bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative ozone anomalies at a high mountain site in northern Italy during 2020: a possible role of COVID-19 lockdowns?
Authors: Cristofanelli Paolo , Arduni Jgor , Serva Federico , Calzolari Francescopiero , Bonasoni Paolo , Busetto Maurizio , Maione Michela , Sprenger Michael , Trisolino Pamela , Putero Davide 
Published: June 2021

Abstract
Several studies investigated the possible impacts of the restriction measures related to the containment of the spread of the COrona VIrus Disease (COVID-19) to atmospheric ozone (O3) at global, regional, and local scales during 2020. O3 is a secondary pollutant with adverse effects on population health and ecosystems and with negative impacts on climate, acting as greenhouse gas. Most of these studies focused on spring 2020 (i.e. March–May) and on observations in the planetary boundary layer (PBL), mostly in the vicinity of urban agglomerates. Here, we analyzed the variability of O3 above the PBL of northern Italy in 2020 by using continuous observations carried out at a high mountain WMO/GAW global station in Italy (Mt. Cimone–CMN; 44°12′ N, 10°42′ E, 2165 m a.s.l.). Low O3 monthly anomalies were observed during spring (MAM) and summer (JJA), when periods of low O3 intertwined with periods with higher O3, within climatological ranges. A similar variability was observed for O3 precursors like NO2 and 15 anthropogenic non-methane volatile organic carbons, but the systematic O3 anomalies were not reflected in these variables. The analysis of meteorological variables and diel O3 cycles did not suggest major changes in the vertical transport related to the thermal circulation system in the mountain area. The analysis of five days back-trajectories suggested that the observed O3 anomalies cannot be explained by differences in the synoptic-scale circulation with respect to the previous years alone. On the other hand, the characterization of two transport patterns (i.e. air masses from the regional PBL or from the free troposphere) and the analysis of back-trajectories suggested an important contribution of transport from the continental PBL during the periods with the lowest O3 at CMN. When proxies of air mass transport from the regional PBL are considered, a lower NO
x
content was pointed out with respect to the previous years, suggesting a lower O3 production in a NO
x
-limited atmosphere. Our study suggested for the first time that, during MAM and JJA 2020, the reduced anthropogenic emissions related to the COVID-19 restrictions lowered the amount of this short-lived climate forcer/pollutant at remote locations above the PBL over northern Italy. This work suggests the importance of limiting anthropogenic precursor emissions for decreasing the O3 amount at remote locations and in upper atmospheric layers.
Carrageenan assisted synthesis of morphological diversity of CdO and Cd (OH)2 with high antibacterial activity
Authors: Mirzaei Akbar , Jamshidi Edris , Morshedloo Ehsan , Javanshir Shahrzad , Manteghi Faranak 
Published: June 2021

Abstract
This research reports a simple and novel method for the controlled synthesis of cadmium oxide (CdO) and cadmium hydroxide (Cd(OH)2) with different new morphologies in the presence of NaBH4 or LiBH4 as reducing agent, by using κ-carrageenan as a capping/stabilizing agent and potassium bromide as a template. The synthesized products were characterized by x-ray diffraction (XRD) and scanning electron microscopy (SEM). The impacts of reducing agent, reaction atmosphere, and concentration of reducing agent on size and morphology of the particles were discussed. We suggested that chemical etching and Kirkendall effect play a key role in the morphology of particles, and the etch rate depends on reducing agent concentration. It was found that by increasing the concentration of the reducing agent, the intensified etching leads to an increase in the size of the particles. The results show an increase in particle size with decreasing reducing agents power. The various morphologies obtained for CdO and Cd(OH)2 such as hollow cube, macro rod, nanoplate, and macroplate were discussed based on the Kirkendall effect and chemical etching. Finally, the antibacterial activity of the synthesized nanoparticles was screened against Escherichia coli (E. coli) and Staphylococcus aureus (s.aureus). The inhibition zones were ranged from 36–47 mm and 25–47 mm for different morphologies of CdO and Cd(OH)2, respectively. Furthermore, the reactive oxygen species (ROS) production assay in the presence of bacteria was performed. The results did not show any positive result of ROS production.
Outcome of environmental change from historical sediment discharge in a Mediterranean fluvial basin, 1500–2019 CE
Authors: Diodato Nazzareno , Ljungqvist Fredrik Charpentier , Bellocchi Gianni 
Published: June 2021

