bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo centromere formation on chromosome fragments with an inactive centromere in maize (Zea mays)
Authors: Douglas Ryan N. , Yang Hua , Zhang Bing , Chen Chen , Han Fangpu , Cheng Jianlin , Birchler James A. 
Published: August 2021

AbstractThe B chromosome of maize undergoes nondisjunction at the second pollen mitosis as part of its accumulation mechanism. Previous work identified 9-Bic-1 (9-B inactivated centromere-1), which comprises an epigenetically silenced B chromosome centromere that was translocated to the short arm of chromosome 9(9S). This chromosome is stable in isolation, but when normal B chromosomes are added to the genotype, it will attempt to undergo nondisjunction during the second pollen mitosis and usually fractures the chromosome in 9S. These broken chromosomes allow a test of whether the inactive centromere is reactivated or whether a de novo centromere is formed elsewhere on the chromosome to allow recovery of fragments. Breakpoint determination on the B chromosome and chromosome 9 showed that mini chromosome B1104 has the same breakpoint as 9-Bic-1 in the B centromere region and includes a portion of 9S. CENH3 binding was found on the B centromere region and on 9S, suggesting both centromere reactivation and de novo centromere formation. Another mini chromosome, B496, showed evidence of rearrangement, but it also only showed evidence for a de novo centromere. Other mini chromosome fragments recovered were directly derived from the B chromosome with breakpoints concentrated near the centromeric knob region, which suggests that the B chromosome is broken at a low frequency due to the failure of the sister chromatids to separate at the second pollen mitosis. Our results indicate that both reactivation and de novo centromere formation could occur on fragments derived from the progenitor possessing an inactive centromere.
What do class comments tell us? An investigation of comment evolution and practices in Pharo Smalltalk
Authors: Rani Pooja , Panichella Sebastiano , Leuenberger Manuel , Ghafari Mohammad , Nierstrasz Oscar 
Published: August 2021

AbstractContextPrevious studies have characterized code comments in various programming languages, showing how high quality of code comments is crucial to support program comprehension activities, and to improve the effectiveness of maintenance tasks. However, very few studies have focused on understanding developer practices to write comments. None of them has compared such developer practices to the standard comment guidelines to study the extent to which developers follow the guidelines.ObjectiveTherefore, our goal is to investigate developer commenting practices and compare them to the comment guidelines.MethodThis paper reports the first empirical study investigating commenting practices in Pharo Smalltalk. First, we analyze class comment evolution over seven Pharo versions. Then, we quantitatively and qualitatively investigate the information types embedded in class comments. Finally, we study the adherence of developer commenting practices to the officialclass comment templateover Pharo versions.ResultsOur results show that there is a rapid increase in class comments in the initial three Pharo versions, while in subsequent versions developers added comments to both new and old classes, thus maintaining a similar code to comment ratio. We furthermore found three times as many information types in class comments as those suggested by the template. However, the information types suggested by the template tend to be present more often than other types of information. Additionally, we find that a substantial proportion of comments follow the writing style of the template in writing these information types, but they are written and formatted in a non-uniform way.ConclusionThe results suggest the need to standardize the commenting guidelines for formatting the text, and to provide headers for the different information types to ensure a consistent style and to identify the information easily. Given the importance of high-quality code comments, we draw numerous implications for developers and researchers to improve the support for comment quality assessment tools.
Testing Children’s Mentalizing in Middle Childhood: Adopting the Child and Adolescent Reflective Functioning Scale with Clinical and Community Children
Authors: Bizzi Fabiola , Charpentier-Mora Simone , Cavanna Donatella , Borelli Jessica L. , Ensink Karin 
Published: August 2021

