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Background: The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) utilizes the Transposase Tn5 to probe open chromatic, which simultaneously reveals multiple transcription factor binding sites (TFBSs) compared to traditional technologies. Deep learning (DL) technology, including convolutional neural networks (CNNs), has successfully found motifs from ATAC-seq data. Due to the limitation of the width of convolutional kernels, the existing models only find motifs with fixed lengths. A Graph neural network (GNN) can work on non-Euclidean data, which has the potential to find ATAC-seq motifs with different lengths. However, the existing GNN models ignored the relationships among ATAC-seq sequences, and their parameter settings should be improved. Results: In this study, we proposed a novel GNN model named GNNMF to find ATAC-seq motifs via GNN and background coexisting probability. Our experiment has been conducted on 200 human datasets and 80 mouse datasets, demonstrated that GNNMF has improved the area of eight metrics radar scores of 4.92% and 6.81% respectively, and found more motifs than did the existing models. Conclusions: In this study, we developed a novel model named GNNMF for finding multiple ATAC-seq motifs. GNNMF built a multi-view heterogeneous graph by using ATAC-seq sequences, and utilized background coexisting probability and the iterloss to find different lengths of ATAC-seq motifs and optimize the parameter sets. Compared to existing models, GNNMF achieved the best performance on TFBS prediction and ATAC-seq motif finding, which demonstrates that our improvement is available for ATAC-seq motif finding. [ABSTRACT FROM AUTHOR]

Previous studies on environmental restorative effects have mainly focused on visual landscapes, and less on the influence of soundscapes on restorative, but soundscapes play a crucial role in restorative environments, especially rural soundscapes, but there is insufficient existing theoretical evidence on the subject. Therefore, this study aims to investigate the influence of Rural Soundscape Perception on Environmental Restoration Perception, and introduces two affective variables, tourism nostalgia and place attachment, to explore the mechanism of Rural Soundscape Perception on Environmental Restoration Perception, as well as the moderating role of the number of trips is also discussed. Based on the theory of restorative environment, this study took the Taohuayuan Scenic Spot in Changde, Hunan Province, China, as the case site, and selected the rural soundscape in the area as the research object; a total of 506 valid data were collected through questionnaire surveys, and structural equation modeling was used to validate the collected data. It was found that rural soundscape perception had a significant positive effect on tourism nostalgia, place attachment, and environmental restoration perception. The results also showed that tourism nostalgia and place attachment mediated the relationship between rural soundscape perception and environmental restoration perception. Additionally, the results revealed that the number of trips did not play a moderating role in the structural relationship between rural soundscape perception and environmental restoration perception. Last, the results of the study shed light on the complex influence path of "rural soundscape perception→tourism nostalgia→place attachment→environmental restoration perception", which provides a new perspective for understanding the mechanism of the rural environment to people's health, and also has a certain guiding significance for the landscape planning of rural tourism sites. [ABSTRACT FROM AUTHOR]

Recall of natural environments evokes human psychophysiological response, there is a lack of systematic, comprehensive analysis in existing research. Moreover, the limited experimental conditions lead to various laboratory research, and more field studies are needed. Employing the field research design and relative environmental psychology methods, this research investigates physical and psychological indexes changes of 60 Chinese university students aged 19–25, which include positive affect (PA), negative affect (NA), heart rate (HR), heart-rate variability (HRV), concentration (Pa), and relaxation (Pm), and regards the Zhangjiajie National Forest Park in China as the experimental site. This study evaluates the psychophysiological effects of the natural forest environment on participates and explores the overall psychophysiological changes, and verifies the positive effect of the natural forest environment on university students. The main findings indicated that the natural forest environment was beneficial for increasing positive affect, decreasing negative affect, affecting HR, and increasing HRV, Pa and Pm. This study adds some basic evidence to a growing theoretical literature emphasizing the role of natural forest environment in psychophysiological restoration. [ABSTRACT FROM AUTHOR]

The rotational spectroscopic properties of reflection-asymmetric nuclei investigated by the reflection-asymmetric axial or triaxial particle rotor model are briefly reviewed. The status of observations of the alternated parity bands in even–even nuclei and the parity doublet bands in odd- A and odd–odd nuclei for the A ∼ 2 2 0 mass region are summarized. The reflection-asymmetric axial particle rotor model has been used to systematically describe the parity doublet bands of the odd- A nuclei in this region. With the triaxial degree of freedom included, the reflection-asymmetric triaxial particle rotor model shows the ability to study the multiple chiral doublet bands with octupole correlations and explore the possible chirality-parity quartet bands. [ABSTRACT FROM AUTHOR]

Stable and radiogenic isotopes represent powerful tools for reconstructing ecological and environmental patterns in ancient ecosystems. The Cretaceous of North America preserves a diverse record of fossil vertebrates well‐suited to analysis using these proxies, contained within many well‐sampled and stratigraphically well‐characterized intervals. Multiple hypotheses have been offered to explain the diverse assemblages of megaherbivores that co‐occurred in the relatively restricted available landmass here, including various forms of niche‐partitioning related to habitat preference, dietary specialization and feeding height stratification. Here we analyse the 87Sr/86Sr, δ13C and δ18O of bioapatite samples obtained from a range of herbivores, faunivores and endemic taxa, from a spatiotemporally‐constrained and intensively‐sampled site in the upper Oldman Formation, to test if megaherbivores partitioned their niches based on spatial patterns of occupation and resource‐use. We also compare measured strontium values to regional 87Sr/86Sr data to assess biogeographical range sizes, habitat breadth and migration potential. We find that hadrosaurs had broad ranges, whereas ankylosaurs and ceratopsids were more spatially restricted. The 87Sr/86Sr ranges of hadrosaurs are much wider and do not overlap with those of other ornithischians, potentially related to dietary differences driven by a combination of feeding height‐stratification and habitat breadth differences. Ankylosaurs and ceratopsids overlapped extensively in 87Sr/86Sr, δ13C and δ18O, indicating overlap in the same habitats and intake of similar resources, and suggesting more complex spatiotemporal variation in resource‐use patterns, fine‐scale dietary differences, and/or sufficient resource‐availability to reduce the degree of competition given this theoretical niche overlap. Additional analyses integrating ecomorphological proxies may elucidate these patterns further. [ABSTRACT FROM AUTHOR]

Identifying cis -regulatory motifs from genomic sequencing data (e.g. ChIP-seq and CLIP-seq) is crucial in identifying transcription factor (TF) binding sites and inferring gene regulatory mechanisms for any organism. Since 2015, deep learning (DL) methods have been widely applied to identify TF binding sites and predict motif patterns, with the strengths of offering a scalable, flexible and unified computational approach for highly accurate predictions. As far as we know, 20 DL methods have been developed. However, without a clear and systematic assessment, users will struggle to choose the most appropriate tool for their specific studies. In this manuscript, we evaluated 20 DL methods for cis -regulatory motif prediction using 690 ENCODE ChIP-seq, 126 cancer ChIP-seq and 55 RNA CLIP-seq data. Four metrics were investigated, including the accuracy of motif finding, the performance of DNA/RNA sequence classification, algorithm scalability and tool usability. The assessment results demonstrated the high complementarity of the existing DL methods. It was determined that the most suitable model should primarily depend on the data size and type and the method's outputs. [ABSTRACT FROM AUTHOR]