AbstractSoil loss is a challenge for sustainable river management, not the least in the Mediterranean region, with climate extremes altering erosion and overland sediment transport. The dynamics of these processes, and their ecological consequences, are poorly documented in the Mediterranen region. For the Arno River Basin (ARB), located by the Tyrrhenian coast of Italy, we estimated changes in annual sediment discharge (SD) as a function of the landscape characteristics within the basin, the seasonal distribution of precipitation and flooding, and the vegetation cover. Owing to a semi-empirical modelling framework, we identified critical erosion-/deposition-prone periods from 1500 to 2019 CE. The long-term estimated mean gross soil erosion in the ARB was ∼900 Mg km−2yr−1, whereas mean net erosion was ∼200 Mg km−2yr−1. The results revealed that during the Little Ice Age (ending ∼1850 CE), increased storms andSDhad a large impact on the landscape and agricultural activity of the ARB. The downward trend inSDobserved after ∼1903 CE occurred with high soil movement, along with environmental change and basin reforestation. The basin area thus experienced, on average, only slight soil losses, with ∼76% of the eroded soil being trapped along the stream reaches, on gently sloping areas as well as in the foot slopes and the valley terrains which divide the basin area. Relying on credible information regardingSDand its hydrological drivers, we showed how historical climatology and parsimonious modelling can be implemented to obtain basin-wide estimates of soil loss, and are appropriate tools for sustainable river basin management.
Women’s rights and critical junctures in constitutional reform in Africa (1951–2019)
Authors: Paulson-Smith Kaden , Tripp Aili Mari 
Published: June 2021

Abstract
Women’s rights are being enshrined in African constitutions today to an unprecedented extent. African countries have on average more constitutional provisions addressing women’s rights than any other region of the world. This longitudinal cross-national study shows that constitutional reforms in African contexts are increasingly evident in the areas of gender equality, customary law, discrimination, violence against women, gender quotas, and citizenship rights, and they sometimes reflect gender-inclusive language. By analysing a novel data set of constitutional reforms across all African countries over 68 years (1951–2019), this article identifies four critical junctures when the adoption of women’s rights reforms arose, namely (i) after independence, particularly in Muslim-majority countries; (ii) after political opening in the 1990s; (iii) after the end of major civil conflicts; and (iv) after the 2011 Arab uprisings. At each juncture, women’s movements capitalized on political openings to advance constitutional reforms that are unmatched on a global scale. This article goes beyond the existing explanations of cumulative gains, international influence, diffusion, learning, and borrowing to show that a ‘critical junctures’ approach may help explain when, why, and how women’s rights reforms occur in constitutions.
Integrative machine learning framework for the identification of cell-specific enhancers from the human genome
Authors: Basith Shaherin , Hasan Md Mehedi , Lee Gwang , Wei Leyi , Manavalan Balachandran 
Published: June 2021

