bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineralogy and geochemistry of Kliripan manganese ore deposit, Hargorejo Village, Kokap District, Kulonprogo Regency
Authors: Islamadina B , Warmada I W 
Published: August 2022

Abstract
This study discusses the mineralogy and geochemistry of manganese deposits in the Kliripan area, where manganese had been mined since the Dutch occupancy until the 1970s. Although mining has been discontinued since then, the demand for manganese has increased in various industries, prompting exploration to continue to meet this demand. We performed petrographic, XRD, and XRF analysis of the ore and wall rock samples. Jasper and grainstone from the Sentolo Formation are the two lithologies where manganese mineralization occurs. Manganese-bearing minerals include pyrolusite, manganite, rhodochrosite, and lithiophorite, while the gangue minerals consist of quartz, calcite, hematite, and clay minerals. We interpret that Jasper is a product of alteration and has MnO content as high as 5.02 wt.%. Meanwhile, the economic grade manganese ore in grainstone has an MnO content up to 48.51 wt.%. The elements Ce, Zr, Co+Ni+Cu, are important discriminants to determine the type of manganese deposit. The results showed that the diagenetic process in reductive water formed the manganese ores. Oxidation of divalent manganese ion formed pyrolusite and manganite. Rhodochrosite crystallized when dilute manganese solution reacts with CO2 from limestone diagenesis. We concluded that the Kliripan manganese ore deposit has both hydrothermal and diagenetic deposits.
Geology and the effect of compaction on base material disposal for the stability of coal disposal slopes in South Kalimantan, Indonesia
Authors: Abdullah B A , Indrawan I G B 
Published: August 2022

Abstract
A mining activity generally removes overburden to extract minerals. Therefore, a certain area is needed to place the overburden material. One of the parameters that can affect the stability of the disposal is the base or the foundation of the disposal area which will later be stockpiled. This study is observe influence of base disposal to the stability of slope. Based on the lithological characteristics and observations of the outcrop, the writer arranges the stratigraphy of the study area in order to determine the stratigraphic arrangement and the distribution of the rock units laterally. In general, the study area is dominated by quartz sandstone, claystone, conglomerate and loose material from older rocks. The stratigraphic sequence of the study area from old to young includes Warukin Sandstone Unit (Tmw), Dahor Layang Member Conglomerate (TQdt) and Dahor Sandstone Unit (TQd). In general, the research area is included in the structural landform unit with geomorphological control that influences the tectonic process (endogenous). Based on the results of the study, there was a significant increase related to the stability of the coal disposal slope with compaction efforts carried out on the base material.
Graphene membrane hosted compact lithium metal anode enabled by capillary force-tuned lithium infiltration
Authors: Zhao Shuaiqin , Ren Zetao , Gu Sichen , Zhang Chen , Han Junwei , Lv Wei 
Published: August 2022

Abstract
Lithium metal anodes, the promising anodes for next-generation batteries, are troubled by the instability and safety issues induced by the dendrite growth. Three-dimensional hosts are widely used to accommodate lithium metal to solve the above problems. However, they are constantly challenged by large thickness and excess space in the host, lowering the volumetric energy density of batteries. Here, we used the reduced graphene oxide membrane (rGOM) assembled with small graphene oxide sheets as the host and obtained a compact, ultrathin (<20 μm) and free-standing lithium metal-rGO composite anode with good flexibility and high volumetric capacity. The overlap sites derived from the stacking of small size of GO act as abundant diffusion channels for the gas release during the spark reduction process, producing narrow interlamellar space in the rGOM and thus enhancing the capillary molten Li infusion to form a compact composite anode. These sites also guide the uniform deposition of Li metal on the surface and interior of the membrane, effectively suppressing the dendrite growth. This compact composite anode delivers a high volumetric capacity (1223 mAh cm−3) and stable cycling performance in the symmetrical cells and the full cells coupled with high mass loading LiFePO4 cathode under a low N/P ratio.
Numerical simulation and performance analysis of the radiofrequency inductive cathode
Authors: QIAO Kuan , CHENG Mousen , ZHANG Fan , YANG Xiong , GUO Dawei , YANG Yuntian , DING Zhenwei 
Published: August 2022