Motivation Transcription factor binding sites (TFBSs) prediction is a crucial step in revealing functions of transcription factors from high-throughput sequencing data. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) provides insight on TFBSs and nucleosome positioning by probing open chromatic, which can simultaneously reveal multiple TFBSs compare to traditional technologies. The existing tools based on convolutional neural network (CNN) only find the fixed length of TFBSs from ATAC-seq data. Graph neural network (GNN) can be considered as the extension of CNN, which has great potential in finding multiple TFBSs with different lengths from ATAC-seq data. Results We develop a motif predictor called MMGraph based on three-layer GNN and coexisting probability of k-mers for finding multiple motifs from ATAC-seq data. The results of the experiment which has been conducted on 88 ATAC-seq datasets indicate that MMGraph has achieved the best performance on area of eight metrics radar score of 2.31 and could find 207 higher-quality multiple motifs than other existing tools. Availability and implementation MMGraph is wrapped in Python package, which is available at https://github.com/zhangsq06/MMGraph.git Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Mechanical properties of fiber-reinforced polymer rebar and bond behavior between the fiber-reinforced polymer rebar and concrete are highly related to rib parameters, including rib depth and rib spacing. Therefore, rib parameters should be taken into account when fiber-reinforced polymer bars are used as the structure reinforcement. In this article, the tensile properties of glass-fiber-reinforced polymer rebars with different rib depths and rib spacings are tested. The influences of different rib depths and rib spacings on the bond behavior between glass-fiber-reinforced polymer rebar and concrete are investigated by pull-out test. Experimental results show that the rib depth has a distinctive effect on the ultimate tensile strength, elastic modulus, and ultimate elongation of glass-fiber-reinforced polymer rebar. The tensile strength and elastic modulus of glass-fiber-reinforced polymer rebar with shallow rib are remarkably higher than those of glass-fiber-reinforced polymer bars with deep rib. However, compared with the glass-fiber-reinforced polymer bars with shallow rib, the glass-fiber-reinforced polymer bars with deep rib contribute larger bond strength with concrete. Besides, the bond strength and basic anchorage length are predicted by taking rib depth and rib spacing into account. A modified Bertero–Popov–Eligehausen model is adopted to simulate the bond stress–slip behavior, and the ascending branch of bond stress–slip curve expressed by rib depth and rib spacing is also proposed. The calculated results are in good agreement with the test ones. [ABSTRACT FROM AUTHOR]

Hominin-animal interactions at Pleistocene archaeological sites have been the main subject of research during human evolution. However, in contrast to that of ungulates, little is known about the evidence of human processing of carnivore species in this time interval of China. In this paper, we present the first case report of an interactive relationship between carnivore species and hunter-gathers in Pleistocene China, based mainly on a detailed taphonomic study of the faunal remains from Shuidonggou Locality 7. It seems highly probable that hominins butchered some individuals of carnivores and roasted bone elements with adhering meat at the site; whereas it's equally feasible that these animals were exploited by hominins mainly for their pelt or fur. In either way, evidence from the site indicates novel strategies in adaptive behaviors adopted by Late Pleistocene foragers in harsh environments of Northwest China. [ABSTRACT FROM AUTHOR]

Scholars have long recognized the importance of organic artifacts to an improved understanding of the economic and social behavior of Palaeolithic hominins. However, in contrast to archaeological studies in other parts of the world, osseous industries from China have received only limited attention. As one of the first steps aiming at tipping this balance, the current paper examines, therefore, a shaped boar tusk—one particular element of hunter-gatherers' tool kit at Shuidonggou Locality 12 (SDG12). Morphological and metrical comparisons of the tusk with both paleontological specimens and bone artifacts from the same site demonstrate that wear pattern on one of the dentin surfaces of the tooth is not significant different from occlusal attritions in living animals, while linear striations on the other dentin facet are most probably artificial grinding marks formed by prehistoric toolmakers in attempts to manufacture a scraper. The tusk specimen from SDG12 represents the first evidence of a ground tooth in Upper Palaeolithic China. The current study indicates that hominins in Shuidonggou area had achieved a deepened understanding of physical properties of osseous material available in environs and ultimately broadened their range of raw material selection by adding a particular element to the inventory of subsistence tools. [ABSTRACT FROM AUTHOR]

Information on Palaeolithic bone technology from China is sparse. Here we present the results of a techno-functional analysis of a bone tool assemblage recovered from Shuidonggou Locality 12 (SDG12), layer 11, Northern China, dated to c. 12-11 cal ka BP. Six bone tool artefact types are identified: wedges, awls, spear points, a knife handle, a possible sewing implement, and a notched carpal. Two other artefacts could not be attributed to a specific type. The artefacts are made of Procapra przewalsikii , Lepus sp., Sus sp., Equus przewalskii , and unidentifiable bone fragments from medium/large size mammals. At least three methods are used to extract blanks: percussion of altered limb bones, longitudinal splitting of Sus sp. canine and large rib, and probably, the groove-and-splinter technique. Grinding and scraping are the dominant shaping techniques together with grooving, notching, polishing, drilling, flaking, and retouching. Tool type variability and function fit the hypothesis according to which the SDG12 and similar sites would be residential camps in which hunter-gatherers produced artefacts enabling them to cope with cold environmental conditions. Our results, however, indicate that not all bone tools match the expectations associated with a serial specialist production. Expedient wedges and awls may have been produced by any member of the group, and whenever the need arose. The SDG12 bone tool assemblage provides a significant contribution to our knowledge about hunter-gatherer adaptations to the Tardiglacial environments of Northern China. [ABSTRACT FROM AUTHOR]

Evidence for "controlled use of fire" by Homo erectus pekinensis at Zhoukoudian Locality 1 was initially discovered in the early 1930s and was widely accepted as the earliest such record in human evolutionary history for more than half a century. However, since the mid-1980s, this evidence has been questioned. Some of the questions were based on new research results, including geochemical and taphonomic studies conducted in the 1990s. Others are hypothetical and to some extent stem from a theoretical shift in ideas about early hominin subsistence capabilities, including hunting big game and using fire. Limited access to Chinese archaeological collections and literature, limited geological sampling, and postdepositional disturbance might all contribute to the results of these recent investigations. A thorough review of original field notes, excavation reports, and research papers leads to the conclusion that fossils, cultural materials, and traces of fire use in certain horizons at the site are abundant, unambiguous, and mutually supportive. New field investigations and laboratory analyses at Locality 1, ongoing since 2009, have yielded new evidence that indicates that Layer 4 contains clear-cut evidence for in situ use of fire. Future research may well reveal similar evidence for Layers 8-9 and 10, potentially resolving this ongoing debate comprehensively. [ABSTRACT FROM AUTHOR]