AbstractBeginning with Ensink’s seminal study (2015), the field entered a new era in which we were able to measure mentalizing in school-aged children. The goal of this work is to continue developing the state of the research within this tradition by exploring the psychometric properties of the Child Reflective Functioning Scale (CRFS) - a measure applied to the Child Attachment Interview and designed to assess RF during middle childhood - within both clinical and normative groups, and to examine if it differentiates between both groups. Participants were 159 Italian children (age range 8–12 years, Mage = 10.66, SD =1.83; 57% males) divided into two groups: 71 children with emotional-behavioral problems (‘clinical group’) and 88 children without emotional-behavioral problems (‘community group’). Demographic data and Verbal Comprehension Index were collected. A two-factor model of CRFS (self- and other-focused RF) was confirmed in both groups, revealing that these intrapersonal and interpersonal indicators of children’s RF are important domains of mentalizing abilities in middle childhood. The results revealed adequate inter-rater reliability of the CRFS. Controlling for the effect of potentially confounding demographic variables, significant differences on CRFS scales between clinical and community groups were found. The clinical group showed lower levels of CRFS scores than normative group, but importantly, the self-focused RF score uniquely predicted clinical/community status. Taken together, the findings showed that the CRFS is a reliable and validity measure for assessing RF in middle childhood with clinical and normative groups, contributing important information to the scientific literature on mentalizing in middle childhood.
Influence of bovine serum albumin on corrosion behaviour of pure Zn in phosphate buffered saline
Authors: Liu Lijun , Lu Lili , Zhang Hai-Jun , Wang Lu-Ning 
Published: August 2021

AbstractZinc (Zn) and its alloys have received increasing attention as new alternative biodegradable metals. However, consensus has not been reached on the corrosion behaviour of Zn. As cardiovascular artery stent material, Zn is supposed to contact with plasma that contains inorganic salts and organic components. Protein is one of the most important constitute in the plasma and could adsorb on the material surface. In this paper, bovine serum albumin (BSA) was used as a typical protein. Influences of BSA on pure Zn corrosion in phosphate buffered saline is investigated as a function of BSA concentrations and immersion durations by electrochemical techniques and surface analysis. Results showed that pure Zn corrosion was progressively accelerated with BSA concentrations (ranging from 0.05 to 5 g L−1) at 0.5 h. With time evolves, formation of phosphates as corrosion product was delayed by BSA adsorption, especially at concentration of 2 g L−1. Within 48 h, the corrosion of pure Zn was alleviated by BSA at concentration of 0.1 g L−1, whereas the corrosion was enhanced after 168 h. Addition of 2 g L−1 BSA has opposite influence on the pure Zn corrosion. Furthermore, schematic corrosion behaviour at protein/Zn interfaces was proposed. This work encourages us to think more about the influence of protein on the material corrosion and helps us to better understand the corrosion behaviour of pure Zn.
Improved cytocompatibility and antibacterial properties of zinc-substituted brushite bone cement based on β-tricalcium phosphate
Authors: Fadeeva Inna V. , Goldberg Margarita A. , Preobrazhensky Ilya I. , Mamin Georgy V. , Davidova Galina A. , Agafonova Nadezhda V. , Fosca Marco , Russo Fabrizio , Barinov Sergey M. , Cavalu Simona , Rau Julietta V. 
Published: August 2021

AbstractFor bone replacement materials, osteoconductive, osteoinductive, and osteogenic properties are desired. The bacterial resistance and the need for new antibacterial strategies stand among the most challenging tasks of the modern medicine. In this work, brushite cements based on powders of Zinc (Zn) (1.4 wt%) substituted tricalcium phosphate (β-TCP) and non-substituted β-TCP were prepared and investigated. Their initial and final phase composition, time of setting, morphology, pH evolution, and compressive strength are reported. After soaking for 60 days in physiological solution, the cements transformed into a mixture of brushite and hydroxyapatite. Antibacterial activity of the cements against Enterococcus faecium, Escherichia coli, and Pseudomonas aeruginosa bacteria strains was attested. The absence of cytotoxicity of cements was proved for murine fibroblast NCTC L929 cells. Moreover, the cell viability on the β-TCP cement containing Zn2+ ions was 10% higher compared to the β-TCP cement without zinc. The developed cements are perspective for applications in orthopedics and traumatology.
Fabrication and characterization of microstructure-controllable COL-HA-PVA hydrogels for cartilage repair
Authors: Xie Jie , Wang Wu , Zhao Ruibo , Lu Wei , chen Liang , Su Weiping , Zeng Min , Hu Yihe 
Published: August 2021

