bluuebunny/crossref_metadata_2025 huggingface dataset:
Picosecond Laser Processing of Photosensitive Glass for Generation of Biologically Relevant Microenvironments
Authors: Jipa Florin , Orobeti Stefana , Butnaru Cristian , Zamfirescu Marian , Axente Emanuel , Sima Felix , Sugioka Koji
Published: December 2020

Various material processing techniques have been proposed for fabrication of smart surfaces that can modulate cellular behavior and address specific clinical issues. Among them, laser-based technologies have attracted growing interest due to processing versatility. Latest development of ultrashort pulse lasers with pulse widths from several tens of femtoseconds (fs) to several picoseconds (ps) allows clean microfabrication of a variety of materials at micro- and nanoscale both at surface and in volume. In this study, we addressed the possibility of 3D microfabrication of photosensitive glass (PG) by high repetition rate ps laser-assisted etching (PLAE) to improve the fabrication efficiency for the development of useful tools to be used for specific biological applications. Microfluidic structures fabricated by PLAE should provide the flow aspects, 3D characteristics, and possibility of producing functional structures to achieve the biologically relevant microenvironments. Specifically, the microfluidic structures could induce cellular chemotaxis over extended periods in diffusion-based gradient media. More importantly, the 3D characteristics could reproduce capillaries for in vitro testing of relevant organ models. Single cell trapping and analysis by using the fabricated microfluidic structures are also essential for understanding individual cell behavior within the same population. To this end, this paper demonstrates: (1) generation of 3D structures in glass volume or on surface for fabrication of microfluidic channels, (2) subtractive 3D surface patterning to create patterned molds in a controlled manor for casting polydimethylsiloxane (PDMS) structures and developing single cell microchambers, and (3) designing glass photo-masks to be used for sequel additive patterning of biocompatible nanomaterials with controlled shapes, sizes, and periodicity. Mesenchymal stem cells grown on laser-processed glass surfaces revealed no sign of cytotoxicity, while a collagen thin coating improved cellular adhesion.
Synergistic Antibacterial Effects of Probiotic Lactic Acid Bacteria with Curcuma longa Rhizome Extract as Synbiotic against Cutibacterium acnes
Authors: Kim Jina , Kim Hyaekang , Jeon Soomin , Jo Jinchul , Kim Younghoon , Kim Heebal
Published: December 2020

Acne is a chronic inflammatory skin disease induced by Cutibacterium acnes. Recently, the effects of probiotics, prebiotics and synbiotics have been researched for the treatment of skin diseases in humans. However, the synbiotic effect of probiotics and prebiotic Curcuma longa rhizome extract (CLE) on C. acnes remains ambiguous. Therefore, the aim of this study was to investigate the synergistic antibacterial activities of probiotic lactic acid bacteria (LAB) with CLE as a synbiotic against C. acnes. Agar well diffusion assays were performed to determine the inhibitory effects of each combination of one of five Lactobacillus sp. with CLE as synbiotics against C. acnes KCTC 3314. Among them, the comparison between the average diameters of inhibition zones showed that the synbiotic combination of Lactobacillus acidophilus A001F8 and CLE significantly increased the inhibition zone diameters against C. acnes, compared to the use of Lactobacillus acidophilus A001F8 or CLE alone (p < 0.05). In conclusion, the synbiotics of probiotic LAB and CLE showed synergistic antibacterial effects against C. acnes, suggesting therapeutic potential for this synbiotic combination in the development of cosmetics or medicine against C. acnes.
Emerging Technologies for Harnessing the Fourth Industrial Revolution in the Energy and Mineral Industries
Authors: Choi Yosoon
Published: December 2020

The Fourth Industrial Revolution provides new ways in which technology can become embedded within societies and even the human body [...]
The Role of Mitochondria in the Dual Effect of Low-Temperature Plasma on Human Bone Marrow Stem Cells: From Apoptosis to Activation of Cell Proliferation
Authors: Belov Sergej V. , Lobachevsky Yakov P. , Danilejko Yurij K. , Egorov Aleksej B. , Simakin Alexander V. , Maleki Alireza , Temnov Andrey A. , Dubinin Mikhail V. , Gudkov Sergey V.
Published: December 2020

The potential use of low-temperature plasma (LTP) for therapeutic purposes has aroused the concern of many researchers. This paper examines the effect of LTP on the morphofunctional state of human bone marrow stem cells (BMSC). It has been established that LTP-induced oxidative stress has a dual effect on the state of stem cells. On the one hand, a cell culture exposed to LTP exhibits the progression of a destructive processes, which is manifested by the perturbation of the cell’s morphology, the initiation of lipid peroxidation and the accumulation of products of this process, like diene conjugates and malondialdehyde, as well as the induction of mitochondrial dysfunction, leading to cell death. On the other hand, the effect of LTP on BMSC located at a distance from the plasma is accompanied by the activation of proliferative processes, as evidenced by the tendency of the activity of mitochondrial biogenesis and fission/fusion processes to increase. The paper discusses the role of mitochondria and reactive oxygen species (ROS) in the cellular response to LTP.
A Coupled Effect Model of Two-Position Local Geometric Deviations on Subsonic Blade Aerodynamic Performance
Authors: Yu Xianjun , Li Mingzhi , An Guangfeng , Liu Baojie
Published: December 2020

