bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution lac insect genome assembly provides genetic insights into lac synthesis and evolution of scale insects
Authors: Wang Weiwei , Chen Xiaoming , Bashir Nawaz Haider , Lu Qin , Zhang Jinwen , Ling Xiaofei , Ding Weifeng , Chen Hang 
Published: February 2023

AbstractLac insect is an important resource insect with great commercial value. However, the lack of its genome information restricts the fundamental biological research and applied studies of this species. Here, we first assembled the contig ofKerria laccausing Illumina and Nanopore sequencing by Hi-C and T2T techniques to obtain the genome ofK. laccaat the chromosome 0 gap level. The genome ofK. laccawas 256.62 Mb and the Scaffold N50 was 28.53 Mb. A total of 56.94 Mb of repeat sequences, constituting 22.19% of the assembled genome, were identified. We annotated 10,696 protein-encoding geneswith 89.74% annotated. By horizontal gene transfer analysis, we obtained a putative gene Isoprenyl diphosphate synthase (IPPS), a key enzyme in the isoprene synthesis pathway in the regulation of lac biosynthesis that transferred horizontally from bacteria to the genome ofK. lacca. Meanwhile, we constructed the lac synthesis biosynthetic pathway and screened 25 putative key genes in the synthesis pathway by transcriptome analysis in different developmental stages and tissues. It provides new research ideas to reveal the molecular mechanism of lac biosynthesis and regulation. The high-quality chromosomal-level genome of lac insect will provide a basis for the study of development, genetics, and the evolution of scale insects.
Gene regulatory patterning codes in early cell fate specification of theC. elegansembryo
Authors: Cole Alison G. , Hashimshony Tamar , Du Zhuo , Yanai Itai 
Published: February 2023

AbstractPattern formation originates during embryogenesis by a series of symmetry-breaking steps throughout an expanding cell lineage. InDrosophila, classic work has shown that the embryo segmentation is established by morphogens within a syncytium, and the subsequent action of the gap, pair-rule, and segment polarity genes. This classic model however does not translate directly to species that lack a syncytium – such asC. elegans– where cell fate is specified by cell-autonomous cell lineage programs and their inter-signaling. Previous single-cell RNA-Seq studies inC. eleganshave analyzed cells from a mixed suspension of cells from many embryos to study late differentiation stages, or individual early stage embryos to study early gene expression in the embryo. To study the intermediate stages of early and late gastrulation (28- to 102- cells stages) missed by these approaches, here we determine the transcriptomes of the 1- to 102-cell stage to identify 119 embryonic cell-states during cell-fate specification, including ‘equivalence-group’ cell identities. We find that gene expression programs are modular according to the sub-cell lineages, each establishing a set of stripes by combinations of transcription factor gene expression across the anterior-posterior axis. In particular, expression of the homeodomain genes establishes a comprehensive lineage-specific positioning system throughout the embryo beginning at the 28-cell stage. Moreover, we find that genes that segment the entire embryo inDrosophilahave orthologs inC. elegansthat exhibit sub-lineage specific expression. These results suggest that theC. elegansembryo is patterned by a juxtaposition of distinct lineage-specific gene regulatory programs each with a unique encoding of cell location and fate. This use of homologous gene regulatory patterning codes suggests a deep homology of cell fate specification programs across diverse modes of development.
The Mexican Cavefish Mount a Rapid and Sustained Regenerative Response Following Skeletal Muscle Injury
Authors: Olsen Luke , Hassan Huzaifa , Keaton Sarah , Rohner Nicolas 
Published: February 2023

SummaryPhysical injury and tissue damage is prevalent throughout the animal kingdom, with the ability to quickly and efficiently regenerate providing a selective advantage. The skeletal muscle possesses a uniquely large regenerative capacity within most vertebrates, and has thus become an important model for investigating cellular processes underpinning tissue regeneration. Following damage, the skeletal muscle mounts a complex regenerative cascade centered around dedicated muscle stem cells termed satellite cells. In non-injured muscle, satellite cells remain in a quiescent state, expressing the canonical markerPax7(Chen et al. 2020). However, following injury, satellite cells exit quiescence, enter the cell cycle to initiate proliferation, asymmetrically divide, and in many cases terminally differentiate into myoblasts, ultimately fusing with surrounding myoblasts and pre-existing muscle fibers to resolve the regenerative process (Chen et al. 2020).
Nanoparticle-Functionalized Acrylic Bone Cement for Local Therapeutic Delivery to Spinal Metastases
Authors: Siddique Ateeque , Cooke Megan E. , Weber Michael H. , Rosenzweig Derek H. 
Published: February 2023

