obtained from a Wistar rat model of isocaloric maternal protein restriction (E18.5, IUGR-like features) and from an eNOS-knockout mouse model (E15 and E18.5, PE-like features). In both rodent models, Rarres1 and 2 were mainly localized in the placental spongiotrophoblast and giant cells. Their placental expression, as well as the expression of the Rarres2 receptor chemokine-like receptor 1 (CmklR1), was largely unaltered at the examined gestational ages in both animal models. Our results have shown that RARRES1 and 2 may have different expression and roles in human and rodent placentas, thereby underlining immanent limitations of comparative interspecies placentology. Further functional studies are required to elucidate the potential involvement of these proteins in early placentogenesis.
Cyclin-Dependent Kinase Inhibitors KRP1 and KRP2 Are Involved in Grain Filling and Seed Germination in Rice (Oryza sativa L.)
Authors: Ajadi Abolore Adijat , Tong Xiaohong , Wang Huimei , Zhao Juan , Tang Liqun , Li Zhiyong , Liu Xixi , Shu Yazhou , Li Shufan , Wang Shuang , Liu Wanning , Tajo Sani Muhammad , Zhang Jian , Wang Yifeng
Published: December 2019

Cyclin-dependent kinase inhibitors known as KRPs (kip-related proteins) control the progression of plant cell cycles and modulate various plant developmental processes. However, the function of KRPs in rice remains largely unknown. In this study, two rice KRPs members, KRP1 and KRP2, were found to be predominantly expressed in developing seeds and were significantly induced by exogenous abscisic acid (ABA) and Brassinosteroid (BR) applications. Sub-cellular localization experiments showed that KRP1 was mainly localized in the nucleus of rice protoplasts. KRP1 overexpression transgenic lines (OxKRP1), krp2 single mutant (crkrp2), and krp1/krp2 double mutant (crkrp1/krp2) all exhibited significantly smaller seed width, seed length, and reduced grain weight, with impaired seed germination and retarded early seedling growth, suggesting that disturbing the normal steady state of KRP1 or KRP2 blocks seed development partly through inhibiting cell proliferation and enlargement during grain filling and seed germination. Furthermore, two cyclin-dependent protein kinases, CDKC;2 and CDKF;3, could interact with KRP1 in a yeast-two-hybrid system, indicating that KRP1 might regulate the mitosis cell cycle and endoreduplication through the two targets. In a word, this study shed novel insights into the regulatory roles of KRPs in rice seed maturation and germination.
Comparative Transcriptomics Provides Insight into Floral Color Polymorphism in a Pleione limprichtii Orchid Population
Authors: Zhang Yiyi , Zhou Tinghong , Dai Zhongwu , Dai Xiaoyu , Li Wei , Cao Mengxia , Li Chengru , Tsai Wen-Chieh , Wu Xiaoqian , Zhai Junwen , Liu Zhongjian , Wu Shasha
Published: December 2019

Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or between similar species. The orchid genus Pleione has a wide variety of flower colors, from violet, rose-purple, pink, to white, but their color formation and its evolutionary mechanism are unclear. Here, we selected the P. limprichtii population in Huanglong, Sichuan Province, China, which displayed three color variations: Rose-purple, pink, and white, providing ideal material for exploring color variations with regard to species evolution. We investigated the distribution pattern of the different color morphs. The ratio of rose-purple:pink:white-flowered individuals was close to 6:3:1. We inferred that the distribution pattern may serve as a reproductive strategy to maintain the population size. Metabolome analysis was used to reveal that cyanindin derivatives and delphidin are the main color pigments involved. RNA sequencing was used to characterize anthocyanin biosynthetic pathway-related genes and reveal different color formation pathways and transcription factors in order to identify differentially-expressed genes and explore their relationship with color formation. In addition, qRT-PCR was used to validate the expression patterns of some of the genes. The results show that PlFLS serves as a crucial gene that contributes to white color formation and that PlANS and PlUFGT are related to the accumulation of anthocyanin which is responsible for color intensity, especially in pigmented flowers. Phylogenetic and co-expression analyses also identified a R2R3-MYB gene PlMYB10, which is predicted to combine with PlbHLH20 or PlbHLH26 along with PlWD40-1 to form an MBW protein complex (MYB, bHLH, and WDR) that regulates PlFLS expression and may serve as a repressor of anthocyanin accumulation-controlled color variations. Our results not only explain the molecular mechanism of color variation in P. limprichtii, but also contribute to the exploration of a flower color evolutionary model in Pleione, as well as other flowering plants.
A Review of Blockchain-Based Systems in Transportation
Authors: Astarita Vittorio , Giofrè Vincenzo Pasquale , Mirabelli Giovanni , Solina Vittorio
Published: December 2019