High sulfur anthracite has high research value and application prospects in the preparation of carbon adsorbent due to its excellent coal quality conditions, but the pore structure changes and sulfur migration dynamics in the preparation process are not clear. In this paper, using SEM, pore structure analysis, Raman, FTIR and XPS, the feasibility of preparing carbon adsorbent from high-sulfur coal blending was analyzed from the perspective of apparent morphology, pore structure parameters, graphite crystal structure, and functional groups and content, while the occurrence form of sulfur in carbon adsorbent was explored. The results showed that the carbon adsorbent prepared from high-sulfur anthracite was mainly microporous, and the specific surface area was up to 1103.23 m2/g, which was the highest among the known high-sulfur coal materials. The degree of disorder of raw coal and the size of graphite crystal particles synergistically formed a rich pore structure. Sulfur in coal mainly exists in the form of thiophene and sulfide. An increase in the bituminous coal proportion promotes the transformation of carbon adsorbent to an alkaline environment. Thiophene sulfur is removed at 900°C, and sulfide is transformed into sulfoxide and sulfone under steam oxidation and Fe catalysis. [ABSTRACT FROM AUTHOR]

Seasonality study of Paleolithic archaeological faunal assemblages is important for reconstructing modes of animal death and ancient hominin strategies for prey acquisition. The dental cementum of animal teeth records the season of an individual animal in which it died, providing the necessary evidence for determining any patterns in season of death. This article presents the procedure and preliminary results of the application of cementum incremental analysis to equid teeth, which comprise the dominant component of the fauna from the Xujiayao Site-an early Late Pleistocene archaeological site in China. Results show multi-seasonal use in both the upper and lower layers of this site. Furthermore, attention is given to the method's future application in seasonality studies at Paleolithic archaeological sites in China. [ABSTRACT FROM AUTHOR]

During the climatic fluctuations in the late Late Pleistocene, hominins in China had experienced some significant changes and adaptations in terms of subsistence strategies. Based on the zooarchaeological analyses of the faunal remains from the Shuidougou site of North China and the Ma'anshan site of South China, the present study demonstratively indicates that the broad-spectrum diet and its closely-related resource intensification for hominins were already at their places roughly at 33-35 cal ka BP. Compared to hominins of earlier period, who would have preferentially exploited large and medium-sized ungulates, hunter-gathers at later period had otherwise incorporated more small-sized animals (especially the quick ones, such as birds and hares) into their diet. Meanwhile, hominins of the later time had also greatly accelerated extractions and exploitations of the nutritional yields from the large and medium-sized animals. However, it seems clear from the current study that there was significant difference regarding the potential mechanisms for the broad-spectrum adaptations of hominins in the late Late Pleistocene of China. [ABSTRACT FROM AUTHOR]

Re-excavation of the Peking man site at Zhoukoudian was initiated in 2009. A taphonomic analysis of the skeletal remains of Cervus ( Sika ) grayi , a dominant species from Layer 3 of the extant West Section of the site strongly negates a role played by hominins in the accumulation and modification of the bones. Instead, it is argued here that some individuals of this medium-sized deer species were probably trapped in the cave by accident and eventually preserved in situ in the Quaternary sediments. The virtual absence of stone artifacts and human skeletal remains from the 2009–2010 field seasons has further strengthened this conclusion. Bearing in mind evidence of a series of cave collapse episodes, we tentatively propose that the cave morphology during the formation of Layer 3 at the West Section was probably inhospitable to Homo erectus pekinensis . [ABSTRACT FROM AUTHOR]

Here we present the results of a techno-functional analysis of 17 bone tools recovered from strata 6, 5 and 3 of the Palaeolithic site of Ma'anshan Cave, Guizhou Province, southern China. Stratum 6, dated to c. 35 cal kyr BP, has yielded three sharp awls. From Stratum 5, dated to c. 34 cal kyr BP, come six probable spear points, awls and a cutting tool. Separated from these layers by a sterile horizon, Stratum 3, dated 23 cal kyr BP to 18 cal kyr BP, has yielded barbed points of two types. Bone tools were shaped by scraping, grinding, and in strata 5 and 3, finished by polishing. Ma'anshan Cave records the oldest formal bone tools from China, and amongst the oldest known evidence of indisputable barbed point manufacture outside Africa. Change in the hunting toolkit between strata 5 and 3 may indicate a shift in prey preference from medium to small size mammals and fish, which needs to be verified by supplementary analyses. The significance of this evidence is discussed in the context of what is known about the origin of bone tool technology in Africa and Eurasia. [ABSTRACT FROM AUTHOR]

Promoters are DNA non-coding regions around the transcription start site and are responsible for regulating the gene transcription process. Due to their key role in gene function and transcriptional activity, the prediction of promoter sequences and their core elements accurately is a crucial research area in bioinformatics. At present, models based on machine learning and deep learning have been developed for promoter prediction. However, these models cannot mine the deeper biological information of promoter sequences and consider the complex relationship among promoter sequences. In this work, we propose a novel prediction model called PromGER to predict eukaryotic promoter sequences. For a promoter sequence, firstly, PromGER utilizes four types of feature-encoding methods to extract local information within promoter sequences. Secondly, according to the potential relationships among promoter sequences, the whole promoter sequences are constructed as a graph. Furthermore, three different scales of graph-embedding methods are applied for obtaining the global feature information more comprehensively in the graph. Finally, combining local features with global features of sequences, PromGER analyzes and predicts promoter sequences through a tree-based ensemble-learning framework. Compared with seven existing methods, PromGER improved the average specificity of 13%, accuracy of 10%, Matthew's correlation coefficient of 16%, precision of 4%, F1 score of 6%, and AUC of 9%. Specifically, this study interpreted the PromGER by the t-distributed stochastic neighbor embedding (t-SNE) method and SHAPley Additive exPlanations (SHAP) value analysis, which demonstrates the interpretability of the model. [ABSTRACT FROM AUTHOR]

Based on optimal foraging theory, prey animals from the Shuidonggou Locality 12 (SDG12) are divided into three types according to body size and defense traits: high-ranked large game, low-ranked slow small game, and low-ranked fast small game. Application of the Reciprocal of Simpson's Index to the three types of animals from SDG12 yields a relatively high level of evenness, which implies a broader meat diet of the SDG12 hominids. Compared to values of taxonomic evenness from Mediterranean sites, it is suggested that this dietary expansion probably resulted from the occurrence of the Broad Spectrum Revolution rather than from climatic changes in the Shuidonggou area. Comparative studies between the Natufian phases in Hayonim Cave and the SDG12 validate this argument. [ABSTRACT FROM AUTHOR]

More than ten thousands of bone fragments were recovered from the Lingjing site, Henan Province during 2005 and 2006. In this paper, through the quantification and statistical analyses of the skeletal elements of the two predominant species in this assemblage, aurochs ( Bos primigenius) and horse ( Equus caballus), the differential influences and weights of a variety of taphonomic agencies in the formation of the assemblage are assessed respectively. Compared to the natural agencies, hominid hunting and the subsequent disarticulation, slaughtering, and their transport of the bone elements of the prey species are the main factors accounting for the formation of the present assemblage. More importantly, this study initiatively identifies hominid's differential treatment of the bones of aurochs and horse in the Paleolithic record of East Asia and demonstrably suggests that hominids at the site have already practiced sophisticated hunting techniques and subsistence strategies and may be quite familiar with the ecological and anatomical characteristics and nutritional values of the large-sized prey animals and can accordingly take different processing and handling strategies at the hunting site. [ABSTRACT FROM AUTHOR]