AbstractPolymethylmethacrylate bone cement is often used to reconstruct critical-sized defects generated by surgical resection of spinal metastases. Residual tumor cells after a resection can drive recurrence and destabilization. Doxorubicin (DOX) is a common chemotherapeutic drug with unwanted side-effects when administered systemically. Mesoporous silica nanoparticles are gaining attention for targeted drug delivery to bypass the negative side effects associated with systemic drug administration. We developed a nanoparticle-functionalized cement for the local release of DOX and tested its ability to suppress cancer cells. DOX was loaded onto nanoparticles which were then mixed into the cement. Drug release profiles were obtained over a period of 4 weeks. Cement constructs were incubated with 2D and 3D cultures of breast and prostate cancer cell lines, and cell metabolic activity and viability were evaluated. Cell migration and spheroid growth were assessed in collagen-coated spheroid cultures. Nanoparticles were homogenously dispersed and did not alter cement mechanical strength. A sustained DOX release profile was achieved with the addition of nanoparticles to the bone cement. The release profile of DOX from nanoparticle cement may be modified by varying the amount of the drug loaded onto the nanoparticles and the proportion of nanoparticles in the cement. Cells treated with the cement constructs showed a dose- and time-dependent inhibition. Cell migration and spheroid growth were impaired in 3D culture. We show that nanoparticles are essential for sustained DOX release from bone cement. DOX-loaded nanoparticle cement can inhibit cancer cells and impair their migration, with strong potential forin vivotranslation studies.
Origin and Development of the Claustrum in Rhesus Macaque
Authors: Li Hong , Duque Alvaro , Rakic Pasko 
Published: February 2023

AbstractUnderstanding the claustrum’s functions has recently progressed thanks to new anatomical and behavioral studies in rodents, which suggest that it plays an important role in attention, salience detection, slow-wave generation, and neocortical network synchronization. Nevertheless, knowledge about the origin and development of the claustrum, especially in primates, is still limited. Here, we show that neurons of rhesus macaque claustrum primordium are generated between embryonic day E48 and E55 and express some neocortical molecular markers, such as NR4A2, SATB2, and SOX5. However, in the early stages, it lacks TBR1 expression, which separates it from other surrounding telencephalic structures. We also found that two waves of neurogenesis (E48 and E55) in the claustrum, corresponding to the birthdates of layers 6 and 5 of the insular cortex, establish a “core” and “shell” cytoarchitecture, which is potentially a basis for differential circuit formation and could influence information processing underlying higher cognitive functions of the claustrum. In addition, parvalbumin-positive interneurons are the dominant interneuron type in the claustrum in fetal macaque, and their maturation is independent of that in the overlaying neocortex. Finally, our study reveals that the claustrum is likely not a continuance of subplate neurons of the insular cortex, but an independent pallial region, suggesting its potentially unique role in cognitive control.Significance StatementThe claustrum is believed to have a role in many high cognitive functions. However, the origin and development of this mysterious structure remain unknown, and the understanding of its relationship with the neocortex is ambiguous. Here we examined neuron origin and development of claustrum in rhesus macaque during the prenatal and postnatal periods. We found that the claustrum is formed as an independent telencephalic area as early as E55, and it seems not related to the subplate of the insula, although it shares some molecular characteristics with the neocortex. The claustrum excitatory neurons are generated sequentially around E48 and E55 and build a “core and shell” structure that may be a basic computing neuronal circuit unit underlying higher cognitive functions.
p53 and RB Cooperate to Suppress Transposable Elements
Authors: Lopez Omar M. , Zhang Michelle , Hendrickson Peter G. , Huang Jianguo , Daniel Andrea R. , Blackmer Jane , Luo Lixia , Attardi Laura D. , Corcoran David , Kirsch David G. 
Published: February 2023