The coupled aerodynamic performance influence of multiple deviations in the blade profile is a complex phenomena. In this paper, a high-pressure compressor rotor blade mid-span profile is studied with the design of experiments (DOE), numerical simulation and surrogate model to analyze the influence of the deviations on the blade aerodynamic performance. The purpose of this work is to provide a new rapid evaluation approach for the blade aerodynamic performance under multiple geometric deviations influence. First, the Hicks-Henne function was used to model the local geometric deviations of the blade profile, and the blade aerodynamic performance was calculated by using the computational fluid dynamics tools. By analyzing the calculation results, the momentum thickness of the boundary layer, the deviations height and the distance between the deviations are combined into a coupled effect model. Then, the coupled effect model was used to rapidly evaluate the blade aerodynamic performance when the two-position local geometric deviations exist on the blade surface. Finally, the evaluated performance were compared with the results predicted by a high-precision surrogate model, which verifies the high accuracy of the coupled effect model in evaluating the positive incidence range of the blade profile.
Engineered Collagen Matrices
Authors: Patil Vaidehi A. , Masters Kristyn S.
Published: December 2020

Collagen is the most abundant protein in mammals, accounting for approximately one-third of the total protein in the human body. Thus, it is a logical choice for the creation of biomimetic environments, and there is a long history of using collagen matrices for various tissue engineering applications. However, from a biomaterial perspective, the use of collagen-only scaffolds is associated with many challenges. Namely, the mechanical properties of collagen matrices can be difficult to tune across a wide range of values, and collagen itself is not highly amenable to direct chemical modification without affecting its architecture or bioactivity. Thus, many approaches have been pursued to design scaffold environments that display critical features of collagen but enable improved tunability of physical and biological characteristics. This paper provides a brief overview of approaches that have been employed to create such engineered collagen matrices. Specifically, these approaches include blending of collagen with other natural or synthetic polymers, chemical modifications of denatured collagen, de novo creation of collagen-mimetic chains, and reductionist methods to incorporate collagen moieties into other materials. These advancements in the creation of tunable, engineered collagen matrices will continue to enable the interrogation of novel and increasingly complex biological questions.
Photo-Based Nanomedicines Using Polymeric Systems in the Field of Cancer Imaging and Therapy
Authors: Husni Patihul , Shin Yuseon , Kim Jae Chang , Kang Kioh , Lee Eun Seong , Youn Yu Seok , Rusdiana Taofik , Oh Kyung Taek
Published: December 2020

The use of photo-based nanomedicine in imaging and therapy has grown rapidly. The property of light in converting its energy into different forms has been exploited in the fields of optical imaging (OI) and phototherapy (PT) for diagnostic and therapeutic applications. The development of nanotechnology offers numerous advantages to overcome the challenges of OI and PT. Accordingly, in this review, we shed light on common photosensitive agents (PSAs) used in OI and PT; these include fluorescent and bioluminescent PSAs for OI or PT agents for photodynamic therapy (PDT) and photothermal therapy (PTT). We also describe photo-based nanotechnology systems that can be used in photo-based diagnostics and therapies by using various polymeric systems.
Development of a Graphene-Based Biosensor for Detecting Recombinant Cyanovirin-N
Authors: de Almeida Pedro Rodrigues , Murad André Melro , Silva Luciano Paulino , Rech Elibio Leopoldo , Alves Elmo Salomão
Published: December 2020

We present a graphene-based biosensor selective to recombinant cyanovirin-N (rCV-N), an antiviral protein that has proven to be an effective microbicide to inhibit HIV replication. We modified the graphene monolayer devices with 1-pyrenebutanoic acid succinimidyl ester, which interacts with both graphene and the primary and secondary amines of antibodies. By monitoring the change in the electrical resistance of the device, we were able to detect rCV-N in solutions in the range of 0.01 to 10 ng/mL, and found that the detection limit was 0.45 pg/mL, which is much smaller than that obtained with currently available techniques. This is important for applications of this microbicide against HIV, since it may be produced at a large scale from soya bean seeds processed using the available industrial processing technologies. The sensor showed high sensitivity, selectivity, and reproducibility.
Patient-Derived Cancer Models
Authors: Di Renzo Maria Flavia , Corso Simona
Published: December 2020