This paper presents a literature review about the application of blockchain-based systems in transportation. The main aim was to identify, through the implementation of a multi-step methodology: current research-trends, main gaps in the literature, and possible future challenges. First, a bibliometric analysis was carried out to obtain a broad overview of the topic of interest. Subsequently, the most influential contributions were analysed in depth, with reference to the following two areas: supply chain and logistics; road traffic management and smart cities. The most important result is that the blockchain technology is still in an early stage, but appears extremely promising, given its possible applications within multiple fields, such as food track and trace, regulatory compliance, smart vehicles’ security, and supply-demand matching. Much effort is still necessary for reaching the maturation stage because several models have been theorized in recent years, but very few have been implemented within real contexts. Moreover, the link blockchain-sustainability was explored, showing that this technology could be the trigger for limiting food waste, reducing exhaust gas emissions, favouring correct urban development, and, in general, improving quality of life.
Adoption Barriers of IoT in Large Scale Pilots
Authors: Padyab Ali , Habibipour Abdolrasoul , Rizk Aya , Ståhlbröst Anna
Published: December 2019

The pervasive connectivity of devices enabled by Internet of Things (IoT) technologies is leading the way in various innovative services and applications. This increasing connectivity comes with its own complexity. Thus, large scale pilots (LSPs) are designed to develop, test and use IoT innovations in various domains in conditions very similar to their operational scalable setting. One of the key challenges facing the diffusion of such innovations within the course of an LSP is understanding the conditions in which their respective users decide to adopt them (or not). Accordingly, in this study we explore IoT adoption barriers in four LSPs in Europe from the following domains: smart cities, autonomous driving, wearables and smart agriculture and farming. By applying Roger’s Diffusion of Innovation as a theoretical lens and using empirical data from workshops and expert interviews, we identify a set of common and domain specific adoption barriers. Our results reveal that trust, cost, perceived value, privacy and security are common concerns, yet shape differently across domains. In order to overcome various barriers, the relative advantage or value of using the innovation needs to be clearly communicated and related to the users’ situational use; while this value can be economic in some domains, it is more hedonic in others. LSPs were particularly challenged in applying established strategies to overcome some of those barriers (e.g., co-creation with end-users) due to the immaturity of the technology as well as the scale of pilots. Accordingly, we reflect on the theoretical choice in the discussion as well as the implications of this study on research and practice. We conclude with providing practical recommendations to LSPs and avenues for future research.
The First Complete Mitochondrial Genomes of Two Sibling Species from Nitidulid Beetles Pests
Authors: Wu Yi , Lan Yangming , Xia Liyuan , Cui Miao , Sun Weiwei , Dong Zhen , Cao Yang
Published: December 2019

Carpophilus dimidiatus (Fabricius, 1792) and Carpophilus pilosellus Motschulsky are two sibling species and economically important storage pests worldwide. The first complete mitochondrial (mt) genomes of both were sequenced using next-generation sequencing. The mt genomes of C. dimidiatus and C. pilosellus are circular, with total lengths of 15,717 bp and 15,686 bp, respectively. Gene order and content for both species are similar to what has been observed in ancestral insects and consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. Comparing the mt genome data of C. dimidiatus and C. pilosellus, they are similar in organization, arrangement patterns, GC contents, transfer RNA (tRNA) secondary structures, and codon usage patterns. Small differences were noted with regards to the nucleotide similarity of coding regions and the control region. This is the first publication of the complete mitochondrial genomes of two sibling species. The mt genome sequences can supplement the nuclear markers of the Carpophilus genus in research species identification, system evolution, and population genetic structure, and also will be valuable molecular marker for further genetic studies.
Reliability of the Scapula Reposition Test in Subjects with Rotator Cuff Tendinopathy and Scapular Dyskinesis
Authors: Fernandez-Matias Ruben , Gallardo-Zamora Pablo , Sanchez-Aguilera Cristina Lorenzo , Mardones-Varela Hector , Gallego-Izquierdo Tomas , Pecos-Martin Daniel
Published: December 2019