AbstractPolyvinyl alcohol (PVA) hydrogel has gained interest in cartilage repair because of its highly swollen, porosity, and viscoelastic properties. However, PVA has some deficiencies, such as its poor biocompatibility and microstructure. This research aimed to design novel hydroxyapatite (HA)-collagen (COL)-PVA hydrogels. COL was added to improve cell biocompatibility, and the microstructure of the hydrogels was controlled by fused deposition modeling (FDM). The feasibility of the COL-HA-PVA hydrogels in cartilage repair was evaluated by in vitro and in vivo experiments. The scanning electron microscopy results showed that the hybrid hydrogels had interconnected macropore structures that contained a COL reticular scaffold. The diameter of the macropore was 1.08–1.85 mm, which corresponds to the diameter of the denatured PVA column. The chondrocytes were then seeded in hydrogels to assess the cell viability and formation of the cartilage matrix. The in vitro results revealed excellent cellular biocompatibility. Osteochondral defects (8 mm in diameter and 8 mm in depth) were created in the femoral trochlear of goats, and the defects were implanted with cell-seeded hydrogels, cell-free hydrogels, or a blank control. The in vivo results showed that the COL-HA-PVA hydrogels effectively repaired cartilage defects, especially the conditions inoculated with chondrocyte in advance. This research suggests that the COL-HA-PVA hydrogels have promising application in cartilage repair.
Biosafety of mesoporous silica nanoparticles: a combined experimental and literature study
Authors: Sun Lue , Sogo Yu , Wang Xiupeng , Ito Atsuo 
Published: August 2021

AbstractMesoporous silica (MS) particles have been explored for various healthcare applications, but universal data about their safety and/or toxicity are yet to be well-established for clinical purposes. Information about general toxicity of hollow MS (HMS) particles and about immunotoxicity of MS particles are significantly lacked. Therefore, acute toxicity and immunotoxicity of HMS particles were experimentally evaluated. A systematic and objective literature study was parallelly performed to analyze the published in vivo toxicity of MS particles. Lethal acute toxicity of MS particles is likely to arise from their physical action after intravenous and intraperitoneal administrations, and only rarely observed after subcutaneous administration. No clear relationship was identified between physicochemical properties of MS particles and lethality as well as maximum tolerated dose with some exceptions. At sub-lethal doses, MS particles tend to accumulate mainly in lung, liver, and spleen. The HMS particles showed lower inflammation-inducing ability than polyinosinic-polycytidylic acid and almost the same allergy-inducing ability as Alum. Finally, the universal lowest observed adverse effect levels were determined as 0.45, 0.81, and 4.1 mg/kg (human equivalent dose) for intravenous, intraperitoneal, and subcutaneous administration of MS particles, respectively. These results could be helpful for determining an appropriate MS particle dose in clinical study.
Effects of actuation of nanoporous gold on cell orientation in a fibroblast sheet
Authors: Wu Peizheng , Sawaki Shogo , Hakamada Masataka , Mabuchi Mamoru 
Published: August 2021

AbstractMechanical stimulation such as flood flow often plays a vital role in the growth and maintenance of a living body, and it is important to investigate cell responses to mechanical stimulation. To date, cell responses to mechanical stimulation have been investigated in detail. However, the cell responses have been little known in a cell sheet. In the present study, a small cyclic strain (CS) of ~0.5% generated by a nanoporous gold actuator was loaded on a cell sheet of fibroblasts, and the effects of the CS on cell orientation were investigated. Individual cells were randomly distributed after the CS application, whereas cells were oriented in a specific direction after the CS application for the cell sheet. Thus, the CS had a different effect on the cell sheet from that on the individual cells. It is suggested that the cadherin/p-120 catenin complex played an important role in the cell response to mechanical stimulation in a cell sheet.
Divergent Molecular and Physiological Response of Two Maize Breeding Lines Under Phosphate Deficiency
Authors: Sun Yanling , Zheng Hongxia 
Published: August 2021