AbstractAccumulating data suggest that the long interspersed nuclear element 1 (LINE1), a major class of transposable elements, can promote tumorigenesis by causing deletions of tumor suppressor genes, amplifications of oncogenes, and chromosomal translocations(1). LINE1 and other transposable elements such as short interspersed nuclear elements (SINEs) can be activated during cancer development. Aberrant transposon expression has been correlated with loss of p53, however, how the loss of p53 or other tumor suppressors leads to activation of transposons during tumorigenesis remains to be fully understood. Here, we investigate the link between loss of the p53 and RB tumor suppressors and derepression of transposable elements. We observe that loss of p53 and RB in mouse embryonic fibroblasts leads to epigenetic changes, such as loss of DNA and histone methylation, which correlate with marked upregulation of LINE and SINE transposable elements. These results suggest that p53 and RB may utilize epigenetic mechanisms that work in tandem to suppress transposons, which may contribute to tumor suppression.SignificanceThe two most commonly mutated genes in human cancer arep53and the retinoblastoma (RB) tumor suppressors. Together, these genes regulate complex interconnecting pathways responsible for the regulation of cell growth, cell death, and genomic integrity. Studies in genetically engineered mouse models demonstrate that the canonical functions of these two tumor suppressors fail to fully explain their tumor suppressive capabilities. Individually, p53 and RB have each been implicated in repressing transposons. Here we show that combined loss of p53 and RB, which rapidly transforms cells, also results in cooperative upregulation of transposable elements and coincides with decreased methylation of DNA and H3K9. Our results present a framework by which p53 and RB work together to restrain the expression of LINE1 and SINEs, which may contribute to tumor suppression.
Paradoxical activation of oncogenic signaling as a cancer treatment strategy
Authors: Dias Matheus Henrique , Friskes Anoek , Wang Siying , Fernandes Neto Joao M. , van Gemert Frank , Mourragui Soufiane , Kuiken Hendrik J. , Mainardi Sara , Alvarez-Villanueva Daniel , Lieftink Cor , Morris Ben , Dekker Anna , van Dijk Emma , Papagianni Chrysa , da Silva Marcelo S. , Jansen Robin , Mulero-Sánchez Antonio , Malzer Elke , Vidal August , Santos Cristina , Salazar Ramón , Wailemann Rosangela A. M. , Torres Thompson E. P. , De Conti Giulia , Raaijmakers Jonne A. , Snaebjornsson Petur , Yuan Shengxian , Qin Wenxin , Kovach John S. , Armelin Hugo A. , Riele Hein te , van Oudenaarden Alexander , Jin Haojie , Beijersbergen Roderick L. , Villanueva Alberto , Medema Rene H. , Bernards Rene 
Published: February 2023

ABSTRACTCancer homeostasis depends on a balance between activated oncogenic pathways driving tumorigenesis and engagement of stress-response programs that counteract the inherent toxicity of such aberrant signaling. While inhibition of oncogenic signaling pathways has been explored extensively, there is increasing evidence that overactivation of the same pathways can also disrupt cancer homeostasis and cause lethality. We show here that inhibition of Protein Phosphatase 2A (PP2A) hyperactivates multiple oncogenic pathways and engages stress responses in colon cancer cells. Genetic and compound screens identify combined inhibition of PP2A and WEE1 as synergistic in multiple cancer models by collapsing DNA replication and triggering premature mitosis followed by cell death. This combination also suppressed the growth of patient-derived tumorsin vivo. Remarkably, acquired resistance to this drug combination suppressed the ability of colon cancer cells to form tumorsin vivo. Our data suggest that paradoxical activation of oncogenic signaling can result in tumor suppressive resistance.
Co-Targeting IL-6 and EGFR signaling for the treatment of schwannomatosis and associated pain
Authors: Yin Zhenzhen , Wu Limeng , Zhang Yanling , Sun Yao , Chen John W. , Subudhi Sonu , Ho William , Lee Grace Y. , Wang Athena , Gao Xing , Ren Jun , Zhu Chao , Zhang Na , Ferraro Gino B. , Muzikansky Alona , Zhang Luo , Stemmer-Rachamimov Anat , Mao Jianren , Plotkin Scott R. , Xu Lei 
Published: February 2023