More than ten thousand bone fragments were recovered from the Lingjing site, Henan Province, during 2005 and 2006. A taphonomic analysis of the faunal remains strongly indicates that hominids have a dominant role in the accumulation and modification of the assemblage. Based on the taphonomic and zooarcheological characteristics of the animal remains, including species richness, mortality patterns, skeletal element profiles, and bone surface-modifications, and on the local ecology, we suggest that the Lingjing site is a Middle Paleolithic kill-butchery site rather than a home base for early humans. The presence of large numbers of stone artifacts may therefore signify a strong sense of planning and farsightedness in the subsistence strategies of early human groups. The Lingjing site is presently the only taphonomically-identified, Middle Paleolithic kill-butchery site known in North China. [ABSTRACT FROM AUTHOR]

This paper presents the results of a detailed study of mortality profiles of the large herbivores from the Middle Palaeolithic (MP) bone assemblage of the Lingjing Xuchang Man Site, Henan Province. Based on the analysis of the crown heights of fossil teeth from this assemblage, we come to a conclusion that aurochs (Bos primigenius) and horse (Equus caballus) are the major prey species in this assemblage and the age structures of these animals can be best described as the "prime-dominated pattern". This study confirmed the well-established notions at many Middle and Upper Palaeolithic sites across Eurasia and Africa that MSA/MP foragers were fully effective in hunting aggressive prey species, particularly aurochs and horse. This find indicates that the hunting behaviors and subsistence strategies were not significantly different between MP and UP (the Upper Palaeolithic) humans in East Asia and hence suggests the early emergence of the modern human behaviors in this area. [ABSTRACT FROM AUTHOR]

Abstract: The Tianyuan cave near Zhoukoudian is among the most special localities in North China for its many porcupine gnawing marks on the bones, as is often the case acknowledged only in South China. But porcupines did not gnaw all the bones, that is gnawing is selective. Skulls, mandibles, tooth roots and long bones are frequently gnawed. The short bones are almost free from gnawing. The selection indicates that, for porcupines, bone gnawing is not only a necessity for attrition of incisors, but also a process of extracting nutrients from the marrow. Additionally, the porcupine gnawing marks can also be employed to determine the provenance of the fossils that were discovered by the local people before the systematic excavation. Those bearing porcupine tooth marks only appear in the upper assemblage. The other significance of the gnawing marks is to infer the habitant of the cave. The bones from the human fossil bearing layer have few tooth marks, which may represent a period of human occupation of the cave. In the upper assemblage, the gnawing marks appear frequently, it may indicate that porcupine and other rodents lived in the cave during this time span. [Copyright &y& Elsevier]

Recombinant antibodies, especially single-chain antibody fragment (scFv), can be applied as detection reagents and even substitute for some reagents used in immunoassays. For scFv fragments, there is no such universal system available up to now. We have constructed vectors for the convenient, rapid expression of a novel compact antibody composed of anti-B-cell-activating factor of the TNF family (BAFF) scFv and the Fc portion (the hinge region, CH2, and CH3 domains) of the human IgG1 in Escherichia coli. After expression in bacteria as inclusion bodies, the recombinant antibody was purified and refolded in vitro. The scFv-Fc antibody was demonstrated to retain high binding affinity to antigen, including membrane-bound BAFF and soluble BAFF, and to possess some human IgG crystallizable fragment domain functions, such as human complement C1q and protein A binding. Both size-exclusion high-performance liquid chromatography column analysis and Western blotting of proteins subjected to nonreducing sodium dodecyl sulfate polyacrylamide gel electrophoresis suggested that scFv-Fc antibody is homodimeric with relative molecular mass of 110 kDa. These findings suggest that the compact antibody may be useful in diagnostic application for the prediction of BAFF relevant to autoimmune diseases in human. [ABSTRACT FROM AUTHOR]

Abstract: A fusion between gene encoding fluoresce-enhanced green fluorescent protein variant (EGFP) and soluble domain of human B-cell-activating factor of the TNF family (sBAFF) was constructed and expressed in Escherichia coli. The EGFP/sBAFF had an apparent molecular weight of 45 kDa and was detected with anti-hsBAFF and anti-His6 monoclonal antibodies. After being purified by immobilized metal affinity chromatography (IMAC), the fusion protein retained similar fluorescence spectra to those of EGFP. Biological activity assays showed the EGFP/sBAFF as well as sBAFF could co-stimulated human B lymphocyte proliferation in vitro. In addition, EGFP/sBAFF has shown specific binding to BAFF receptors positive-cells and the stained cells could be analyzed with flow cytometry. Thus, the fusion protein represents a readily obtainable source of biologically active sBAFF that may prove useful in further studies on BAFF and its receptors. [Copyright &y& Elsevier]

Background: Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene regulation. Deep learning technologies including convolutional neural networks (CNNs) and graph neural networks (GNNs), have achieved success in finding ATAC-seq motifs. However, CNN-based methods are limited by the fixed width of the convolutional kernel, which makes it difficult to find multiple transcription factor binding sites with different lengths. GNN-based methods has the limitation of using the edge weight information directly, makes it difficult to aggregate the neighboring nodes' information more efficiently when representing node embedding. Results: To address this challenge, we developed a novel graph attention network framework named MMGAT, which employs an attention mechanism to adjust the attention coefficients among different nodes. And then MMGAT finds multiple ATAC-seq motifs based on the attention coefficients of sequence nodes and k-mer nodes as well as the coexisting probability of k-mers. Our approach achieved better performance on the human ATAC-seq datasets compared to existing tools, as evidenced the highest scores on the precision, recall, F1_score, ACC, AUC, and PRC metrics, as well as finding 389 higher quality motifs. To validate the performance of MMGAT in predicting TFBSs and finding motifs on more datasets, we enlarged the number of the human ATAC-seq datasets to 180 and newly integrated 80 mouse ATAC-seq datasets for multi-species experimental validation. Specifically on the mouse ATAC-seq dataset, MMGAT also achieved the highest scores on six metrics and found 356 higher-quality motifs. To facilitate researchers in utilizing MMGAT, we have also developed a user-friendly web server named MMGAT-S that hosts the MMGAT method and ATAC-seq motif finding results. Conclusions: The advanced methodology MMGAT provides a robust tool for finding ATAC-seq motifs, and the comprehensive server MMGAT-S makes a significant contribution to genomics research. The open-source code of MMGAT can be found at https://github.com/xiaotianr/MMGAT, and MMGAT-S is freely available at https://www.mmgraphws.com/MMGAT-S/. [ABSTRACT FROM AUTHOR]

A practical electrochemical strategy for the direct synthesis of arenesulfonyl fluorides from industrial feedstock nitroarenes is described. The key to success lies in using a cheap ionic liquid N-methylimidazolium p-toluenesulfonate ([Mim]TolSO3) as an effective additive and electrolyte to facilitate the selective reduction of nitroarenes to the corresponding aniline intermediate, promoting the desired fluorosulfonylation with broad functional group tolerance under mild conditions. [ABSTRACT FROM AUTHOR]

The nuclear Chirality-Parity (ChP) violation, a simultaneous breaking of chiral and reflection symmetries in the intrinsic frame, is investigated with a reflection-asymmetric triaxial particle rotor model. A new symmetry for an ideal ChP violation system is found and the corresponding selection rules of the electromagnetic transitions are derived. The fingerprints for the ChP violation including the nearly degenerate quartet bands and the selection rules of the electromagnetic transitions are provided. These fingerprints are examined for ChP quartet bands by taking a two- j shell h 11 / 2 and d 5 / 2 with typical energy spacing for A = 130 nuclei. [ABSTRACT FROM AUTHOR]