For many decades, basic and preclinical cancer research has been based on the use of established, commercially available cell lines, originally derived from patients’ samples but adapted to grow indefinitely in artificial culture conditions, and on xenograft models developed by injection of these cells in immunocompromised animals [...]
Survival Outcomes Following Combination of First-Line Platinum-Based Chemotherapy with S-1 in Patients with Advanced Gastric Cancer
Authors: Koumarianou Anna , Ntavatzikos Anastasios , Vallilas Christos , Kampoli Katerina , Kakoseou Zoi , Karamouzis Michalis V.
Published: December 2020

The efficacy of S-1 combined with a platinum agent in the first-line setting and in patients with advanced gastric adenocarcinoma has been previously demonstrated in randomized clinical trials. However, real-world data regarding S-1 efficacy in European patients remains limited. In the present study, we reviewed the data of a European cohort of patients with advanced gastric cancer treated with first-line therapy consisting of S-1 in combination with a platinum agent. Forty-eight patients (29 with locally advanced/inoperable and 19 with metastatic disease) were treated with S-1 plus oxaliplatin (33 patients) or S1 plus cisplatin (15 patients). The Cox regression analysis, adjusted with propensity score, indicated that the use of cisplatin as compared to oxaliplatin was associated with increased risk of death (HR 9.634, p = 0.000). Four SAEs (serious adverse events) GIII were recorded (1 fatigue, 1 neutropenia, 1 anemia, 1 diarrhea) in 3 patients. S-1 combination with a platinum agent in the first-line setting in European patients with advanced gastric cancer results to similar survival outcomes and toxicity with previously reported data from Asian populations. S-1 combination with oxaliplatin seems to be associated with superior efficacy as compared to cisplatin.
Metabolic Regulation of Epigenetic Modifications and Cell Differentiation in Cancer
Authors: Saggese Pasquale , Sellitto Assunta , Martinez Cesar A. , Giurato Giorgio , Nassa Giovanni , Rizzo Francesca , Tarallo Roberta , Scafoglio Claudio
Published: December 2020

Metabolic reprogramming is a hallmark of cancer, with consistent rewiring of glucose, glutamine, and mitochondrial metabolism. While these metabolic alterations are adequate to meet the metabolic needs of cell growth and proliferation, the changes in critical metabolites have also consequences for the regulation of the cell differentiation state. Cancer evolution is characterized by progression towards a poorly differentiated, stem-like phenotype, and epigenetic modulation of the chromatin structure is an important prerequisite for the maintenance of an undifferentiated state by repression of lineage-specific genes. Epigenetic modifiers depend on intermediates of cellular metabolism both as substrates and as co-factors. Therefore, the metabolic reprogramming that occurs in cancer likely plays an important role in the process of the de-differentiation characteristic of the neoplastic process. Here, we review the epigenetic consequences of metabolic reprogramming in cancer, with particular focus on the role of mitochondrial intermediates and hypoxia in the regulation of cellular de-differentiation. We also discuss therapeutic implications.
Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk
Authors: Logotheti Stella , Marquardt Stephan , Richter Christin , Sophie Hain Renée , Murr Nico , Takan Işıl , Pavlopoulou Athanasia , Pützer Brigitte M.
Published: December 2020

Mechanisms governing tumor progression differ from those of initiation. One enigmatic prometastatic process is the recapitulation of pathways of neural plasticity in aggressive stages. Cancer and neuronal cells develop reciprocal interactions via mutual production and secretion of neuronal growth factors, neurothrophins and/or axon guidance molecules in the tumor microenvironment. Understanding cancer types where this process is active, as well as the drivers, markers and underlying mechanisms, has great significance for blocking tumor progression and improving patient survival. By applying computational and systemic approaches, in combination with experimental validations, we provide compelling evidence that genes involved in neuronal development, differentiation and function are reactivated in tumors and predict poor patient outcomes across various cancers. Across cancers, they co-opt genes essential for the development of distinct anatomical parts of the nervous system, with a frequent preference for cerebral cortex and neural crest-derived enteric nerves. Additionally, we show that p73, a transcription factor with a dual role in neuronal development and cancer, simultaneously induces neurodifferentiation and stemness markers during melanoma progression. Our data yield the basis for elucidating driving forces of the nerve–tumor cell crosstalk and highlight p73 as a promising regulator of cancer neurobiology.
Lysophosphatidic Acid Signaling in Cancer
Authors: Brindley David N.
Published: December 2020

This Special Issue aims to highlight the impact of discoveries made over the last 25 years on the role of autotaxin (ATX) and lysophosphatidic acid (lysophosphatidate, LPA) signaling in tumor growth, metastasis and the treatment of cancers by chemotherapy, radiotherapy and immunotherapy [...]
Utility of Circulating Tumor DNA in Different Clinical Scenarios of Breast Cancer
Authors: Mesquita Alexandra , Costa José Luís , Schmitt Fernando
Published: December 2020