The Scapula Reposition Test (SRT) is proposed to determine if a relationship exists between scapular dyskinesis and shoulder pathology. The purpose of this study was to evaluate intra-rater and inter-rater reliability of the SRT in subjects with rotator cuff tendinopathy and scapular dyskinesis. In addition, we compared subjective strength findings from the test to an objective measure made by dynamometry. The SRT was independently and randomly performed by two physical therapists in 42 subjects. The percent agreement, Cohen’s kappa (κ), maximum attainable κ, prevalence and bias indexes, and prevalence-adjusted-bias-adjusted kappa were used as intra- and inter-rater reliability estimates. Finally, the point-biserial correlation coefficient (rpb) was used for correlation analysis of objective and subjective strength findings. A moderate intra-rater (κ = 0.43; CI 95%, 0.14 to 0.73; p = 0.004) and poor inter-rater (κ = 0.08; CI 95%, −0.22 to 0.38; p = 0.61) agreement was found. Subjective strength changes during SRT and dynamometry were poorly correlated (rpb = 0.137; CI 95%, −0.175 to 0.423; p = 0.389). The SRT cannot be recommended for clinical practice. More studies evaluating its reliability are needed as well as further research on the capability of a rater to manually detect strength changes.
Gastrointestinal Bleeding in Patients with Hereditary Hemorrhagic Telangiectasia: Risk Factors and Endoscopic Findings
Authors: Mora-Luján José María , Iriarte Adriana , Alba Esther , Sánchez-Corral Miguel Ángel , Berrozpe Ana , Cerdà Pau , Cruellas Francesc , Ribas Jesús , Castellote Jose , Riera-Mestre Antoni
Published: December 2019

Background: We aimed to describe risk factors for gastrointestinal (GI) bleeding and endoscopic findings in patients with hereditary hemorrhagic telangiectasia (HHT). Methods: This is a prospective study from a referral HHT unit. Endoscopic tests were performed when there was suspicion of GI bleeding, and patients were divided as follows: with, without, and with unsuspected GI involvement. Results: 67 (27.9%) patients with, 28 (11.7%) patients without, and 145 (60.4%) with unsuspected GI involvement were included. Age, tobacco use, endoglin (ENG) mutation, and hemoglobin were associated with GI involvement. Telangiectases were mostly in the stomach and duodenum, but 18.5% of patients with normal esophagogastroduodenoscopy (EGD) had GI involvement in video capsule endoscopy (VCE). Telangiectases ≤ 3 mm and ≤10 per location were most common. Among patients with GI disease, those with hemoglobin < 8 g/dL or transfusion requirements (65.7%) were older and had higher epistaxis severity score (ESS) and larger telangiectases (>3 mm). After a mean follow-up of 34.2 months, patients with GI involvement required more transfusions and more emergency department and hospital admissions, with no differences in mortality. Conclusions: Risk factors for GI involvement have been identified. Patients with GI involvement and severe anemia had larger telangiectases and higher ESS. VCE should be considered in patients with suspicion of GI bleeding, even if EGD is normal.
Trends, Patient and Prescriber Characteristics in Gabapentinoid Use in a Sample of United States Ambulatory Care Visits from 2003 to 2016
Authors: Zhou Lili , Bhattacharjee Sandipan , Kwoh C. Kent , Tighe Patrick J. , Malone Daniel C. , Slack Marion , Wilson Debbie L. , Brown Joshua D. , Lo-Ciganic Wei-Hsuan
Published: December 2019

Increasing gabapentinoid use has raised concerns of misuse and abuse in the United States (US). Little is known about the characteristics of gabapentinoid use in general clinical practice over time. This cross-sectional study used data from the National Ambulatory Medical Care Survey. We examined the trends of patient and prescriber characteristics and the diagnoses associated with US ambulatory care visits involving gabapentinoids for adult visits from 2003 to 2016. Using multivariable logistic regression, we estimated the adjusted proportion of gabapentinoid-involved visits among all visits and tested for trend significance. Among the weighted estimate of 260.1 million gabapentinoid-involved visits (aged 18–64 years: 61.8%; female: 61.9%; white: 85.5%), the adjusted annual proportion of gabapentinoid-involved visits nearly quadrupled from 2003 to 2016 (9.1 to 34.9 per 1000 visits; Ptrend < 0.0001), driven mainly by gabapentin. Nearly half had concurrent use with opioids (32.9%) or benzodiazepines (15.3%). Primary care physicians (45.8%), neurologists (8.2%), surgeons (6.2%), and psychiatrists (4.8%) prescribed two-thirds of the gabapentinoids. Most (96.6%) of the gabapentinoid visits did not have an approved indication for gabapentinoids among the first three diagnoses. Among US ambulatory care visits from 2003 to 2016, gabapentinoid use increased substantially, commonly prescribed by primary care physicians.
α-Cyclodextrin-Based Polypseudorotaxane Hydrogels
Authors: Domiński Adrian , Konieczny Tomasz , Kurcok Piotr
Published: December 2019