The deformed relativistic Hartree–Bogoliubov theory in continuum (DRHBc) has been proved as one of the best models to probe the exotic structures in deformed nuclei. In DRHBc, the potentials and densities are expressed in terms of the multipole expansion with Legendre polynomials, the dependence on which has only been touched for light nuclei so far. In this paper, taking a light nucleus 2 0 Ne and a heavy nucleus 2 4 2 U as examples, we investigated the dependence on the multipole expansion of the potentials and densities in DRHBc. It is shown that the total energy converges well with the expansion truncation both in the absence of and presence of the pairing correlation, either in the ground state or at a constrained quadrupole deformation. It is found that to reach the same accuracy of the total energy, even to the same relative accuracy by percent, a larger truncation is required by a heavy nucleus than a light one. The dependence of the total energy on the truncation increases with deformation. By decompositions of the neutron density distribution, it is shown that a higher-order component has a smaller contribution. With the increase of deformation, the high-order components get larger, while at the same deformation, the high-order components of a heavy nucleus play a more important role than that of a light one. [ABSTRACT FROM AUTHOR]

Abstract When, how, and following which paths hominins created the innovations that allowed them to colonize regions of the planet that were not suited to their thermal physiology is still a matter of inquiry. In this paper, we elaborate a theoretical framework to investigate the origin and diversification of bone needles, summarize the evidence for their emergence, create a large database of their morphometric and stylistic characters, and present results of the study of an exceptionally well-preserved collection of needles from Shuidonggou Locality 12 (SDG12), a site located in the Ningxia Hui Autonomous Region, Northern China, dated to ca. 11.2 ka BP. Bone needles are reported from 271 sites and 355 archaeological layers. Revision of the evidence shows they represent an original cultural innovation that emerged in Eurasia between 45–40 ka BP. Size differences between the earliest known specimens, found in Siberia and China, indicate needles may have been invented independently in these two regions. Needles from Eastern Europe may represent either an independent invention or a geographic extension of earlier Siberian and Caucasian sewing traditions. In Western Europe, needles appear during the Solutrean. The wider size range characteristic of Magdalenian specimens supports the idea that needles of different sizes were used in a variety of tasks. In China, the robust sub-circular needles found at sites dated between 35–25 ka BP are followed, between 26–23 ka BP, by small flat needles, which may represent an innovation associated with the microblades/microcores toolkit. At SDG12, technological, functional, and morphometric analyses of finished needles and manufacturing by-products identify two previously undetected reduction sequences for the production of needles of different size and, probably, function. The bone needles found at Paleoindian sites are the smallest and reflect a never previously achieved mastery in the production of such tools. [ABSTRACT FROM AUTHOR]

Liquefaction residue of Heishan bituminous coal (HLR) was subject to two hydroconversion reactions under 5 MPa initial pressure of hydrogen at 300°C for 3 h, without catalyst and with acid supported catalyst (ASC), respectively. The reaction products were analyzed with gas chromatography/mass spectrometer (GC/MS). The results show that 222 organic compounds were detected totally in the products and they can be divided into alkanes, aromatic hydrocarbons (AHCs), phenols, ketones, ethers, and other species (OSs). The yield of hydroconversion over the ASC is much higher than that without catalyst. The most abundant products are aromatic hydrocarbons in the reaction products from both catalytic and noncatalytic reactions of HLR. The yield of aromatic hydrocarbons in the reaction product from hydroconversion with the ACS is considerably higher than that from hydroconversion without a catalyst. [ABSTRACT FROM AUTHOR]

Plants play a very important role in landscape construction. In order to explore whether different living environment will affect people's preference for the structural features of plant organs, this study examined 26 villagers and 33 college students as the participants, and pictures of leaves, flowers and fruits of plants as the stimulus to conduct eye-tracking and EEG detection experiments. We found that eye movement indicators can explain people's visual preferences, but they are unable to find differences in preferences between groups. EEG indicators can make up for this deficiency, which further reveals the difference in psychological and physiological responses between the two groups when viewing stimuli. The final results show that the villagers and the students liked leaves best, preferring aciculiform and leathery leaves; solitary, purple and capitulum flowers; and medium-sized, spathulate, black and pear fruits. In addition, it was found that the overall attention of the villagers when watching stimuli was far lower than that of the students, but the degree of meditation was higher. With regard to eye movement and EEG, the total duration of fixations is highly positively correlated with the number of fixations, and the average pupil size has a weak negative correlation with attention. On the contrary, the average duration of fixations has a weak positive correlation with meditation. Generally speaking, we believe that Photinia×fraseri, Metasequoia glyptostroboides, Photinia serratifolia, Koelreuteria bipinnata and Cunninghamia lanceolata are superior landscape building plants in rural areas and on campuses; Pinus thunbergii, Myrica rubra, Camellia japonica and other plants with obvious features and bright colours are also the first choice in rural landscapes; and Yulania biondii, Cercis chinensis, Hibiscus mutabilis and other plants with simple structures are the first choice in campus landscapes. This study is of great significance for selecting plants for landscape construction and management according to different environments and local conditions. [ABSTRACT FROM AUTHOR]

One of the key factors to improve electrochemical properties is to find exceptional electrode materials. In this work, the nickel-cobalt layered double hydroxide (CNT@CoS/NiCo-LDH) with the structure of a hollow nanocage was prepared by etching CNT@CoS with zeolitic imidazolate framework-67 (ZIF-67) as a template. The results show that the addition of nickel has a great influence on the structure, morphology and chemical properties of materials. The prepared material CNT@CoS/NiCo-LDH-100 (C@CS/NCL-100) inherited the rhombic dodecahedral shape of ZIF-67 well and the CNTs were evenly interspersed among the rhombic dodecahedrons. The presence of CNTs improved the conductivity and surface area of the samples. The C@CS/NCL-100 demonstrates a high specific capacitance of 2794.6 F·g−1 at 1 A·g−1. Furthermore, as an assemble device, the device of C@CS/NCL-100 as a positive electrode exhibits a relatively high-energy density of 35.64 Wh·kg−1 at a power density of 750 W·kg−1 Further, even at the high-power density of 3750 W·kg−1, the energy density can still retain 26.38 Wh·kg−1. Hence, the superior performance of C@CS/NCL-100 can be ascribed to the synergy among CNTs, CoS and NiCo LDH, as well as the excellent three-dimensional structure obtained by used ZIF-67 as a template. [ABSTRACT FROM AUTHOR]

Research undertaken over the last three decades has substantially transformed our understanding of avian exploitation in the prehistory. We now know that, as early as the European Middle Palaeolithic, birds were introduced in the cultural adaptive systems of prehistoric human groups for their meat, their bones for the manufacture of tools and their feathers either for symbolic and/or technological purpose. However, studies on avian exploitation mainly focus on the European and Levantine archaeological record, leaving vast regions of the Old World undocumented. Here we present the study of the avian assemblage recovered at Shuidonggou Locality 12, a c. 10.5 ka site from Northern China. Our zooarchaeological, taphonomic and technological approach shows clear difference in skeletal element representation by order as well as in the anthropogenic modifications present on these remains. More than ten taxa of birds are identified. Galliformes dominate the avian assemblage followed by Falconiformes and Strigiformes. While Galliformes appear to have been hunted for their meat, raptor wings were likely collected on the landscape and their feathers removed, likely to be used as ornament alongside stone beads. Furthermore, some bird bone may have been used in the manufacture of bone tools. Contextual evidence from the associated bone tool assemblage suggests nets and/or snares may have been used to catch the birds. Finally, the SDG12 visitors may have used projectiles equipped with blunt points to selectively hunt male pheasants. [ABSTRACT FROM AUTHOR]