Breast cancer is a complex disease whose molecular mechanisms are not completely understood. Developing target therapies is a promising approach. Therefore, understanding the biological behavior of the tumor is a challenge. Tissue biopsy in the metastatic setting remains the standard method for diagnosis. Nevertheless, it has been associated with some disadvantages: It is an invasive procedure, it may not represent tumor heterogeneity, and it does not allow for treatment efficacy to be assessed or early recurrences to be detected. Analysis of circulating tumor DNA (ctDNA) may help to overcome this as it is a non-invasive method of monitoring the disease. In early-stage disease, it can detect early recurrences and monitor tumors’ genomic profiles, identifying the emergence of new genetic alterations which can be related to tumor-acquired resistance. In the metastatic setting, the analysis of ctDNA may also allow for the anticipation of clinical and radiological progression of the disease, selection of targeted therapies, and for a photogram of tumor heterogeneity to be provided. It may also detect disease progression earlier in locally advanced tumors submitted to neoadjuvant treatment, and identify minimal residual disease. ctDNA analysis may guide clinical decision-making in different scenarios, in a precision medicine era, once it acts as a repository of genetic tumor material, allowing for a comprehensive mutation profiling analysis. In this review, we focused on recent advances towards the implementation of ctDNA in a clinical routine for breast cancer.
Photocatalytic Transformation of Triclosan. Reaction Products and Kinetics
Authors: Schröder Sophie , San-Román Mª-Fresnedo , Ortiz Inmaculada
Published: December 2020

5-Chloro-2-[2,4-dichlorophenoxy]-phenol, or triclosan (TCS), is an antimicrobial and antifungal agent with high resistance to conventional wastewater treatments, thus, more effective remediation technologies are necessary, where photocatalytic processes deserve special attention due to the high degradation rates of TCS, and the use of a renewable source of energy. However, different by-products may be formed during the treatment, sometimes more harmful than the parent compounds. Efforts to detail reaction pathways continually feed into related literature; however, knowing the transformation kinetics and the dependence on the operating variables is essential for the correct design of the abovementioned remediation technologies. This work contributes to increasing the knowledge necessary for the application of photocatalytic processes for the degradation of emerging pollutants, with TCS as a case study. First, an experimental plan to analyze the influence of the operating variables was carried out, determining time courses of the parent and intermediate compounds. Next, the kinetic model and parameters that are capable of predicting TCS concentration and its derivatives as a function of the operating conditions are provided. This constitutes a very useful tool to predict the performance of wastewater remediation treatment both in the degradation of the original pollutant and in the reduction of the toxicity in the treated water.
Highly Active Trifloaluminate Ionic Liquids as Recyclable Catalysts for Green Oxidation of 2,3,6-Trimethylphenol to Trimethyl-1,4-Benzoquinone
Authors: Latos Piotr , Siewniak Agnieszka , Barteczko Natalia , Jurczyk Sebastian , Boncel Sławomir , Chrobok Anna
Published: December 2020

An effective method for the synthesis of 2,3,6-trimethyl-1,4-benzoquinone via the oxidation of 2,3,6-trimethylphenol as the key step in the in the preparation of vitamin E was presented. An aqueous solution of H2O2 was used as the oxidant and Lewis acidic trifloaluminate ionic liquids [emim][OTf]-Al(OTf)3, χAl(OTf)3 = 0.25 or 0.15 as catalysts. Trifloaluminate ionic liquids were synthesised by the simple reaction between 1-ethyl-3-methylimidazolium trifluoromethanesulfonate (triflate) [emim][OTf] and aluminium triflate used in sub-stoichiometric quantities. The influence of the reaction parameters on the reaction course, such as the amount and concentration of the oxidant, the amount of catalyst, the amount and the type of organic solvent, temperature, and the reaction time was investigated. Finally, 2,3,6-trimethyl-1,4-benzoquinone was obtained in high selectivity (99%) and high 2,3,6-trimethylphenol conversion (84%) at 70 °C after 2 h of oxidation using a 4-fold excess of 60% aqueous H2O2 and acetic acid as the solvent. The catalytic performance of trifloaluminate ionic liquids supported on multiwalled carbon nanotubes (loading of active phase: 9.1 wt.%) was also demonstrated. The heterogeneous ionic liquids not only retained their activity compared to the homogenous counterparts, but also proved to be a highly recyclable catalysts.
Dental Materials Coatings: Effect on the Clinical Behavior
Authors: Lo Giudice Roberto , Tribst João Paulo Mendes
Published: December 2020

n/a
Femtosecond Laser-Induced Self-Assembly of Ce3+-Doped YAG Nanocrystals
Authors: Shimotsuma Yasuhiko , Tomura Kotaro , Okuno Tatsuya , Shimizu Masahiro , Miura Kiyotaka
Published: December 2020