AbstractEnhancers are deoxyribonucleic acid (DNA) fragments which when bound by transcription factors enhance the transcription of related genes. Due to its sporadic distribution and similar fractions, identification of enhancers from the human genome seems a daunting task. Compared to the traditional experimental approaches, computational methods with easy-to-use platforms could be efficiently applied to annotate enhancers’ functions and physiological roles. In this aspect, several bioinformatics tools have been developed to identify enhancers. Despite their spectacular performances, existing methods have certain drawbacks and limitations, including fixed length of sequences being utilized for model development and cell-specificity negligence. A novel predictor would be beneficial in the context of genome-wide enhancer prediction by addressing the above-mentioned issues. In this study, we constructed new datasets for eight different cell types. Utilizing these data, we proposed an integrative machine learning (ML)-based framework called Enhancer-IF for identifying cell-specific enhancers. Enhancer-IF comprehensively explores a wide range of heterogeneous features with five commonly used ML methods (random forest, extremely randomized tree, multilayer perceptron, support vector machine and extreme gradient boosting). Specifically, these five classifiers were trained with seven encodings and obtained 35 baseline models. The output of these baseline models was integrated and again inputted to five classifiers for the construction of five meta-models. Finally, the integration of five meta-models through ensemble learning improved the model robustness. Our proposed approach showed an excellent prediction performance compared to the baseline models on both training and independent datasets in different cell types, thus highlighting the superiority of our approach in the identification of the enhancers. We assume that Enhancer-IF will be a valuable tool for screening and identifying potential enhancers from the human DNA sequences.
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation
Authors: Cui Chunmei , Zhou Yuan , Cui Qinghua 
Published: June 2021

AbstractAnimal models have a certain degree of similarity with human in genes and physiological processes, which leads them to be valuable tools for studying human diseases and for assisting drug development. However, translational researches adopting animal models are largely restricted by the species heterogeneity, which is also a major reason for the failure of drug research. Currently, computational method for exploring the functional differences between orthologous genes is still insufficient. For this purpose, here, we presented an algorithm, functional divergence score (FDS), by comprehensively evaluating the functional differences between the microRNAs regulating the paired orthologous genes. Given that mouse is one of the most popular model animals, currently, FDS was designed to dissect the functional divergence of orthologous genes between human and mouse. The results showed that gene FDS value is significantly associated with gene evolutionary characteristics and can discover expression divergence of human–mouse orthologous genes. Moreover, FDS performed well in distinguishing the targets of approved drugs and the failed ones. These results suggest that FDS is a valuable tool to evaluate the functional divergence of paired human and mouse orthologous genes. In addition, for each orthologous gene pair, FDS can provide detailed differences in functions and phenotypes. Our study provided a useful tool for quantifying the functional difference between human and mouse, and the presented framework is easily to be extended to the orthologous genes between human and other species. An online server of FDS is available at http://www.cuilab.cn/fds/.
Embeddings of genomic region sets capture rich biological associations in lower dimensions
Authors: Gharavi Erfaneh , Gu Aaron , Zheng Guangtao , Smith Jason P , Cho Hyun Jae , Zhang Aidong , Brown Donald E , Sheffield Nathan C 
Published: June 2021

AbstractMotivationGenomic region sets summarize functional genomics data and define locations of interest in the genome such as regulatory regions or transcription factor binding sites. The number of publicly available region sets has increased dramatically, leading to challenges in data analysis.ResultsWe propose a new method to represent genomic region sets as vectors, or embeddings, using an adapted word2vec approach. We compared our approach to two simpler methods based on interval unions or term frequency-inverse document frequency and evaluated the methods in three ways: First, by classifying the cell line, antibody or tissue type of the region set; second, by assessing whether similarity among embeddings can reflect simulated random perturbations of genomic regions; and third, by testing robustness of the proposed representations to different signal thresholds for calling peaks. Our word2vec-based region set embeddings reduce dimensionality from more than a hundred thousand to 100 without significant loss in classification performance. The vector representation could identify cell line, antibody and tissue type with over 90% accuracy. We also found that the vectors could quantitatively summarize simulated random perturbations to region sets and are more robust to subsampling the data derived from different peak calling thresholds. Our evaluations demonstrate that the vectors retain useful biological information in relatively lower-dimensional spaces. We propose that vector representation of region sets is a promising approach for efficient analysis of genomic region data.Availability and implementationhttps://github.com/databio/regionset-embedding.Supplementary informationSupplementary data are available at Bioinformatics online.
Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures
Authors: N’Guessan Arnaud , Brito Ilana Lauren , Serohijos Adrian W R , Shapiro B Jesse 
Published: June 2021