Supramolecular hydrogels that are based on inclusion complexes between α-cyclodextrin and (co)polymers have gained significant attention over the last decade. They are formed via dynamic noncovalent bonds, such as host–guest interactions and hydrogen bonds, between various building blocks. In contrast to typical chemical crosslinking (covalent linkages), supramolecular crosslinking is a type of physical interaction that is characterized by great flexibility and it can be used with ease to create a variety of “smart” hydrogels. Supramolecular hydrogels based on the self-assembly of polypseudorotaxanes formed by a polymer chain “guest” and α-cyclodextrin “host” are promising materials for a wide range of applications. α-cyclodextrin-based polypseudorotaxane hydrogels are an attractive platform for engineering novel functional materials due to their excellent biocompatibility, thixotropic nature, and reversible and stimuli-responsiveness properties. The aim of this review is to provide an overview of the current progress in the chemistry and methods of designing and creating α-cyclodextrin-based supramolecular polypseudorotaxane hydrogels. In the described systems, the guests are (co)polymer chains with various architectures or polymeric nanoparticles. The potential applications of such supramolecular hydrogels are also described.
Anisotropic Grain Growth in (111) Nanotwinned Cu Films by DC Electrodeposition
Authors: Lu Tien-Lin , Shen Yu-An , Wu John A. , Chen Chih
Published: December 2019

We have reported a method of fabricating (111)-orientated nanotwinned copper (nt-Cu) by direct current electroplating. X-ray analysis was performed for the samples annealed at 200 to 350 °C for an hour. X-ray diffraction indicates that the (200) signal intensity increases while (111) decreases. Abnormal grain growth normally results from transformation of surface energy or strain energy density. The average grain size increased from 3.8 µm for the as-deposited Cu films to 65–70 µm after the annealing at 250 °C for 1 h. For comparison, no significant grain growth behavior was observed by random Cu film after annealing for an hour. This research shows the potential for its broad electric application in interconnects and three-dimensional integrated circuit (3D IC) packaging.
Mathematical Modeling of Breast Tumor Destruction Using Fast Heating during Radiofrequency Ablation
Authors: Paruch Marek
Published: December 2019

In oncology, hyperthermia is understood as a planned, controlled technique of heating cancerous changes in order to destroy their cells or stop their growth. In clinical practice, hyperthermia is used in combination with radiotherapy, chemotherapy, or immunological therapy. During the hyperthermia, the tissue is typically exposed to a temperature in the range of 40–45 °C, the exception is thermoablation, during which the temperatures reach much higher values. Thermoablation is characterized by the use of high temperatures up to 90 °C. The electrode using the radiofrequency is inserted into the central area of the tumor. Interstitial thermoablation is used to treat, among others, breast and brain cancer. The therapy consists of inducing coagulation necrosis in an area that is heated to very high temperatures. Mathematical modeling is based on the use of a coupled thermo-electric model, in which the electric field is described by means of the Laplace equation, while the temperature field is based on the Pennes equation. Coupling occurs at the level of the additional source function in the Pennes equation. The temperature field obtained in this way makes it possible to calculate the Arrhenius integral as a determinant of the destruction of biological tissue. As a result of numerical calculations regarding the temperature field and the Arrhenius integral, it can be concluded that, with the help of numerical tools and mathematical modeling, one can simulate the process of destroying cancerous tissue.
Quantitative and Qualitative HPLC Analysis of Mycosporine-Like Amino Acids Extracted in Distilled Water for Cosmetical Uses in Four Rhodophyta
Authors: Chaves-Peña Patricia , de la Coba Francisca , Figueroa Felix L. , Korbee Nathalie
Published: December 2019

Mycosporine-like amino acids (MAAs) have gained considerable attention as highly active photoprotective candidates for human sunscreens. However, more studies are necessary to evaluate the extraction efficiencies of these metabolites in cosmetic compatible solvents, as well as, their subsequent HPLC analysis. In the present study, MAA extraction using distilled water and 20% aqueous methanol in four Rhodophyta was investigated. Different re-dissolution solvents and a C8 and C18 columns were tested for the HPLC analysis. Porphyra-334, shinorine, palythine, palythine-serine, asterina-330, and palythinol were identified by HPLC/ESI-MS. The separation of these MAAs were improved employing the C8-column, and using methanol as re-dissolution solvent. Regarding total MAAs concentrations, no differences between the two solvents were found. The highest MAA amounts were observed injecting them directly in the HPLC. According to these results, distilled water could be an excellent extraction solvent for MAAs. Nevertheless, the re-dissolution in pure methanol after dryness would be the best option for the qualitative analysis of the most common MAAs in these red algae. Our results entail important implications regarding the use of red macroalgae as promising candidates as environment-friendly sources of natural sunscreens.
Marine Bacteria versus Microalgae: Who Is the Best for Biotechnological Production of Bioactive Compounds with Antioxidant Properties and Other Biological Applications?
Authors: Hamidi Masoud , Kozani Pouya Safarzadeh , Kozani Pooria Safarzadeh , Pierre Guillaume , Michaud Philippe , Delattre Cédric
Published: December 2019