Abstract
The radiofrequency (RF) inductive cathode has great prospects in space missions with long mission cycles, large speed increments, and rapid response requirements as the main electron source and neutralizer in Hall thrusters and ion thrusters. This paper proposes a comprehensive multi-physics RF inductive cathode model in which the RF electromagnetic field, electrostatic field for extracting electrons, flow field, plasma transport and electrochemical reaction process are all accounted for. Each physical field mentioned above can form a closed partial differential equation. The two-dimensional finite element code COMSOL is used to solve the multi-physics model. With this model, the formation process of the anode spot is exhibited and demonstrates the non-bipolar flow theory in practice. The simulation results demonstrate that the current jump in the RF inductive cathode is caused by the anode spot. Furthermore, the influences of preset discharge parameters such as RF power, bias voltage and actuating gas flow as well as structural parameters like the coil structure, discharge chamber size and ion collector area, emission hole size, distance between the anode target and the emission hole etc on the cathode performance are investigated, and some important optimal parameters are proposed.
Metric learning for kernel ridge regression: assessment of molecular similarity
Authors: Fabregat Raimon , van Gerwen Puck , Haeberle Matthieu , Eisenbrand Friedrich , Corminboeuf Clémence 
Published: August 2022

Abstract
Supervised and unsupervised kernel-based algorithms widely used in the physical sciences depend upon the notion of similarity. Their reliance on pre-defined distance metrics—e.g. the Euclidean or Manhattan distance—are problematic especially when used in combination with high-dimensional feature vectors for which the similarity measure does not well-reflect the differences in the target property. Metric learning is an elegant approach to surmount this shortcoming and find a property-informed transformation of the feature space. We propose a new algorithm for metric learning specifically adapted for kernel ridge regression (KRR): metric learning for kernel ridge regression (MLKRR). It is based on the Metric Learning for Kernel Regression framework using the Nadaraya-Watson estimator, which we show to be inferior to the KRR estimator for typical physics-based machine learning tasks. The MLKRR algorithm allows for superior predictive performance on the benchmark regression task of atomisation energies of QM9 molecules, as well as generating more meaningful low-dimensional projections of the modified feature space.
Predicting ncRNA–protein interactions based on dual graph convolutional network and pairwise learning
Authors: Zhuo Linlin , song bosheng , liu yuansheng , Li Zejun , Fu Xiangzheng 
Published: August 2022

Abstract
Noncoding RNAs (ncRNAs) have recently attracted considerable attention due to their key roles in biology. The ncRNA–proteins interaction (NPI) is often explored to reveal some biological activities that ncRNA may affect, such as biological traits, diseases, etc. Traditional experimental methods can accomplish this work but are often labor-intensive and expensive. Machine learning and deep learning methods have achieved great success by exploiting sufficient sequence or structure information. Graph Neural Network (GNN)-based methods consider the topology in ncRNA–protein graphs and perform well on tasks like NPI prediction. Based on GNN, some pairwise constraint methods have been developed to apply on homogeneous networks, but not used for NPI prediction on heterogeneous networks. In this paper, we construct a pairwise constrained NPI predictor based on dual Graph Convolutional Network (GCN) called NPI-DGCN. To our knowledge, our method is the first to train a heterogeneous graph-based model using a pairwise learning strategy. Instead of binary classification, we use a rank layer to calculate the score of an ncRNA–protein pair. Moreover, our model is the first to predict NPIs on the ncRNA–protein bipartite graph rather than the homogeneous graph. We transform the original ncRNA–protein bipartite graph into two homogenous graphs on which to explore second-order implicit relationships. At the same time, we model direct interactions between two homogenous graphs to explore explicit relationships. Experimental results on the four standard datasets indicate that our method achieves competitive performance with other state-of-the-art methods. And the model is available at https://github.com/zhuoninnin1992/NPIPredict
BERN2: an advanced neural biomedical named entity recognition and normalization tool
Authors: Sung Mujeen , Jeong Minbyul , Choi Yonghwa , Kim Donghyeon , Lee Jinhyuk , Kang Jaewoo 
Published: August 2022

Abstract In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.Availability and implementationWeb service of BERN2 is publicly available at http://bern2.korea.ac.kr. We also provide local installation of BERN2 at https://github.com/dmis-lab/BERN2.Supplementary informationSupplementary data are available at Bioinformatics online.
A tale of two recoveries: uncovering the imbalance between state-driven production and private consumption in post-pandemic Wuhan, China
Authors: Li Ziming , Chen Xiangming , Wang Lei 
Published: August 2022