AbstractPatients with Schwannomatosis (SWN) overwhelmingly present with intractable, debilitating chronic pain. There are no effective therapies to treat SWN. The drivers of pain response and tumor progression in SWN are not clear. The pain is not proportionally linked to tumor size and is not always relieved by tumor resection, suggesting that mechanisms other than mechanical nerve compression exist to cause pain. SWN research is limited by the lack of clinically-relevant models. Here, we established novel patient-derived xenograft (PDX) models, dorsal root ganglia (DRG) imaging model, and combined with single-cell resolution intravital imaging and RNASeq, we discovered: i) schwannomas on the peripheral nerve cause macrophage influx into the DRG, via secreting HMGB1 to directly stimulate DRG neurons to express CCL2, the key macrophage chemokine, ii) once recruited, macrophages cause pain response via overproduction of IL-6, iii) IL-6 blockade in a therapeutic setting significantly reduces pain but has modest efficacy on tumor growth, iv) EGF signaling is a potential driver of schwannoma growth and escape mechanism from anti-IL6 treatment, and v) combined IL-6 and EGFR blockade simultaneously controlled pain and tumor growth in SWN models. Our findings prompted the initiation of phase II clinical trial (NCT05684692) for pain relief in patients with SWN.
A COVID-19 DNA Vaccine Candidate Elicits Broadly Neutralizing Antibodies Against Multiple SARS-CoV-2 Variants Including the Currently Circulating Omicron BF.5, BF.7, BQ.1 and XBB
Authors: Ding Yuan , Fan Feng , Xu Xin , Zhao Gan , Zhang Xin , Zhao Huiyun , Wang Limei , Wang Bin , Gao Xiao-Ming 
Published: February 2023

ABSTRACTWaves of breakthrough infections by SARS-CoV-2 Omicron subvariants pose a global challenge to pandemic control today. We have previously reported a pVAX1-based DNA vaccine candidate, pAD1002, which encodes a receptor-binding domain (RBD) chimera of SARS-CoV-1 and Omicron BA.1. In mouse and rabbit models, pAD1002 plasmid induced cross-neutralizing Abs against heterologous Sarbecoviruses, including SARS-CoV-1 and SARS-CoV-2 prototype, Delta and Omicron variants. However, these antisera failed to block the recent emerging Omicron subvariants BF.7 and BQ.1. To solve this problem, we replaced the BA.1-encoding DNA sequence in pAD1002 with that of BA.4/5. The resulting construct, namely pAD1016, elicited SARS-CoV-1 and SARS-CoV-2 RBD-specific IFN-γ+cellular responses in BALB/c and C57BL/6 mice. More importantly, pAD1016 vaccination in mice and rabbits generated serum Abs capable of neutralizing pseudoviruses representing multiple SARS-CoV-2 Omicron subvariants including BA.2, BA.4/5, BF.7, BQ.1 and XBB. As a booster vaccine for inactivated SARS-CoV-2 virus preimmunization in C57BL/6 mice, pAD1016 broadened the serum Ab neutralization spectrum to cover the Omicron BA.4/5, BF7 and BQ.1 subvariants. These data highlight the potential benefit of pAD1016 in eliciting neutralizing Abs against broad spectrum Omicron subvariants in individuals previously vaccinated with inactivated prototype SARS-CoV-2 virus and suggests that pAD1016 is worthy further translational study as a COVID-19 vaccine candidate.
Stacking multiple optimal transport policies to map functional connectomes
Authors: Dadashkarimi Javid , Rosenblatt Matthew , Karbasi Amin , Scheinost Dustin 
Published: February 2023