AbstractPangenomes—the cumulative set of genes encoded by a population or species—arise from the interplay of horizontal gene transfer, drift, and selection. The balance of these forces in shaping pangenomes has been debated, and studies to date focused on ancient evolutionary time scales have suggested that pangenomes generally confer niche adaptation to their bacterial hosts. To shed light on pangenome evolution on shorter evolutionary time scales, we inferred the selective pressures acting on mobile genes within individual human microbiomes from 176 Fiji islanders. We mapped metagenomic sequence reads to a set of known mobile genes to identify single nucleotide variants (SNVs) and calculated population genetic metrics to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation without the need to invoke the adaptive value of mobile genes to either bacterial or human hosts. These results stand in contrast with the apparent adaptive value of pangenomes over longer evolutionary time scales. In general, the most highly mobile genes (i.e., those present in more distinct bacterial host genomes) tend to have higher metagenomic read coverage and an excess of low-frequency SNVs, consistent with their rapid spread across multiple bacterial species in the gut. However, a subset of mobile genes—including those involved in defense mechanisms and secondary metabolism—showed a contrasting signature of intermediate-frequency SNVs, indicating species-specific selective pressures or negative frequency-dependent selection on these genes. Together, our evolutionary models and population genetic data show that gene-specific selective pressures predominate over human or bacterial host-specific pressures during the relatively short time scales of a human lifetime.
Temporal transcriptomic landscape of postnatal mouse ovaries reveals dynamic gene signatures associated with ovarian aging
Authors: Zhou Zixue , Yang Xi , Pan Yuncheng , Shang Lingyue , Chen Siyuan , Yang Jialin , Jin Li , Zhang Feng , Wu Yanhua 
Published: June 2021

Abstract
The ovary is the most important organ for maintaining female reproductive health, but it fails before most other organs. Aging-associated alterations in gene expression patterns in mammalian ovaries remain largely unknown. In this study, the transcriptomic landscape of postnatal mouse ovaries over the reproductive lifespan was investigated using bulk RNA sequencing in C57BL/6 mice. Gene expression dynamics revealed that the lifespan of postnatal mouse ovaries comprised four sequential stages, during which 2517 genes were identified as differentially enriched. Notably, the DNA repair pathway was found to make a considerable and specific contribution to the process of ovarian aging. Temporal gene expression patterns were dissected to identify differences in gene expression trajectories over the lifespan. In addition to DNA repair, distinct biological functions (including hypoxia response, epigenetic modification, fertilization, mitochondrial function, etc.) were overrepresented in particular clusters. Association studies were further performed to explore the relationships between known genes responsible for ovarian function and differentially expressed genes identified in this work. We found that the causative genes of human premature ovarian insufficiency were specifically enriched in distinct gene clusters. Taken together, our findings reveal a comprehensive transcriptomic landscape of the mouse ovary over the lifespan, providing insights into the molecular mechanisms underlying mammalian ovarian aging and supporting future etiological studies of aging-associated ovarian disorders.
Incorporating Research into an Undergraduate Animal Behavior Course using Zoos and Webcams
Authors: Davis-Berg Elizabeth C , Rafacz Michelle L 
Published: June 2021

AbstractIn our nonmajors animal behavior class, we developed a semester-long research project assignment that incorporates project-based learning (PBL) and the opportunity for Course-Based Undergraduate Research Experiences (CUREs) that introduces, assesses, and applies the course concepts. This project can easily be adapted for nonmajors biology, majors biology, or other more general survey classes, including remote courses. This student-led project involves a field trip for data collection at our local zoo, additional data collection using webcams, and writing and presenting a scientific report. Students apply the scientific method to design their research project and formulate a hypothesis. Throughout the semester, students learn about different behavioral sampling methods and how to develop and use an ethogram in class using animal webcams from zoos. At the zoo, students conduct a comparative behavior project by collecting data from their main animal and two related animals using multiple trials, so students can observe differences in behavior. At the conclusion of the project, students write a report demonstrating their data analysis, graphing, explanation, and interpretation of their own scientific data. We discuss how others can design and implement PBL and CUREs in their classes and what we have learned from our experiences.
Transfer of conservative discrete differential operators between staggered grids: construction and duality relations
Authors: Goudon Thierry , Krell Stella , Llobell Julie , Minjeaud Sebastian 
Published: June 2021