Natural bioactive compounds with antioxidant activity play remarkable roles in the prevention of reactive oxygen species (ROS) formation. ROS, which are formed by different pathways, have various pathological influences such as DNA damage, carcinogenesis, and cellular degeneration. Incremental demands have prompted the search for newer and alternative resources of natural bioactive compounds with antioxidant properties. The marine environment encompasses almost three-quarters of our planet and is home to many eukaryotic and prokaryotic microorganisms. Because of extreme physical and chemical conditions, the marine environment is a rich source of chemical and biological diversity, and marine microorganisms have high potential as a source of commercially interesting compounds with various pharmaceutical, nutraceutical, and cosmeceutical applications. Bacteria and microalgae are the most important producers of valuable molecules including antioxidant enzymes (such as superoxide dismutase and catalase) and antioxidant substances (such as carotenoids, exopolysaccharides, and bioactive peptides) with various valuable biological properties and applications. Here, we review the current knowledge of these bioactive compounds while highlighting their antioxidant properties, production yield, health-related benefits, and potential applications in various biological and industrial fields.
Halogenated Diterpenes with In Vitro Antitumor Activity from the Red Alga Sphaerococcus coronopifolius
Authors: Smyrniotopoulos Vangelis , de Andrade Tomaz Anna Cláudia , Vanderlei de Souza Maria de Fátima , Leitão da Cunha Emídio Vasconcelos , Kiss Robert , Mathieu Véronique , Ioannou Efstathia , Roussis Vassilios
Published: December 2019

Eight new (1–8) structurally diverse diterpenes featuring five different carbocycles were isolated from the organic extracts of the red alga Sphaerococcus coronopifolius collected from the coastline of the Ionian Sea in Greece. The structures of the new natural products, seven of which were halogenated, and the relative configuration of their stereocenters were determined on the basis of comprehensive spectroscopic analyses, including NMR and HRMS data. Compounds 5 and 8 were found to possess in vitro antitumor activity against one murine and five human cancer cell lines with mean IC50 values 15 and 16 μM, respectively.
High-Throughput Identification of Putative Antimicrobial Peptides from Multi-Omics Data of the Lined Seahorse (Hippocampus erectus)
Authors: Chen Xiyang , Yi Yunhai , You Xinxin , Liu Jie , Shi Qiong
Published: December 2019

Lined seahorse (Hippocampus erectus), the most widely cultivated seahorse in China, has been in short supply because of its important medicinal value; meanwhile, unnatural deaths caused by various diseases (especially enteritis) have limited their practical large-scale aquaculture. Antimicrobial peptides (AMPs), as the best alternative to antibiotics, have been extensively applied in agricultural practices. In this study, we identified 290 putative AMP sequences from our previously published genome and transcriptome data of the lined seahorse. Among them, 267 are novel, and 118 were validated by our proteome data generated in the present study. It seems that there is a tissue preference in the distribution of AMP/AMP precursor transcripts, such as lectins in the male pouch. In addition, their transcription levels usually varied during development. Interestingly, the representative lectins kept extremely high levels at the pre-pregnancy stage while at relatively lower levels at other stages. Especially Lectin25, with the highest transcription levels and significant developmental changes, has been reported to be involved in seahorse and human pregnancy. The comparison of transcriptome data between one-day and three-month juveniles indicated that Hemoglobin2 (Hemo2) was significantly upregulated in the body, haslet, and brain. Our proteome data of female and male individuals revealed three putative AMP precursors with sexual specificity, including two male-biased cyclin-dependent kinases (CDK-like16 and CDK-like23) and one female-biased bovine pancreatic trypsin inhibitor 2 (BPTI2). In conclusion, our present high-throughput identification of putative AMP sequences from multi-omics (including genomics, transcriptomics, and proteomics) data provides an overview of AMPs in the popular lined seahorse, which lays a solid foundation for further development of AMP-based fish food additives and human drugs.
Characterization of the Jumbo Squid (Dosidicus gigas) Skin By-Product by Shotgun Proteomics and Protein-Based Bioinformatics
Authors: Carrera Mónica , Ezquerra-Brauer Josafat Marina , Aubourg Santiago P.
Published: December 2019

Jumbo squid (Dosidicus gigas) is one of the largest cephalopods, and represents an important economic fishery in several regions of the Pacific Ocean, from southern California in the United States to southern Chile. Large and considerable discards of this species, such as skin, have been reported to constitute an important source of potential by-products. In this paper, a shotgun proteomics approach was applied for the first time to the characterization of the jumbo squid (Dosidicus gigas) skin proteome. A total of 1004 different peptides belonging to 219 different proteins were identified. The final proteome compilation was investigated by integrated in-silico studies, including gene ontology (GO) term enrichment, pathways, and networks studies. Potential new valuable bioactive peptides such as antimicrobial, bioactive collagen peptides, antihypertensive and antitumoral peptides were predicted to be present in the jumbo squid skin proteome. The integration of the global proteomics results and the bioinformatics analysis of the jumbo squid skin proteome show a comprehensive knowledge of this fishery discard and provide potential bioactive peptides of this marine by-product.
Design of Wear-Resistant Diecast AlSi9Cu3(Fe) Alloys for High-Temperature Components
Authors: Timelli Giulio , Fabrizi Alberto , Vezzù Simone , De Mori Alessandro
Published: December 2019