AbstractConnectomics is a popular approach for understanding the brain with neuroimaging data. However, a connectome generated from one atlas is different in size, topology, and scale compared to a connectome generated from another. Consequently, connectomes generated from different atlases cannot be used in the same analysis. This limitation hinders efforts toward increasing sample size and demonstrating generalizability across datasets. Recently, we proposed Cross Atlas Remapping via Optimal Transport (CAROT) to find a spatial mapping between a pair of atlases based on a set of training data. The mapping transforms timeseries fMRI data parcellated with an atlas to form a connectome based on a different one. Crucially, CAROT does not need raw fMRI data and thus does not require re-processing, which can otherwise be time-consuming and expensive. The current CAROT implementation leverages information from several source atlases to create robust mappings for a target atlas. In this work, we extend CAROT to combine existing mappings between a source and target atlas for an arbitrary number of mappings. This extension (labeled Stacking CAROT) allows mappings between a pair of atlases to be created once and re-used with other pre-trained mappings to create new mappings as needed. Reconstructed connectomes from Stacking CAROT perform as well as those from CAROT in downstream analyses. Importantly, Stacking CAROT significantly reduces training time and storage requirements compared to CAROT. Overall, Stacking CAROT improves previous versions of CAROT.
Introduction “stalking: what do we know about working with people who stalk and where do we go?”
Authors: Wheatley Rachael 
Published: February 2023

Purpose
There is an absence of qualitative research with individuals who have stalked. This special issue of articles draws on one study, rich with the meaning-making of experts by experience. That is, people who have stalked, been convicted and detained in UK prisons. The purpose of this issue is to provide forensic practitioners with an overview of current considerations for intervening with individuals who stalk. It does this by drawing together empirically derived interpreted experiences of men who stalk, expanding key discussions with expert practitioners in the field, working with those who stalk. It highlights current thinking on the psychology of stalking and multidisciplinary options for risk management. Furthermore, it provides an overview of necessary future directions.

Design/methodology/approach
Research findings from a recent, novel, mixed methods study (Wheatley, 2019 and Wheatleya et al., 2020) are discussed with other experienced stalking practitioners in the UK for reflection and discussion. The papers synthesise the research findings, existing psychological literature and practitioner experience to discuss implications for psychological practice with those who stalk.

Findings
The key findings resonated with current practitioners, providing a springboard for expanding thinking around stalking and crucial themes such as narcissistic vulnerability, deterrence, labelling and developing alternative meaningful activities.

Research limitations/implications
In providing this marriage of experiential expert insights, this Special Issue advances the practice of psychology in relation to those who stalk, having clear applications to the processes of risk assessment, intervention and management. Pivotally, how to enhance engagement opportunities to develop working and therapeutic relationships.

Originality/value
This issue introduces new subtopics, some of which have never been written about before. It provides discussion papers marrying research with practitioner experience, with a focus on practical applications within criminal psychology and future directions.
Leadership and firm value among couples in charge: Evidence from Chinese listed family firms
Authors: Wu Na , Xia Xinping , Li Yuguo 
Published: February 2023

AbstractThis study investigates how leadership by married couples affects the firm value of family businesses in the institutional context of the Chinese capital market. Marital leadership is found to significantly decrease firm value compared with other family firms, which is supported by a battery of estimation strategies. Aggravating the principal–principal problem, tunnelling behaviour and financial fraud are confirmed as potential economic mechanisms. Moreover, monitoring from the internal corporate governance and external institution environment helps marital leadership focus on shareholder wealth beyond family interest. Our findings indicate that marital leadership implies more of a collusion effect than a collaboration effect in China.
Rio Tinto as a niche for acidophilus enzymes of industrial relevance
Authors: Daddaoua Abdelali , Álvarez Consolación , Oggerin Monika , Rodriguez Nuria , Duque Estrella , Amils Ricardo , Armengaud Jean , Segura Ana , Ramos Juan Luis 
Published: February 2023

AbstractLignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5–5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre‐industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.
Marketmaking Middlemen
Authors: Gautier Pieter , Hu Bo , Watanabe Makoto 
Published: February 2023

AbstractThis article develops a model in which market structure is determined endogenously by the choice of intermediation mode. There are two representative modes of intermediation that are widely used in real‐life markets: one is a middleman mode where an intermediary purchases inventory from the wholesale market and resells to buyers; the other is a market‐making mode where an intermediary offers a platform for buyers and sellers to meet and trade. We show that a marketmaking middleman, who adopts a mixture of these two intermediation modes, can emerge in a directed search equilibrium and discuss implications for the market structure.