Direct three-dimensional laser writing of crystallization inside glass has been intensely studied as an attractive technique for fabricating photonic devices. In particular, polarization-dependent periodic nanostructures composed of the partial crystallization in glass can be self-assembled through focused irradiation of femtosecond pulses. Here, we report on the Y3Al5O12 (YAG) crystal precipitation in nanoscale by femtosecond laser irradiation inside Al2O3-Y2O3 glass. Furthermore, we focus on the white emission by Ce: YAG in which a part of Y3+ site was replaced by Ce3+, the effect on photoluminescence (PL) characteristics by changing of ligand field induced by nanostructure formation was observed.
Extrusive Luxation Injuries in Young Patients: A Retrospective Study with 5-Year Follow-Up
Authors: Spinas Enrico , Pipi Laura , Dettori Claudia
Published: December 2020

(1) Background: The purpose of this study was to analyze the influence of the chosen diagnostic and therapeutic approach (repositioning and splinting methods) on the risk, frequency and timing of the onset of pulp canal obliteration and pulp necrosis following extrusive luxation in young patients with permanent dentition. (2) Methods: From an initial sample of 50 subjects affected by extrusive luxation, were selected the clinical data of 13 patients presenting extrusive luxation but no other type of injury to the dental hard tissue. All teeth were examined according to a standardized protocol. Follow-up examinations were performed at regular intervals for 5 years. Statistical associations between pulp consequences and several covariates were assessed using the Mann–Whitney test and Fisher’s exact test. (3) Results: Among the 13 studied teeth, only 1 healed completely, whereas 9 showed pulp obliteration and 3 developed pulp necrosis. No tooth with obliteration developed pulp necrosis. The average time to treatment was 11.9 h. The treatment approaches used were manual repositioning, orthodontic repositioning and stabilization splinting. “Time to treatment” was the only covariate that showed a weak statistical association with the onset of pulp consequences. (4) Conclusions: There is still uncertainty over the most appropriate therapeutic approach to adopt in young patients with extrusive luxation injuries, particularly for repositioning of the injured tooth. Extruded teeth should be treated as soon as possible after the traumatic event. This study highlighted the value of orthodontic repositioning of the extruded tooth, which does not seem to aggravate the conditions of the dental pulp. In addition, the study confirmed that prophylactic endodontic treatment is not appropriate for immature teeth affected by extrusive luxation injuries, given the extreme rarity of pulp necrosis in teeth already affected by pulp obliteration.
Fostering Critical Reflection in Primary Education through STEAM Approaches
Authors: Bassachs Marcel , Cañabate Dolors , Nogué Lluís , Serra Teresa , Bubnys Remigijus , Colomer Jordi
Published: December 2020

This paper describes a quantitative study that explores teaching practices in primary education to sustain the hypothesis that students’ critical thinking may be activated through individual and group reflection. The study examines the quality of the reflections from primary school students during group processing when participating in Science, Technology, Engineering, Arts, and Math (STEAM) instructional approaches. The project’s core methodology lies in scientific (physics) and artistic (dance) instructional activities which were executed in a continuous reflective and cooperative learning environment. The educational approach was refined by analyzing the reflective discussions from focus groups where descriptive, argumentative, reflective and critical reflective knowledge about acquired knowledge, competences, beliefs, attitudes and emotions were considered. While the educational intervention proved that 1st-year (K-7) students essentially reflected at the level of description, 3rd-year (K-9) and 5th-year (K-11) students, however, attained higher levels of individual critical reflection development than initially anticipated. The STEAM approaches were found to produce significant use and understanding of both science and artistic concepts and to increase a sense of competence readiness and a perception of modes of cooperation such as individual responsibility and promotive interaction.
Estimating Micro-Level On-Road Vehicle Emissions Using the K-Means Clustering Method with GPS Big Data
Authors: Hu Hyejung , Lee Gunwoo , Kim Jae Hun , Shin Hyunju
Published: December 2020

Due to the advanced spatial data collection technologies, the locations of vehicles on roads are now being collected nationwide, so there is a demand for applying a micro-level emission calculation methods to estimate regional and national emissions. However, it is difficult to apply this method due to the low data collection rate and the complicated calculation procedure. To solve these problems, this study proposes a vehicle trajectory extraction method for estimating micro-level vehicle emissions using massive GPS data. We extracted vehicle trajectories from the GPS data to estimate the emission factors for each link at a specific time period. Vehicle trajectory data was divided into several groups through a k-means clustering method, in which the ratios of each operating mode were used as variables for clustering similar vehicle trajectories. The results showed that the proposed method has an acceptable accuracy in estimating emissions. Furthermore, it was also confirmed that the estimated emission factors appropriately reflected the driving characteristics of links. If the proposed method were utilized to update the link-based micro-level emission factors using continuously accumulated trajectory data for the road network, it would be possible to efficiently calculate the regional- or national-level emissions only using traffic volume.
Application of Transfer Effect Models for Predicting Growth and Survival of Genetically Selected Scots Pine Seed Sources in Sweden
Authors: Hayatgheibi Haleh , Berlin Mats , Haapanen Matti , Kärkkäinen Katri , Persson Torgny
Published: December 2020