Abstract
The world’s first epicentre of Covid-19 that contained the virus early and recovered quickly, Wuhan, the capital city of China’s Hubei province, offers a rare case for examining the effective but unbalanced role of the Chinese state in recovering a post-Covid city against a continued zero-Covid policy. Due to institutional inertia in policy-making, Wuhan has experienced a two-track recovery of (i) rapid GDP growth from infrastructure investment fuelled by government stimuli and large state-owned enterprises, and (ii) a weak recovery for small private businesses and grassroots consumption. Combining analyses of city-level data and survey/interview information, this paper examines the unbalanced role of the Chinese state in producing Wuhan’s uneven two-track economic recovery and its implications for recalibrating the roles of the central versus local governments and empowering the latter to rebalance from production to consumption and to improve livelihood.
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
Authors: Chen Qingyu , Allot Alexis , Leaman Robert , Islamaj Rezarta , Du Jingcheng , Fang Li , Wang Kai , Xu Shuo , Zhang Yuefu , Bagherzadeh Parsa , Bergler Sabine , Bhatnagar Aakash , Bhavsar Nidhir , Chang Yung-Chun , Lin Sheng-Jie , Tang Wentai , Zhang Hongtong , Tavchioski Ilija , Pollak Senja , Tian Shubo , Zhang Jinfeng , Otmakhova Yulia , Yepes Antonio Jimeno , Dong Hang , Wu Honghan , Dufour Richard , Labrak Yanis , Chatterjee Niladri , Tandon Kushagri , Laleye Fréjus A A , Rakotoson Loïc , Chersoni Emmanuele , Gu Jinghang , Friedrich Annemarie , Pujari Subhash Chandra , Chizhikova Mariia , Sivadasan Naveen , VG Saipradeep , Lu Zhiyong 
Published: August 2022

Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature—at a rate of about 10 000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200 000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g. Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text-mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset—consisting of over 30 000 articles with manually reviewed topics—was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181 and 0.9394 for macro-F1-score, micro-F1-score and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g. 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.
Database URL https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/
EfGD: the Erianthus fulvus genome database
Authors: Qian Zhenfeng , Li Xuzhen , He Lilian , Gu Shujie , Shen Qingqing , Rao Xibing , Zhang Rongqiong , Di Yining , Xie Linyan , Wang Xianhong , Chen Shuying , Dong Yang , Li Fusheng 
Published: August 2022

Abstract
Erianthus fulvus (TaxID: 154759) is a valuable germplasm resource in sugarcane breeding and research and has excellent agronomic traits, such as drought resistance, cold resistance, barren tolerance and high brix. With a stable chromosome number (2n = 20) and a small genome (0.9 Gb), it is an ideal candidate for research on sugarcane. Next-generation sequencing technology has enabled a growing number of studies to focus on genomics. Due to the large amount of omics data available, a centralized platform is necessary for ensuring the consistency, independence and maintainability of these large-scale datasets through storage, analysis and integration. Here, we present a comprehensive database for the E. fulvus genome, EfGD. By using the new high-quality reference genome and its annotations, the EfGD provides the largest whole-genome sequencing reference dataset for E. fulvus, which archives 27 165 protein-coding genes and 55 564 488 SNPs from 202 newly resequenced genomes. Furthermore, we created a user-friendly graphical interface for visualizing genomic diversity, population structure and evolution and provided other tools on an open platform.
Database URL: https://efgenome.ynau.edu.cn
‘Open’ or ‘Closed’? Participation in English Manorial Presentment Juries, c.1310–c.1600: A Quantitative Approach
Authors: Gibbs Spike 
Published: August 2022

Abstract
Historians of both the medieval and early modern eras have characterised the governing structures of rural communities as being dominated by local elites. However, interpretations are hampered by a lack of clear criteria against which to evaluate whether a village-governance regime was ‘open,’ and characterised by wide participation, or ‘closed’, and characterised by the narrow restriction of office to an elite group, making it difficult to draw comparisons across time and space. This article uses a set of quantitative methodologies to solve this problem. It examines presentment juries in the manorial court, a governing institution which straddles the late medieval and early modern period, in three case-study communities for the period from 1310 to 1600. By applying four measures of participation, the article reveals that post-Black Death juries were characterised by a nuanced system of restriction. They were open in the sense that a large proportion of the male population, drawn from a wide range of families, acted as jurors and there was a continuous turnover in jury panels. However, they were also closed in that a small group of prominent individuals and families served a disproportionately frequent number of times. The results also question an established narrative of increasing monopolisation of village governance by a new ‘middling sort’ over the sixteenth century. Instead, change over time and space reveals a variable set of trends, with no universal linear pattern. The inflexibility of manorial institutions, combined with local demographic regimes and trends in landholding, led to significant differences in political participation between communities.
A novel Candida glabrata doxycycline-inducible system for in vitro/in vivo use
Authors: Schrevens S , Sanglard D 
Published: August 2022