AbstractInorganic phosphate (Pi) deficiency is a main limiting factor on crops growth and to select low-Pi tolerant breeding lines is very significant for crop breeding. Here, two contrasting maize (Zea maysL.) breeding lines showed different physiological response to Pi deficiency. The low-Pi tolerant QXN233 maintained normal growth, including high fresh weight, green leaves, strong shoots, and numerous roots relative to that of the sensitive MH05-4, mainly due to QXN233’ high Pi content in shoots under Pi deficiency. Importantly, some Pi-responsive genes were detected, and among them, Pi transportersZmPHT1;1andZmPHT1;9as well as phytase geneZmphytase 2were expressed increasingly in QXN233 compared to MH05-4 under Pi deprivation or Pi resupply. Moreover, QXN233 had higher proline content, soluble sugar content, and SOD activity than MH05-4, related with its tolerance. Taken together, this study enriches the understanding of the mechanism of maize responding to Pi deficiency.
Clinical trial registries as Scientometric data: A novel solution for linking and deduplicating clinical trials from multiple registries
Authors: Thiele Christian , Hirschfeld Gerrit , von Brachel Ruth 
Published: August 2021

AbstractRegistries of clinical trials are a potential source for scientometric analysis of medical research and serve important functions for the research community and the public at large. Clinical trials that recruit patients in Germany are usually registered in the German Clinical Trials Register (DRKS) or in international registries such as ClinicalTrials.gov. Furthermore, the International Clinical Trials Registry Platform (ICTRP) aggregates trials from multiple primary registries. We queried the DRKS, ClinicalTrials.gov, and the ICTRP for trials with a recruiting location in Germany. Trials that were registered in multiple registries were linked using the primary and secondary identifiers and a Random Forest model based on various similarity metrics. We identified 35,912 trials that were conducted in Germany. The majority of the trials was registered in multiple databases. 32,106 trials were linked using primary IDs, 26 were linked using a Random Forest model, and 10,537 internal duplicates on ICTRP were identified using the Random Forest model after finding pairs with matching primary or secondary IDs. In cross-validation, the Random Forest increased the F1-score from 96.4% to 97.1% compared to a linkage based solely on secondary IDs on a manually labelled data set. 28% of all trials were registered in the German DRKS. 54% of the trials on ClinicalTrials.gov, 43% of the trials on the DRKS and 56% of the trials on the ICTRP were pre-registered. The ratio of pre-registered studies and the ratio of studies that are registered in the DRKS increased over time.
Leveraging full-text article exploration for citation analysis
Authors: La Quatra Moreno , Cagliero Luca , Baralis Elena 
Published: August 2021

AbstractScientific articles often include in-text citations quoting from external sources. When the cited source is an article, the citation context can be analyzed by exploring the article full-text. To quickly access the key information, researchers are often interested in identifying the sections of the cited article that are most pertinent to the text surrounding the citation in the citing article. This paper first performs a data-driven analysis of the correlation between the textual content of the sections of the cited article and the text snippet where the citation is placed. The results of the correlation analysis show that the title and abstract of the cited article are likely to include content highly similar to the citing snippet. However, the subsequent sections of the paper often include cited text snippets as well. Hence, there is a need to understand the extent to which an exploration of the full-text of the cited article would be beneficial to gain insights into the citing snippet, considering also the fact that the full-text access could be restricted. To this end, we then propose a classification approach to automatically predicting whether the cited snippets in the full-text of the paper contain a significant amount of new content beyond abstract and title. The proposed approach could support researchers in leveraging full-text article exploration for citation analysis. The experiments conducted on real scientific articles show promising results: the classifier has a 90% chance to correctly distinguish between the full-text exploration and only title and abstract cases.
Analysis of scientific collaboration network of Italian Institute of Technology
Authors: di Bella Enrico , Gandullia Luca , Preti Sara 
Published: August 2021