We used a regression model approach to examine transferability of the 1.5-generation Swedish Scots pine orchard plus trees using the estimated coefficients of the transfer models recently developed for growth and survival of unimproved Scots pine in Sweden and Finland. Differences between observed and predicted values obtained for height and survival of 3214 plus tree progenies, tested at 58 progeny trials, were regressed on latitudinal transfers (∆LAT). In order to evaluate rates of improvement in height and survival of selected progenies over unimproved trees, average percentage differences in performances (∆g%) between the tree groups were calculated. Results indicate that the adopted models can further predict performances of more advanced-generation orchard trees, as there was no evidence of any systematic pattern in the slope of regression functions. Overall, ∆g% estimates obtained for height of progenies were greater than those of survival, suggesting Swedish Scots pine breeding activities are generating gain in the height growth. Moreover, ∆g% estimates obtained for height and survival of half-sib progenies were higher than those of full-sib ones, as a result of response to higher selection intensity applied in the reselection of their parents. This indicates that, in addition to the gain in growth, a gain in survival is also achievable from 1.5-generation seed orchards, depending on the intensity of selection and intended deployment site.
Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes
Authors: Dupin Julia , Raimondeau Pauline , Hong-Wa Cynthia , Manzi Sophie , Gaudeul Myriam , Besnard Guillaume
Published: December 2020

The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae’s diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae.
A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach
Authors: Vizzari Maria Teresa , Benazzo Andrea , Barbujani Guido , Ghirotto Silvia
Published: December 2020

There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago.
Traffic Safety Perception, Attitude, and Feeder Mode Choice of Metro Commute: Evidence from Shenzhen
Authors: Guo Yuanyuan , Yang Linchuan , Huang Wenke , Guo Yi
Published: December 2020

Like many other transit modes, the metro provides stop-to-stop services rather than door-to-door services, so its use undeniably involves first- and last-mile issues. Understanding the determinants of the first- and last-mile mode choice is essential. Existing literature, however, mostly overlooks the mode choice effects of traffic safety perception and attitudes toward the mode. To this end, based on a face-to-face questionnaire survey in Shenzhen, China, this study uses the two-sample t-test to confirm the systematic differences in traffic safety perception and attitudes between different subgroups and develops a series of multinomial logistic (MNL) models to identify the determinants of first- and last-mile mode choice for metro commuters. The results of this study show that: (1) Walking is the most frequently used travel mode, followed by dockless bike-sharing (DBS) and buses; (2) Variances in traffic safety perception and attitude exist across gender and location; (3) Vehicle-related crash risks discourage metro commuters from walking to/from the metro station but encourage them to use DBS and buses as feeder modes; (4) DBS–metro integration is encouraged by the attitude that DBS is quicker than buses and walking, and positive attitudes toward the bus and DBS availability are decisive for the bus–metro and DBS–metro integration, respectively; and (5) Substantial differences exist in the mode choice effects of traffic safety perception and attitudes for access and egress trips. This study provides a valuable reference for metro commuters’ first- and last-mile travel mode choice, contributing to developing a sustainable urban transport system.
Drugs as Soulmates: The Construction and Validation of a 12-Item Soulmate Scale to Measure Substance Addiction and Loneliness
Authors: Lo T. Wing , Yeung Jerf W. K. , Lee Gabriel K. W. , Tam Cherry H. L. , Chan Gloria H. Y.
Published: December 2020

Substance users use substances to tackle psychological stress, frustrations, poor social support and poor-quality relationships. Such experience resembles seeking a soulmate for receiving comfort, a sense of security and satisfaction to relieve feelings of loneliness. Against this backdrop, the study aims to develop a Soulmate Scale to measure substance use and loneliness. Data were collected from 507 drug abusers between 18–71 years of age who were receiving drug addiction treatment in Hong Kong. Both exploratory factor analysis and confirmatory factor analysis were conducted. Results show a valid and reliable scale with three factors: psychological release and shelter, staunch and supportive friendship, and spiritual solace and companionship. This study offers additional support for understanding the drug-taking experience of substance users from their perspective. The Scale provides a useful tool to assess the underlying reasons for substance users to persistently take drugs and formulate corresponding intervention plans to achieve drug abstinence.
Adverse Childhood Experiences and Risk of Subsequently Engaging in Self-Harm and Violence towards Other People—“Dual Harm”
Authors: Carr Matthew J. , Steeg Sarah , Mok Pearl L. H. , Pedersen Carsten Bøcker , Antonsen Sussie , Kapur Nav , Webb Roger T.
Published: December 2020