Type AlSi9Cu3(Fe) alloy has been modified by alloying with iron, manganese, and chromium elements to develop wear-resistant diecast hypoeutectic Al–Si–Cu alloys that can be applied for high-temperature applications. Several alloys have been produced by varying iron, manganese, and chromium levels (0.80, 1.00, 1.20 wt.% for Fe; 0.25, 0.40, 0.55 wt.% for Mn, and 0.06, 0.10 wt.% for Cr). Brinell hardness measurements and pin-on-disk wear tests have been conducted from room temperature up to 200 °C. The microstructural changes that occurred with the different alloying levels have been quantitatively examined by metallographic and image analysis techniques. The results showed how the increasing content of the Fe, Mn, and Cr promoted the precipitation of both primary and secondary Fe-enriched particles, mainly with polyhedral, blocky, and star-like morphologies. These compounds showed high hardness that is not affected by chemical composition and morphology variation. At high temperatures, the diecast alloys always showed lower average hardness and wear resistance, especially at 200 °C; however, a greater amount of Fe-rich particles can compensate the alloy softening.
An Innovative Technique for Comprehensive Utilization of High Aluminum Iron Ore via Pre-Reduced-Smelting Separation-Alkaline Leaching Process: Part I: Pre-Reduced-Smelting Separation to Recover Iron
Authors: Li Siwei , Pan Jian , Zhu Deqing , Guo Zhengqi , Shi Yue , Chou Jianlei , Xu Jiwei
Published: December 2019

In this study, a novel process was established for extraction of Fe and Al from a complex high aluminum iron ore (33.43% Fetotal and 19.09% Al2O3). The main steps in the proposed process included pre-reducing high alumina iron ore and subsequent smelting to produce pig iron and rich-alumina slag, followed by alkaline leaching of the slag to obtain sodium aluminate solution and a clean slag. When smelting the pre-reduced high alumina iron ore pellets at 1625 °C for 30 min with a slag basicity of 0.40, the pig iron yielded 97.08% Fe and extracted 0.13% Al2O3, together with an iron recovery of 94.54%. In addition, more than 68.93% Al2O3 was recovered by leaching the slag, which was achieved by firstly roasted the slag at 900 °C for 2 h and then alkaline leaching at 95 °C for 2 h with a liquid-to-solid ratio of 10 mL/g. In addition, the alkaline leaching slag could potentially be used as raw material for construction purpose, which mainly consisted of SiO2 and CaO.
In Vivo Mitochondrial Function in Idiopathic and Genetic Parkinson’s Disease
Authors: Dossi Gabriele , Squarcina Letizia , Rango Mario
Published: December 2019

Parkinson’s disease (PD) is associated with brain mitochondrial dysfunction. High-energy phosphates (HEPs), which rely on mitochondrial functioning, may be considered potential biomarkers for PD. Phosphorus magnetic resonance spectroscopy (31P-MRS) is a suitable tool to explore in vivo cerebral energetics. We considered 10 31P-MRS studies in order to highlight the main findings about brain energetic compounds in patients affected by idiopathic PD and genetic PD. The studies investigated several brain areas such as frontal lobes, occipital lobes, temporoparietal cortex, visual cortex, midbrain, and basal ganglia. Resting-state studies reported contrasting results showing decreased as well as normal or increased HEPs levels in PD patients. Functional studies revealed abnormal PCr + βATP levels in PD subjects during the recovery phase and abnormal values at rest, during activation and recovery in one PD subject with PINK1 gene mutation suggesting that mitochondrial machinery is more impaired in PD patients with PINK1 gene mutation. PD is characterized by energetics impairment both in idiopathic PD as well as in genetic PD, suggesting that mitochondrial dysfunction underlies the disease. Studies are still sparse and sometimes contrasting, maybe due to different methodological approaches. Further studies are needed to better assess the role of mitochondria in the PD development.
Numerical Study of Paramagnetic Elliptical Microparticles in Curved Channels and Uniform Magnetic Fields
Authors: Sobecki Christopher , Zhang Jie , Wang Cheng
Published: December 2019