The process of the Middle to Upper Palaeolithic transition has been hotly debated for many years, but East Asia has not been a significant part of that debate until recently. The Shuidonggou (SDG) site complex, yielding Initial Upper Paleolithic (IUP) blade-rich assemblages, has been given more and more importance since its discovery and first excavation in the 1920s. This paper presents a specific study of the archaeological remains yielded by three years of systematic, modern excavations at Shuidonggou locality 7 (SDG7), an important locality within the SDG site cluster. Although the archaeological deposits of SDG7 had undergone some hydraulic disturbances, detailed lithic analyses identified two distinct technological systems. One is termed autochthonous and is a predominantly flake-tool technology, and the other is an allochthonous Levallois-like technology which coexisted within the same Lower Concentrated Layer for some time before disappearing, implying the potential existence of technological diffusion and interaction between the two different technologies. The technological variability and change suggested by the evidence from SDG7 reveal a kind of cultural mosaic, rather than the replacement of one lithic technology by another. We believe the new round of excavations and research in the SDG site will provide more evidence for answering key questions about the process of the Middle–Upper Paleolithic transition in North China. [ABSTRACT FROM AUTHOR]

Highlights: [•] Dynamic load economic dispatch with wind power (DLEDW) model is established. [•] Markov chains combined with scenario analysis method are used to predict wind power. [•] Chance constrained technique is used to simulate the impacts of wind forecast error. [•] Improved artificial physical optimization algorithm is proposed to solve DLEDW. [•] Heuristic search strategies are applied to handle the constraints of DLEDW. [Copyright &y& Elsevier]

Highlights: [•] Second-order cone programming (SOCP) is proposed to solve unit commitment. [•] Unit commitment is transformed to SOCP model with tight lower bounds. [•] Conic quadratic constraints representation of UC problem is suggested. [•] Effectiveness of the proposed method is verified with different test systems. [•] SOCP is expanded to solve large-scale mixed integer nonlinear optimization problem. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome virus is one of the main pathogens threatening the global pig industry, and there is still a lack of effective therapeutic drugs. Sanggenon C is a flavanone Diels-Alder adduct compound extracted from the root bark of the mulberry genus, which has blood pressure-reducing, anti-atherosclerotic, anti-oxidative, and anti-inflammatory effects. In our previous study, Sanggenon C was confirmed to significantly inhibit PRRSV replication in vitro. However, its antiviral potential to inhibit PRRSV infection in vivo has not been evaluated in piglets. Here, the antiviral effect of Sanggenon C was evaluated in PRRSV-challenged piglets based on assessments of rectal temperature, viral load, pathological changes of lung tissue and secretion of inflammatory cytokines. The results showed that Sanggenon C treatment relieved the clinical symptoms, reduced the viral loads in the lungs and bloods, alleviated the pathological damage of lung tissue, decreased the secretion of inflammatory cytokines, and shorten the excretion time of virus from the oral and nasal secretions and feces of piglets after PRRSV infection. The results indicated that Sanggenon C is a promising anti-PRRSV drug, which provides a new strategy for the prevention and control of PRRS in clinical practice. • Sanggenon C relieved the clinical symptoms of PRRSV-challenged piglets. • Sanggenon C reduced viral loads in the lungs and bloods of infected piglets. • Sanggenon C alleviated the pathological damage of lung tissues in infected piglets. • Sanggenon C shorten the excretion time of virus from oral and nasal secretions and feces of piglets. [ABSTRACT FROM AUTHOR]

In this paper, cut marks on the long bones of class II sized animals in the Ma'anshann site are studied. Based on the location and frequencies of the long bone cut marks, the distribution characteristics are analyzed as follows: (1) cut mark frequencies in the lower layer (LL) are much higher than those of the upper; (2) in the LL cut mark frequency of the upper limbs is the highest, and that of the middle and lower limbs is lower and the lowest; (3) In the upper layer (UL) the cut mark frequency, does not spread as orderly as in the LL. The data are compared to those of the experiment and it is demonstrated that values of the LL all fall into the experimental 95% confidence intervals, and the cut mark frequencies of the upper, middle and lower limbs coincide with those of the experiment; while the values of the UL are much lower, of which, those of the humerus, femur and radius are out of the intervals, and the frequencies of the upper, middle and lower limbs are far more different from those of the experiment. It implies that the earlier hominids (of the LL) defleshed the limbs of the class II sized animals with stone tools more completely than the later hominids. With the evidence of burning marks, it is suggested that the difference on the roasting behaviors derived the cut mark difference of the Ma'anshan UL and LL. [ABSTRACT FROM AUTHOR]

The Tianyuan Cave is the only human fossil-bearing site containing rich mammalian fossils found in the last decades near Zhoukoudian. Up to now more than 34 specimens of the human body have been recovered, and the mammalian fossils can be put into 29 species. Cervids dominate the fauna, and carnivores are very rare. Based on the primary examination, the human fossils can be attributed to the species Homo sapiens. All the mammalian fossils, except one between tooth of Crocuta belong to the species that still exist today. But some of them are the first records in fossil form north of the Yellow River, such as Arctonyx and Capricornis. Based on the mammalian fauna study, it seems that the Tianyuan Cave can be correlated with the Upper Cave. Sixty-three percent of the species of the mammalian fauna from the Tianyuan Cave are also present in the Upper Cave. The characters of the deposits also share some similarities between the Tianyuan Cave and the Upper Cave; both of them are mainly composed of breccia without cement. The dating using the U-series method on deer tooth samples indicates that the geological age of the new site is around 25 thousand years B.P. This is the first discovery of human sites outside the core area of the Peking Man Site at Zhoukoudian, which throws new light onto this world famous site complex. [ABSTRACT FROM AUTHOR]

Glioma is the main type of malignant brain tumor in adults, and the status of isocitrate dehydrogenase (IDH) mutation highly affects the diagnosis, treatment, and prognosis of gliomas. Radiographic medical imaging provides a noninvasive platform for sampling both inter and intralesion heterogeneity of gliomas, and previous research has shown that the IDH genotype can be predicted from the fusion of multimodality radiology images. The features of medical images and IDH genotype are vital for medical treatment; however, it still lacks a multitask framework for the segmentation of the lesion areas of gliomas and the prediction of IDH genotype. In this paper, we propose a novel three-dimensional (3D) multitask deep learning model for segmentation and genotype prediction (SGPNet). The residual units are also introduced into the SGPNet that allows the output blocks to extract hierarchical features for different tasks and facilitate the information propagation. Our model reduces 26.6% classification error rates comparing with previous models on the datasets of Multimodal Brain Tumor Segmentation Challenge (BRATS) 2020 and The Cancer Genome Atlas (TCGA) gliomas' databases. Furthermore, we first practically investigate the influence of lesion areas on the performance of IDH genotype prediction by setting different groups of learning targets. The experimental results indicate that the information of lesion areas is more important for the IDH genotype prediction. Our framework is effective and generalizable, which can serve as a highly automated tool to be applied in clinical decision making. [ABSTRACT FROM AUTHOR]