The etiology of “dual harm” (the co-occurrence of self-harm and externalized violence in the same individual) is under-researched. Risk factors have mostly been investigated for each behavior separately. We aimed to examine adversities experienced between birth and age 15 years among adolescents and young adults with histories of self-harm and violent criminality, with a specific focus on dual harm. Three nested case-control studies were delineated using national interlinked Danish registers; 58,409 cases in total aged 15–35 were identified: 28,956 with a history of violent criminality (but not self-harm), 25,826 with a history of self-harm (but not violent criminality), and 3987 with dual-harm history. Each case was matched by date of birth and gender to 20 controls who had not engaged in either behavior. We estimated exposure prevalence for cases versus controls for each of the three behavior groups, and incidence rate ratios (IRRs). Experiencing five or more childhood adversities was more prevalent among individuals with dual-harm history (19.3%; 95% CI 18.0, 20.8%) versus self-harm (10.9%; 10.5, 11.3%) and violence (11.4%; 11.0%, 11.8%) histories. The highest IRRs for dual harm were linked with parental unemployment (5.15; 95% CI 4.71, 5.64), parental hospitalization following self-harm (4.91; 4.40, 5.48) or assault (5.90; 5.07, 6.86), and parental violent criminality (6.11; 5.57, 6.70). Growing up in environments that are characterized by poverty, violence, and substance misuse, and experiencing multiple adversities in childhood, appear to be especially strongly linked with elevated dual-harm risk. These novel findings indicate potential etiologic pathways to dual harm.
Dietary Thiols: A Potential Supporting Strategy against Oxidative Stress in Heart Failure and Muscular Damage during Sports Activity
Authors: Brancaccio Mariarita , Mennitti Cristina , Cesaro Arturo , Fimiani Fabio , Moscarella Elisabetta , Caiazza Martina , Gragnano Felice , Ranieri Annaluisa , D’Alicandro Giovanni , Tinto Nadia , Mazzaccara Cristina , Lombardo Barbara , Pero Raffaela , Limongelli Giuseppe , Frisso Giulia , Calabrò Paolo , Scudiero Olga
Published: December 2020

Moderate exercise combined with proper nutrition are considered protective factors against cardiovascular disease and musculoskeletal disorders. However, physical activity is known not only to have positive effects. In fact, the achievement of a good performance requires a very high oxygen consumption, which leads to the formation of oxygen free radicals, responsible for premature cell aging and diseases such as heart failure and muscle injury. In this scenario, a primary role is played by antioxidants, in particular by natural antioxidants that can be taken through the diet. Natural antioxidants are molecules capable of counteracting oxygen free radicals without causing cellular cytotoxicity. In recent years, therefore, research has conducted numerous studies on the identification of natural micronutrients, in order to prevent or mitigate oxidative stress induced by physical activity by helping to support conventional drug therapies against heart failure and muscle damage. The aim of this review is to have an overview of how controlled physical activity and a diet rich in antioxidants can represent a “natural cure” to prevent imbalances caused by free oxygen radicals in diseases such as heart failure and muscle damage. In particular, we will focus on sulfur-containing compounds that have the ability to protect the body from oxidative stress. We will mainly focus on six natural antioxidants: glutathione, taurine, lipoic acid, sulforaphane, garlic and methylsulfonylmethane.
Time Trends in Spain from 2001 to 2018 in the Incidence and Outcomes of Hospitalization for Urinary Tract Infections in Patients with Type 2 Diabetes Mellitus
Authors: López-de-Andrés Ana , Albaladejo-Vicente Romana , Palacios-Ceña Domingo , Carabantes-Alarcon David , Zamorano-Leon José Javier , de Miguel-Diez Javier , Lopez-Herranz Marta , Jiménez-García Rodrigo
Published: December 2020

We aim to examine the incidences, clinical characteristics, and in-hospital outcomes of type 2 diabetes (T2DM) patients hospitalized with urinary tract infections (UTIs) in Spain and to identify the factors associated with in-hospital mortality (IHM). A retrospective observational study was carried out with a sample that included all adult patients who were hospitalized for UTIs between 2001 and 2018 and collected in the Spanish National Health System Hospital Discharge Database. We identified 850,276 patients with UTIs (25.49% with T2DM). The incidence of UTIs increased in patients with and without diabetes from 290.76 and 74.79 cases per 100,000 inhabitants in the period from year 2001 to year 2003 to 568.45 and 144.0 in the period from 2016 to 2018, respectively (p < 0.001). Adjusted incidence of UTIs was higher in T2DM patients (incidence rate ratio (IRR) 4.36; 95% CI 4.35–4.39). The multivariable analysis showed a significant reduction in the IHM over time for men and women with T2DM. In T2DM, patients’ higher IHM was associated with older age, comorbidities, and Staphylococcus aureus isolation. Women with T2DM had a higher risk of dying than men. The risk of IHM with an episode of UTIs was independent of the presence of T2DM (odds ratio (OR) 0.97; 95% CI 0.91–1.01). We conclude that the incidence of UTIs was over four times higher in T2DM than nondiabetic patients and has increased over time.
Recruiting and Engaging American Indian and Alaska Native Teens and Young Adults in a SMS Help-Seeking Intervention: Lessons Learned from the BRAVE Study
Authors: Stephens David , Peterson Roger , Singer Michelle , Johnson Jacqueline , Rushing Stephanie Craig , Kelley Allyson
Published: December 2020