We numerically investigated the dynamics of a paramagnetic elliptical particle immersed in a low Reynolds number Poiseuille flow in a curved channel and under a uniform magnetic field by direct numerical simulation. A finite element method, based on an arbitrary Lagrangian-Eulerian approach, analyzed how the channel geometry, the strength and direction of the magnetic field, and the particle shape affected the rotation and radial migration of the particle. The net radial migration of the particle was analyzed after executing a π rotation and at the exit of the curved channel with and without a magnetic field. In the absence of a magnetic field, the rotation is symmetric, but the particle-wall distance remains the same. When a magnetic field is applied, the rotation of symmetry is broken, and the particle-wall distance increases as the magnetic field strength increases. The causation of the radial migration is due to the magnetic angular velocity caused by the magnetic torque that constantly changes directions during particle transportation. This research provides a method of magnetically manipulating non-spherical particles on lab-on-a-chip devices for industrial and biological applications.
Polarizability-Dependent Sorting of Microparticles Using Continuous-Flow Dielectrophoretic Chromatography with a Frequency Modulation Method
Authors: Giesler Jasper , Pesch Georg R. , Weirauch Laura , Schmidt Marc-Peter , Thöming Jorg , Baune Michael
Published: December 2019

The separation of microparticles with respect to different properties such as size and material is a research field of great interest. Dielectrophoresis, a phenomenon that is capable of addressing multiple particle properties at once, can be used to perform a chromatographic separation. However, the selectivity of current dielectrophoretic particle chromatography (DPC) techniques is limited. Here, we show a new approach for DPC based on differences in the dielectrophoretic mobilities and the crossover frequencies of polystyrene particles. Both differences are addressed by modulating the frequency of the electric field to generate positive and negative dielectrophoretic movement to achieve multiple trap-and-release cycles of the particles. A chromatographic separation of different particle sizes revealed the voltage dependency of this method. Additionally, we showed the frequency bandwidth influence on separation using one example. The DPC method developed was tested with model particles, but offers possibilities to separate a broad range of plastic and metal microparticles or cells and to overcome currently existing limitations in selectivity.
Design Optimization of a Compact Double-Ended-Tuning-Fork-Based Resonant Accelerometer for Smart Spindle Applications
Authors: Chen Yu-Hsuan , Li Wei-Chang , Xiao Xi-Wen , Yang Chieh-Cheng , Liu Chien-Hao
Published: December 2019

With the rapid developments of the Industrial Era 4.0, numerous sensors have been employed to facilitate and monitor the quality of machining processes. Among them, accelerometers play an important role in chatter detection and suppression for reducing the tool down-time and increasing manufacturing efficiency. To date, most commonly seen accelerometers have relatively large sizes such that they can be installed only on the housing of spindles or the surfaces of workpieces that may not be able to directly capture actual vibration signals or obstruct the cutting process. To address this challenge, this research proposed a compact, wide-bandwidth resonant accelerometer that could be embedded inside high-speed spindles for real-time chatter monitoring and prediction. Composed of a double-ended tuning fork (DETF), a proof mass, and a support beam, the resonant accelerometer utilizes the resonance frequency shift of the DETF due to the bending motions of the structure during out-of-plane accelerations as the sensing mechanism. The entire structure based on commercially available quartz tuning forks (QTFs) with electrodes for symmetric-mode excitations. The advantages of this structure include low noise and wide operation bandwidth thanks to the frequency modulation scheme. A theoretical model and finite element analysis were conducted for designs and optimizations. Simulated results demonstrated that the proposed accelerometer has a size of 9.76 mm × 4.8 mm × 5.5 mm, a simulated sensitivity of 0.94 Hz/g, and a simulated working bandwidth of 3.5 kHz. The research results are expected to be beneficial for chatter detection and intelligent manufacturing.
Zika Virus Infection in Pregnancy: Advanced Diagnostic Approaches in Dengue-Naive and Dengue-Experienced Pregnant Women and Possible Implication for Cross-Reactivity and Cross-Protection
Authors: Zavattoni Maurizio , Rovida Francesca , Percivalle Elena , Cassaniti Irene , Sarasini Antonella , Arossa Alessia , Tassis Beatrice , Bollani Lina , Lombardi Giuseppina , Orcesi Simona , Baldanti Fausto
Published: December 2019

Zika virus (ZIKV) infection has been linked to congenital defects in fetuses and infants, as exemplified by the microcephaly epidemic in Brazil. Given the overlapping presence of Dengue virus (DENV) in the majority of ZIKV epidemic regions, advanced diagnostic approaches need to be evaluated to establish the role of pre-existing DENV immunity in ZIKV infection. From 2015 to 2017, five pregnant women with suspected ZIKV infection were investigated in Pavia, Italy. Among the five pregnant women, three were DENV–ZIKV immunologically cross-reactive, and two were DENV-naïve. Advanced diagnosis included the following: (i) NS1 blockade-of-binding (BOB) ELISA assay for ZIKV specific antibodies and (ii) ELISpot assay for the quantification of effector memory T cells for DENV and ZIKV. These novel assays allowed to distinguish between related flavivirus infections. The three DENV-experienced mothers did not transmit ZIKV to the fetus, while the two DENV-naive mothers transmitted ZIKV to the fetus. Pre-existing immunity in DENV experienced mothers might play a role in cross-protection.
A Deeper Look into the Biodiversity of the Extremely Acidic Copahue volcano-Río Agrio System in Neuquén, Argentina
Authors: Lopez Bedogni Germán , Massello Francisco L. , Giaveno Alejandra , Donati Edgardo Rubén , Urbieta María Sofía
Published: December 2019