AbstractThis paper is concerned with the construction of a discrete conservative operator on a mesh, knowing a conservative operator on a different mesh. We analyse the possibility of defining such a transfer based on the preservation of conservation properties and provide practical procedures, which can be effectively implemented for schemes that work on staggered grids. We show that such a transfer can be applied to obtain a discrete balance equation on a mesh starting from a discrete balance equation on a different mesh, and to prove local discrete duality relations for standard discrete operators defined on staggered grids.
A Vertex Model for LLT Polynomials
Authors: Corteel Sylvie , Gitlin Andrew , Keating David , Meza Jeremy 
Published: June 2021

Abstract
We describe a novel Yang–Baxter integrable vertex model. From this vertex model we construct a certain class of partition functions that we show are essentially equal to the LLT polynomials of Lascoux, Leclerc, and Thibon. Using the vertex model formalism, we give alternate proofs of many properties of these polynomials, including symmetry and a Cauchy identity.
Integration of Singular Foliations via Paths
Authors: Garmendia Alfonso , Villatoro Joel 
Published: June 2021

Abstract
We give a new construction of the holonomy and fundamental groupoids of a singular foliation. In contrast with the existing construction of Androulidakis and Skandalis, our method proceeds by taking a quotient of an infinite-dimensional space of paths. This strategy is a direct extension of the classical construction for regular foliations and mirrors the integration of Lie algebroids via paths (per Crainic and Fernandes). In this way, we obtain a characterization of the holonomy and fundamental groupoids of a singular foliation that more clearly reflects the homotopic character of these invariants. As an application of our work, we prove that the constructions of the fundamental and holonomy groupoid of a foliation have functorial properties.
High prevalence of circulating dual-class resistant Mycoplasma genitalium in asymptomatic MSM in Tokyo, Japan
Authors: Ando Naokatsu , Mizushima Daisuke , Takano Misao , Mitobe Morika , Miyake Hirofumi , Yokoyama Keiko , Sadamasu Kenji , Aoki Takahiro , Watanabe Koji , Uemura Haruka , Yanagawa Yasuaki , Gatanaga Hiroyuki , Oka Shinichi 
Published: June 2021

Abstract

Objectives
To assess the prevalence and antibiotic resistance profile of Mycoplasma genitalium detected from urogenital/rectal swab samples obtained from MSM in Tokyo, Japan.

Methods
We performed PCR-based screening for M. genitalium urogenital/rectal infection in 982 asymptomatic MSM between 1 January 2019 and 5 November 2020. Mutations in the antibiotic resistance-associated genes gyrA and parC and the 23S rRNA of M. genitalium were analysed.

Results
The prevalence of M. genitalium infection was 6.1%: the prevalence of rectal and urogenital infection was 4.7% and 1.4%, respectively. Among the cases, 48 were successfully analysed for 23S rRNA, 41 for parC mutations and 37 for gyrA mutations. Macrolide- and quinolone-resistance associated mutations (23S rRNA and parC mutations) were observed in 43 (89.6%) and 28 (68.3%) cases, respectively. The quinolone-resistance associated mutation-harbouring variants also harboured macrolide-resistance associated mutations. The S83I mutation in the parC gene was most commonly identified (24 cases, 58.5%), and its combination with M95I or D99N mutation in the gyrA gene was observed in 9 of 36 successfully analysed cases (25.0%). No significant association was observed between the presence of antibiotic resistance and antibiotic exposure for either macrolides or fluoroquinolones (P = 0.785 and 0.402, respectively).

Conclusions
In Tokyo, there is an alarmingly high prevalence of M. genitalium harbouring macrolide and/or quinolone resistance-associated mutations in MSM, irrespective of antibiotic exposure. The high prevalence of M. genitalium strains with both parC and gyrA mutations limits the efficacy of sitafloxacin. Therefore, suitable alternatives are required to treat such M. genitalium infections.