This paper shares lessons learned recruiting and engaging participants in the BRAVE study, a randomized controlled trial carried out by the Northwest Portland Area Indian Health Board and the mHealth Impact Lab. The team recruited 2330 American Indian/Alaska Native (AI/AN) teens and young adults nationwide (15–24 years old) via social media channels and text message and enrolled 1030 to participate in the 9 month study. Teens and young adults who enrolled in this study received either: 8 weeks of BRAVE text messages designed to improve mental health, help-seeking skills, and promote cultural pride and resilience; or 8 weeks of Science Technology Engineering and Math (STEM) text messages, designed to elevate and re-affirm Native voices in science, technology, engineering, math and medicine; and then received the other set of messages. Results indicate that social media channels like Facebook and Instagram can be used to recruit AI/AN teens and young adults. Retention in this study was high, with 87% of participants completing both the BRAVE and STEM intervention arms. Lessons learned from this process may help teen and young adult-serving organizations, prevention programs, policy makers, researchers, and educators as they support the next generation of AI/AN change makers.
DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina
Authors: Macari Gabriele , Toti Daniele , Pasquadibisceglie Andrea , Polticelli Fabio
Published: December 2020

Motivation: Bringing a new drug to the market is expensive and time-consuming. To cut the costs and time, computer-aided drug design (CADD) approaches have been increasingly included in the drug discovery pipeline. However, despite traditional docking tools show a good conformational space sampling ability, they are still unable to produce accurate binding affinity predictions. This work presents a novel scoring function for molecular docking seamlessly integrated into DockingApp, a user-friendly graphical interface for AutoDock Vina. The proposed function is based on a random forest model and a selection of specific features to overcome the existing limits of Vina’s original scoring mechanism. A novel version of DockingApp, named DockingApp RF, has been developed to host the proposed scoring function and to automatize the rescoring procedure of the output of AutoDock Vina, even to nonexpert users. Results: By coupling intermolecular interaction, solvent accessible surface area features and Vina’s energy terms, DockingApp RF’s new scoring function is able to improve the binding affinity prediction of AutoDock Vina. Furthermore, comparison tests carried out on the CASF-2013 and CASF-2016 datasets demonstrate that DockingApp RF’s performance is comparable to other state-of-the-art machine-learning- and deep-learning-based scoring functions. The new scoring function thus represents a significant advancement in terms of the reliability and effectiveness of docking compared to AutoDock Vina’s scoring function. At the same time, the characteristics that made DockingApp appealing to a wide range of users are retained in this new version and have been complemented with additional features.
Androgen Deprivation Induces Transcriptional Reprogramming in Prostate Cancer Cells to Develop Stem Cell-Like Characteristics
Authors: Verma Shiv , Shankar Eswar , Kalayci F. Naz Cemre , Mukunda Amrita , Alassfar Malek , Singh Vaibhav , Chan E. Ricky , MacLennan Gregory T. , Gupta Sanjay
Published: December 2020

Enzalutamide, an antiandrogen, is approved for therapy of castration resistant prostate cancer. Clinical applications have shown that approximately 30% of patients acquire resistance after a short period of treatment. However, the molecular mechanisms underlying this resistance is not completely understood. To identify transcriptomic signatures associated with acquisition of drug resistance we profiled gene expression of paired enzalutamide sensitive and resistant human prostate cancer LNCaP (lymph node carcinoma of the prostate) and C4-2B cells. Overlapping genes differentially regulated in the enzalutamide resistant cells were ranked by Ingenuity Pathway Analysis and their functional validation was performed using ingenuity knowledge database followed by confirmation to correlate transcript with protein expression. Analysis revealed that genes associated with cancer stem cells, such as POU5F1 (OCT4), SOX2, NANOG, BMI1, BMP2, CD44, SOX9, and ALDH1 were markedly upregulated in enzalutamide resistant cells. Amongst the pathways enriched in the enzalutamide-resistant cells were those associated with RUNX2, hedgehog, integrin signaling, and molecules associated with elastic fibers. Further examination of a patient cohort undergoing ADT and its comparison with no-ADT group demonstrated high expression of POU5F1 (OCT4), ALDH1, and SOX2 in ADT specimens, suggesting that they may be clinically relevant therapeutic targets. Altogether, our approach exhibits the potential of integrative transcriptomic analyses to identify critical genes and pathways of antiandrogen resistance as a promising approach for designing novel therapeutic strategies to circumvent drug resistance.