AbstractIt has been proven that collaboration between authors leads to a positive influence on research. This paper aims to analyse the complex structure of the co-authorship network among researchers of the Italian Institute of Technology. In this paper, we examine two different co-authorship networks created starting from the data of the papers published by the Italian Institute of Technology during the period 2006–2019. We apply the main Social Network Analysis techniques to describe the relational structure of the group of researchers and its evolution over time. The structure and characteristics of the networks are analysed both at macro and micro levels, and an attempt is made to identify a possible relationship between the position of researchers in the graphs and their scientific productivity and quality.
A big picture: bibliometric study of academic publications from post-Soviet countries
Authors: Chankseliani Maia , Lovakov Andrey , Pislyakov Vladimir 
Published: August 2021

AbstractThe world’s largest community of scientists disintegrated following the dissolution of the Soviet Union. With extremely scarce resources and limited academic freedom as starting points, researchers in this region have been creating new knowledge; they have been building on rich scientific traditions in selected disciplines and, at times, paving new paths in non-traditional disciplines. At present, the cumulative contribution of post-Soviet countries to global research output is only three percent, indicating that these countries are not key players on the global research scene. This study uses bibliometric methods to offer novel empirical insight into the quantity and impact of academic publications; it also looks at the quality of journals in which the output is published. The findings reveal that fifteen post-Soviet countries differ considerably in terms of how much they have prioritised research, as well as the quantity, quality, and impact of their publications. The research productivity across the region has not been high and, taken together, these countries have produced publications of considerably lower quality and lower impact when viewed in the context of global research output. At the same time, researchers from post-Soviet countries tap into international collaborative networks actively, resulting in an exceptionally large proportion of publications from this region being internationally co-authored. In the historical context of Soviet research being known as one of the least collaborative globally, this finding indicates that researchers in the region are attractive to international collaborators and may be seeking such partnerships due to relatively modest research capacity at home.
Scaling Features of Diurnal Variation of Galactic Cosmic Rays
Authors: Modzelewska Renata , Krasińska Agata , Wawrzaszek Anna , Gil Agnieszka 
Published: August 2021

AbstractWe analyze the scaling properties of the diurnal variation of galactic cosmic rays (GCRs) in Solar Cycle 24 and the solar minima between Solar Cycles 23/24 and 24/25 for 2007 – 2019 based on the count rates of the Oulu, Newark, Hermanus, and Potchefstroom neutron monitors. The scaling features of the GCR diurnal variation are studied by evaluating the Hurst exponent, a quantitative parameter used as an indicator of the state of the randomness of a time series. We estimate the Hurst exponents for GCR diurnal-variation parameters amplitude and phase using structure-function and detrended-fluctuation-analysis methods. Results show that the Hurst exponents for the GCR diurnal variation vary in the range from $\approx0.3$
≈
0.3
to $\approx0.9$
≈
0.9
, with a general tendency of being systematically above 0.5. It suggests that the GCR diurnal variation reveals a more persistent structure than Brownian motion. However, the time series of GCR diurnal-variation amplitude and phase evolve from a more persistent structure in the solar minimum between Solar Cycles 23/24 in 2007 – 2009 to a more random character in and near the solar maximum 2012 – 2014. This observation seems to be in agreement with the general configuration of the heliosphere through the 11-year solar-activity cycle. Moreover, the temporal profile of the Hurst exponent for GCR diurnal amplitude and phase around the beginning of the solar minimum between Solar Cycles 24/25 (2018 – 2019) differs from the solar minimum between Solar Cycles 23/24 in 2007 – 2009, suggesting a dependence on solar-magnetic polarity. These findings could shed more light on GCR particle transport in the turbulent heliosphere over the solar cycle.