Substantial quantities of sediments are known to enter the deep lithosphere at subduction zones, but the extent to which sediments melt and the process involved in sediment contribution to the deep lithosphere are inadequately understood. Vigorous debate continues about whether the subducted sediment component is terrigenous or pelagic and transported as a hydrous melt, an aqueous fluid, or bulk sediment. In this contribution, we conduct an integrated study on a variety of deep-seated xenoliths in the Neogene Hannuoba basalts from the northern margin of the North China Craton. Among these xenoliths, clinopyroxenite xenoliths are compositionally and isotopically distinct. Mineral chemistry shows that the clinopyroxenite xenoliths come from a depth near the MOHO, rather than from the mantle as suggested previously. The clinopyroxenite xenoliths have extremely evolved Sr-Nd-Hf isotopic compositions and are interpreted to have a late Archean protolith age. The extremely low contents of Cr and Ni for the clinopyroxenite xenoliths preclude a magmatic origin. Instead, a metasomatic origin is suggested, which is strongly supported for the clinopyroxenites by the occurrence of hydrous minerals and high contents of large-ion-lithophile elements (K, Rb, Ba, Th and Sr) and light rare earth elements, as well as elevated δ18O (9.9–11.3‰) and light δ26Mg (−1.04‰ to −1.42‰) isotopic compositions. Furthermore, their high high-field-strength element (Nb, Ta, Zr and Hf) contents indicate that the metasomatic agent is a hydrous melt, rather than an aqueous fluid. The metasomatic melts are considered to be derived from a mixed source of sedimentary carbonates and ancient, felsic continental materials. A combination of zircon ages and oxygen isotope data for the clinopyroxenite xenoliths further restricts the timing of metasomatism to the late Paleozoic. Considering the regional tectonic setting, the sediments most likely came from the subducted Paleo-Asian oceanic slab. Thus the Hannuoba clinopyroxenite xenoliths provide direct evidence for melting of the subducted Paleo-Asian oceanic slab sediment and its interaction with the deep lithosphere. The data show that melting of subducted sediments can take place at a much shallower depth than commonly thought and place an independent constraint on future models of slab geotherms. [ABSTRACT FROM AUTHOR]

In western Yunnan, potassic felsic suites with important Cu mineralization have been interpreted as being genetically associated with the Ailao Shan-Red River (ASRR) shear zone. In this paper, we show that the magmatism is unrelated to the shear zone, but shares many characteristics in common with potassic suites along the Jinsha suture to the north and northwest on the northern Tibetan Plateau, representing a magmatic response to the continued India-Asia convergence since the collision in the early Eocene. These felsic suites include syenite, monzogranite porphyries and granite porphyries. We dated 15 representative samples using zircon U-Pb method that gives a tight emplacement age of ~37–35 Ma. On 45 representative samples, we have done bulk-rock major element, trace element and Sr-Nd-Pb isotope analysis. We use these data, together with zircon Hf isotope data and the literature data on potassic mafic suites in the region to discuss the petrogenesis of these rocks. We conclude that the petrogenesis of the felsic potassic suites is most consistent with a scenario of deep (≥ 40 km) melting of thickened crust. The crustal melting is caused by intrusion and underplating of potassic mafic melts derived from melting of metasomatized mantle lithosphere. The mafic potassic suites in the region result from such mantle melts. Mixing of the mafic melts with the felsic melts explains the syenite and monzogranite porphyries and their extended fractional crystallization gives rise to the granite porphyries. The potassic suites along the Jinsha suture, including those from northern Tibet, western Yunnan and Vietnam, share the same tectonic setting during the Eocene-Oligocene. In response to the continued India-Asia convergence, removal of the lower continental lithospheric mantle triggered by Rayleigh-Taylor convective instability induces asthenosphere upwelling, partial melting of the metasomatized mantle lithosphere. We hypothesize that the eastward migration of the potassic magmatism along the Jinsha suture in the period of Eocene-Oligocene results from eastward thickening and removing of the continental lithospheric mantle along the suture, which, in time and space, correlates with the dischronal subduction of the torn Indian continental slab at ca. 52 Ma along the India-Asia collision zone. • The 35-37 Ma potassic suites in western Yunnan result from lower crust melting. • Their varied felsic compositions result from varying extent of fractional crystallization. • The removal of lithospheric mantle along the Jinsha suture was eastward-migrating. [ABSTRACT FROM AUTHOR]

• Cat (Felis catus) BAFF and its receptor BAFF-R were cloned. • csBAFF, EGFP/csBAFF, and cBAFF-R were expressed in E. coli and purified using a Ni2+ column. • csBAFF cellular localization was assessed. • csBAFF promoted B-cell survival in vitro. • Ligand–receptor interaction was assessed. B-cell survival depends on signals induced by binding of B-cell activating factor (BAFF) to its receptor (BAFF-R). In this study, the full-length cDNAs of cat BAFF (cBAFF) and BAFF-R (cBAFF-R) were amplified from the spleen by reverse transcription PCR. The open reading frame of cBAFF cDNA encodes a protein of 285 amino acids containing a predicted transmembrane domain and a furin protease cleavage site, similar to mammalian, avian, and reptile BAFFs. The cBAFF-R gene encodes a 189 amino acid protein. Real-time quantitative PCR analyses revealed that the two genes are predominantly expressed in the spleen. csBAFF, EGFP/csBAFF, and cBAFF-R were efficiently expressed in Escherichia coli BL21 (DE3), as confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting analyses. After purification, the EGFP/csBAFF fusion protein showed a fluorescence spectrum similar to that of EGFP. Confocal laser scanning microscopy showed that EGFP/csBAFF bound to its receptor. In vitro , csBAFF promoted the survival of cat and mouse splenic B cells with/without a priming agent (Staphylococcus aureus Cowan 1, SAC) or anti-mouse IgM. Furthermore, it stimulated the survival of mouse B cells, similar to msBAFF. Recombinant cBAFF-R blocked the function of sBAFF in vitro. These findings indicate that csBAFF plays an important role in the survival of cat B cells and has functional cross reactivity between cats and other mammals, and suggest a role for the BAFF–BAFF-R system in regulating B-cell survival. Therefore, BAFF and BAFF-R show promise for enhancing the immune systems of animals. [ABSTRACT FROM AUTHOR]