The Copahue volcano-Río Agrio system, on Patagonia Argentina, comprises the naturally acidic river Río Agrio, that runs from a few meters down the Copahue volcano crater to more than 40 km maintaining low pH waters, and the acidic lagoon that sporadically forms on the crater of the volcano, which is studied for the first time in this work. We used next-generation sequencing of the 16S rRNA gene of the entire prokaryotic community to study the biodiversity of this poorly explored extreme environment. The correlation of the operational taxonomic units (OTUs)s presence with physicochemical variables showed that the system contains three distinct environments: the crater lagoon, the Upper Río Agrio, and the Salto del Agrio waterfall, a point located approximately 12 km down the origin of the river, after it emerges from the Caviahue lake. The prokaryotic community of the Copahue Volcano-Río Agrio system is mainly formed by acidic bacteria and archaea, such as Acidithiobacillus, Ferroplasma, and Leptospirillum, which have been isolated from similar environments around the world. These results support the idea of a ubiquitous acidic biodiversity; however, this highly interesting extreme environment also has apparently autochthonous species such as Sulfuriferula, Acidianus copahuensis, and strains of Acidibacillus and Alicyclobacillus.
Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles
Authors: Khadka Bijendra , Persaud Dhillon , Gupta Radhey S.
Published: December 2019

SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
Riverine Sediment Geochemistry as Provenance Fingerprints along the Eastern Coast of China: Constraint, Approach, and Application
Authors: Chen Jie , Liu Ping , Sun Dandan , Zhang Dan , Miao Bingdi , Chen Jing
Published: December 2019

Sediment geochemistry is affected by sediment granularity and chemical partition, which may greatly influence the accuracy of sediment source identification. In this study, we analyzed Ca, Co, Zr, V, Cr, Ti, Sc, Th, and Al in the sediments of major rivers and a Holocene core along the eastern coast of China to reveal the constraints on sediment geochemistry related to granularity and chemical partition and to try and identify the sources of the sediments present in the core. The results reveal that the element concentrations have a significant positive correlation with Al concentration in all these riverine sediments. There are significant differences in the element contents of the bulk sample and the residual sediment leached with acid, including in their ratios. The ratios of Cr/Th–Sc/Th, which is often used for provenance discrimination, reveal that uncertainty of provenance discrimination will increase if the impact of sediment granularity and chemical phase on the index system is not considered. We applied this geochemical approach for provenance on a Holocene core of the East China Sea using Cr/Th–Al, Sc/Th–Al, Ti/Zr–Al, and Cr/Th–Sc/Th with the same granularity as the residue sediments. Based on this approach, we identified the core sediments to have had a large component derived from the western Taiwanese rivers since the mid-Holocene. This study sheds light on the sediment geochemistry used to identify the provenance of marginal seas with multiple rivers entering them.
Assessment of Thermal Performance of Textile Materials Modified with PCM Microcapsules Using Combination of DSC and Infrared Thermography Methods
Authors: Nejman Alicja , Gromadzińska Ewa , Kamińska Irena , Cieślak Małgorzata
Published: December 2019

The aim of the study was the combination of two measurement methods, the differential scanning calorimetry (DSC) and infrared thermography to evaluate thermal performance of woven and knitted fabrics coated with acrylic pastes containing 20% (P/20) and 40% (P/40) of microcapsules of phase change materials (MPCM) with transition temperatures of 28 °C (MPCM28) and 43 °C (MPCM43). The DSC analysis showed that the phase transition processes for materials modified with pastes P/20 occur in a narrower temperature range than those modified with P/40 pastes. The initial temperatures TOnset (S-S) and TOnset (S-L) are higher for materials modified respectively with pastes P/20 and P/40. The melting and crystallization enthalpy values of both P/20 coated materials are lower by about 45% and 35% compared to P/40. Infrared thermography analysis showed that materials modified with P/20 are heating up faster than modified with P/40 for both MPCM. In the cooling process for modified fabrics the highest temperature decrease was observed in the first 30s. Materials modified with paste P/40 were cooled more slowly in comparison with paste P/20, both for MPCM28 and MPCM43.