Abstract
Candida glabrata is an important pathogen causing superficial to invasive disease in human. Conditional expression systems are helpful in addressing the function of genes and especially when they can be applied to in vivo studies. Tetracycline-dependent regulation systems have been used in diverse fungi to turn-on (Tet-on) or turn-off (Tet-off) gene expression either in vitro but also in vivo in animal models. Up to now, only a Tet-off expression has been constructed for gene expression in C. glabrata. Here, we report a Tet-on gene expression system which can be used in vitro and in vivo in any C. glabrata genetic background. This system was used in a mice model of systemic infection to demonstrate that the general amino acid permease Gap1 is important for C. glabrata virulence.
Differential hydroxylation efficiency of the two non-heme carotene hydroxylases: DcBCH1, rather than DcBCH2, plays a major role in carrot taproot
Authors: Li Tong , Liu Jie-Xia , Deng Yuan-Jie , Duan Ao-Qi , Liu Hui , Zhuang Fei-Yun , Xiong Ai-Sheng 
Published: August 2022

Abstract
Carotene hydroxylase plays an important role in catalyzing the hydroxylation of carotene to xanthopylls, including two types: non-heme carotene hydroxylase (BCH type) and heme-containing cytochrome P450 hydroxylase (P450 type). Two BCH-encoding genes were annotated in the carrot genome. However, the role of BCHs and whether there are functional interactions between the duplicated BCHs in carrot remains unclear. In this study, two BCH encoding genes, DcBCH1 and DcBCH2, were cloned from carrot. The relative expression level of DcBCH1 was much higher than that of DcBCH2 in carrot taproots with different carotene accumulation levels. Overexpression of DcBCH1 in ‘KRD’ (high carotene accumulated) carrot changed the taproot color from orange to yellow, accompanied by substantial reductions in α-carotene and β-carotene. There was no obvious change in taproot color between transgenic ‘KRD’ carrot overexpressing DcBCH2 and control carrot. Simultaneously, the content of α-carotene in the taproot of DcBCH2-overexpressing carrot decreased, but the content of β-carotene did not change significantly in comparison with control carrot. Using the CRISPR/Cas9 system to knock out DcBCH1 in ‘KRD’ carrot lightened the taproot color from orange to pink-orange; the content of α-carotene in the taproot increased slightly, while the β-carotene content was still significantly decreased, compared with control carrot. In DcBCH1-knockout carrot, the transcript level of DcBCH2 was significantly increased. These results indicated that in carrot taproot, DcBCH1 played the main function of BCH enzyme, which could hydroxylate α-carotene and β-carotene; DcBCH1 and DcBCH2 had functional redundancy, and these two DcBCHs could partially compensate for each other.
Introgression of clubroot resistant gene into
Brassica oleracea
L. from
Brassica rapa
based on homoeologous exchange
Authors: Zhu Mingzhao , Yang Limei , Zhang Yangyong , Zhuang Mu , Ji Jialei , Hou Xilin , Li Zhansheng , Han Fengqing , Fang Zhiyuan , Lv Honghao , Wang Yong 
Published: August 2022

Abstract
Clubroot is a soil-borne disease in cabbage (Brassica oleracea L. var. capitata L.) caused by Plasmodiophora brassicae, which poses a great threat to cabbage production. However, clubroot resistance (CR) genes in Brassica rapa could be introduced into the cabbage via breeding to make it clubroot resistant. In this study, CR genes from B. rapa were introduced into the cabbage genome and the mechanism of gene introgression was explored. Two methods were used to create CR materials: (i) The fertility of CR Ogura CMS cabbage germplasms containing CRa was restored by using an Ogura CMS restorer. After cytoplasmic replacement and microspore culture, CRa-positive microspore individuals were obtained. (ii) Distant hybridization was performed between cabbage and B. rapa, which contained three CR genes (CRa, CRb, and Pb8.1). Finally, BC2 individuals containing all three CR genes were obtained. Inoculation results showed that both CRa-positive microspore individuals and BC2 individuals containing three CR genes were resistant to race 4 of P. brassicae. Sequencing results from CRa-positive microspore individuals with specific molecular markers and genome-wide association study (GWAS) showed penetration at the homologous position of the cabbage genome by a 3.42 Mb CRa containing a fragment from B. rapa; indicating homoeologous exchange (HE) as the theoretical basis for the introgression of CR resistance. The successful introduction of CR into the cabbage genome in the present study can provide useful clues for creating introgression lines within other species of interest.