Abstract B cell activating factor from the TNF family (BAFF) is implicated in not only the physiology of normal B cells, but also the pathophysiology of aggressive B cells related to malignant and autoimmune diseases. Autophagy plays a crucial role in balancing the beneficial and detrimental effects of immunity and inflammation. However, little is known about whether and how excessive BAFF mediates autophagy contributing to B-cell proliferation and survival. Here, we show that excessive human soluble BAFF (hsBAFF) inhibited autophagy with a concomitant reduction of LC3-II in normal and B-lymphoid (Raji) cells. Knockdown of LC3 not only potentiated hsBAFF inhibition of autophagy, but also attenuated hsBAFF activation of Akt/mTOR pathway, thereby diminishing hsBAFF-induced B-cell proliferation/viability. Further, we found that hsBAFF inhibition of autophagy was Akt/mTOR-dependent. This is supported by the findings that hsBAFF increased mTORC1-mediated phosphorylation of ULK1 (Ser757); Akt inhibitor X, mTORC1 inhibitor rapamycin, mTORC1/2 inhibitor PP242, expression of dominant negative Akt, or knockdown of mTOR attenuated hsBAFF-induced phosphorylation of ULK1, decrease of LC3-II level, and increase of cell proliferation/viability. Chelating intracellular free Ca2+ ([Ca2+] i) with BAPTA/AM or preventing [Ca2+] i elevation using EGTA or 2-APB profoundly blocked hsBAFF-induced activation of Akt/mTOR, phosphorylation of ULK1 and decrease of LC3-II, as well as increase of cell proliferation/viability. Similar effects were observed in the cells where CaMKII was inhibited by KN93 or knocked down by CaMKII shRNA. Collectively, these results indicate that hsBAFF inhibits autophagy promoting cell proliferation and survival through activating Ca2+-CaMKII-dependent Akt/mTOR signaling pathway in normal and neoplastic B-lymphoid cells. Our findings suggest that manipulation of intracellular Ca2+ level or CaMKII, Akt, or mTOR activity to promote autophagy may be exploited for prevention of excessive BAFF-induced aggressive B lymphocyte disorders and autoimmune diseases. Graphical abstract Unlabelled Image Highlights • hsBAFF promotes B-cell proliferation and survival by inhibiting autophagy. • Downregulation of LC3 protein level is critical for hsBAFF inhibition in B cells. • hsBAFF-activated Akt/mTOR signaling represses autophagy via phosphorylating ULK1 (Ser757) in B cells. • hsBAFF inhibits autophagy by activating Ca2+-CaMKII-dependent Akt/mTOR signaling pathway in B cells. [ABSTRACT FROM AUTHOR]

Gamma-interferon-inducible lysosomal thiol reductase (GILT) plays an important role in the processing of major histocompatibility complex (MHC) class II-restricted antigens by catalyzing disulfide bonds reduction. Herein, a GILT homolog (ScGILT) was identified from silver carp. Its open reading frame covers 771 base pairs, encoding a protein of 256 amino acids that possesses GILT signature sequence CQHGX 2 ECX 2 NX 4 C, active-site CXXC motif, and two potential N-linked glycosylation sites. The predicted tertiary structures of ScGILT and other GILTs were quite similar in shape and positional arrangement of the key motifs. ScGILT mRNA was constitutively expressed in all detected tissues, with high-level expression in fish immune organs, spleen and head kidney. After stimulation with lipopolysaccharide, the expression of ScGILT mRNA significantly increased in spleen and head kidney cells, and ScGILT protein translocated to late endosomes and lysosomes in HeLa cells. Recombinant ScGILT fused with a His 6 tag was expressed and purified, and could reduce the interchain disulfide bonds of IgG at pH 4.5. These results suggested that ScGILT was capable of catalyzing disulfide bonds reduction, and then might play an important role in the processing of MHC class II-restricted antigens in silver carp. [ABSTRACT FROM AUTHOR]

A series of Cenozoic post-collisional mantle-derived magmas developed in the Southeastern Tibetan Plateau (the SE Plateau), which can be utilized to trace source components and mantle metasomatism, and further constrain the mantle evolution. In this paper, we present a systematic study on petrography, whole-rock major and trace element, Sr-Nd-Pb-Mg isotopes of Miocene-Holocene alkali basalts at the southeastern margin of the SE Plateau. These Miocene-Holocene alkali basalts were the products of the northward extension of the Cenozoic mantle-derived magmatism in Southeast Asia (SE Asia), since they are comparable in terms of geographical distributions, petrographic characteristics, geochronology patterns, and geochemical compositions. The alkali basalts in this study are mainly basanite and trachybasalt, characterized by enriched LILEs, depleted Sr-Nd-Pb isotopes, positive anomaly in HFSEs, and significantly lighter Mg isotopes (−0.51‰ to −0.32‰) relative to primitive mantle. Integrated Sr-Nd-Mg isotopes and seismic tomography suggest a source regions from the mantle transition zone that has been enriched by significant carbonate sediments. The decoupling of high Sr contents and depleted Sr Nd isotopes in the alkali basalts indicate that the mantle carbonation is subjected to recent subduction events and is possibly related to the subduction of the Neo-Tethyan seafloor. The calculated melting temperature of these basalts are generally high (1487–1583 °C), which is consistent with that of Cenozoic basalts in SE Asia (1470–1480 °C) and Hainan island (1480–1530 °C), showing a high-temperature gradient similar to that of mantle plume-related magmatism. Consequently, the generation of Miocene-Holocene alkali basalts is plausibly associated with the Hainan plume. • Sanjiang alkaline basalts are the northward extension of basalts in Southeast Asia. • Sanjiang alkali basalts are originated from the mantle transition zone. • Alkali basalts in the southeastern Plateau originated from the carbonated mantle. • Alkali basalts are related to the Hainan mantle plume. [ABSTRACT FROM AUTHOR]

The spin symmetry in the Dirac sea has been investigated with relativistic Brueckner–Hartree–Fock theory using the bare nucleon–nucleon interaction. Taking the nucleus 16 O as an example and comparing the theoretical results with the data, the definition of the single-particle potential in the Dirac sea is studied in detail. It is found that if the single-particle states in the Dirac sea are treated as occupied states, the ground state properties are in better agreement with experimental data. Moreover, in this case, the spin symmetry in the Dirac sea is better conserved and it is more consistent with the findings using phenomenological relativistic density functionals. [ABSTRACT FROM AUTHOR]

A systematic and specific pattern due to the effects of the tensor forces is found in the evolution of spin–orbit splittings in neutron drops. This result is obtained from relativistic Brueckner–Hartree–Fock theory using the bare nucleon–nucleon interaction. It forms an important guide for future microscopic derivations of relativistic and nonrelativistic nuclear energy density functionals. [ABSTRACT FROM AUTHOR]

Wheat straw (WS) was thermally pretreated at 200, 300 and 400 °C in a muffle furnace, respectively, before co-gasified with Shengli lignite (SL). The results from thermogravimetric analyzer (TGA) experiments showed that interaction of solid phases between SL and the pretreated WSs occurred at the gasification stage rather than the pyrolysis stage and the synergy varied with the biomass pretreatment temperature. Co-gasification of WS-200/SL had an inhibitory effect, and there was no synergy effect during WS-300/SL co-gasification. In contrast, co-gasification of WS-400/SL had a positive effect in the gasification stage. The investigation of co-gasification in a fixed-bed reactor, however, found synergies in product gas yields and carbon conversion for both WS-200/SL and WS-400/SL. The (H 2 +CO) yield and carbon conversion increased by 3.95% and 18.32%, respectively, for co-gasification of WS-400/SL blends compared with the calculated values based on individual materials. From the results of both the TGA and fixed-bed experiments, it is concluded that 400 °C of pyrolysis temperature for WS is the best to produce hydrogen for co-gasification with SL. The maximum synergetic effect was explained by the relatively high surface area and high content of alkali metals in WS-400. [ABSTRACT FROM AUTHOR]