bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pangenome analysis pipeline provides insights into functional gene identification in rice
Authors: Wang Jian , Yang Wu , Zhang Shaohong , Hu Haifei , Yuan Yuxuan , Dong Jingfang , Chen Luo , Ma Yamei , Yang Tifeng , Zhou Lian , Chen Jiansong , Liu Bin , Li Chengdao , Edwards David , Zhao Junliang 
Published: January 2023

Abstract
Background
A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking.

Results
To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants’ position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS).

Conclusions
Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.
Seasonal changes in the diversity, host preferences and infectivity of mosquitoes in two arbovirus-endemic regions of Costa Rica
Authors: Romero-Vega Luis M. , Piche-Ovares Marta , Soto-Garita Claudio , Barantes Murillo Daniel Felipe , Chaverri Luis Guillermo , Alfaro-Alarcón Alejandro , Corrales-Aguilar Eugenia , Troyo Adriana 
Published: January 2023

Abstract
Background
Mosquitoes are vectors of various arboviruses belonging to the genera Alphavirus and Flavivirus, and Costa Rica is endemic to several of them. The aim of this study was to describe and analyze the community structure of such vectors in Costa Rica.

Methods
Sampling was performed in two different coastal locations of Costa Rica with evidence of arboviral activity during rainy and dry seasons. Encephalitis vector surveillance traps, CDC female gravid traps and ovitraps were used. Detection of several arboviruses by Pan-Alpha and Pan-Flavi PCR was attempted. Blood meals were also identified. The Normalized Difference Vegetation Index (NDVI) was estimated for each area during the rainy and dry seasons. The Chao2 values for abundance and Shannon index for species diversity were also estimated.

Results
A total of 1802 adult mosquitoes belonging to 55 species were captured, among which Culex quinquefasciatus was the most caught species. The differences in NDVI were higher between seasons and between regions, yielding lower Chao-Sørensen similarity index values. Venezuelan equine encephalitis virus, West Nile virus and Madariaga virus were not detected at all, and dengue virus and Zika virus were detected in two separate Cx. quinquefasciatus specimens. The primary blood-meal sources were chickens (60%) and humans (27.5%). Both sampled areas were found to have different seasonal dynamics and population turnover, as reflected in the Chao2 species richness estimation values and Shannon diversity index.

Conclusion
Seasonal patterns in mosquito community dynamics in coastal areas of Costa Rica have strong differences despite a geographical proximity. The NDVI influences mosquito diversity at the regional scale more than at the local scale. However, year-long continuous sampling is required to better understand local dynamics.

Graphical Abstract
Long-term study reveals central European aerial insectivores as an unusual group of hosts that harbor mostly helminths that are unable to complete life-cycles in the nesting quarters of their hosts
Authors: Sitko Jiljí , Heneberg Petr 
Published: January 2023

AbstractBackgroundCentral European aerial insectivores are long-distance migrants that winter in sub-Saharan Africa. Most of them employ the fly-and-forage migrating strategy and differ in their food composition. The composition and structure of helminth component communities of these hosts are poorly understood, and information regarding seasonality and long-term changes is unavailable.MethodsFrom 1963 to 2022, we analyzed the population trends of helminths in five aerial insectivore species. Namely, we examinedApus apus,Hirundo rustica,Delichon urbicum,Riparia riparia, andFicedula albicollis; all originated from the Czech Republic.ResultsWe identified central European aerial insectivores as hosts that are parasitized mostly by helminths that cannot complete their life-cycles in the nesting quarters of their hosts. This phenomenon is unknown in other bird host species. In contrast, only a single dominant trematode species that completes its life-cycle locally colonized the central European aerial insectivores. All other dominant species of Trematoda, all Nematoda, and all Acanthocephala were dependent on intermediate hosts unavailable in the nesting quarters of the examined bird hosts. Surprisingly, these helminths transmitted from winter quarters or migratory routes were diverse, and many of them were abundant in terms of both prevalence and intensity of infection. The helminth component communities of aerial insectivores were dynamic systems. During the study period, three species became new and regularly encountered members of helminth fauna of examined hosts, and other species gradually increased or decreased their intensity of infection. In contrast to other groups of bird hosts, the dominant helminth species of aerial insectivores did not experience local extinctions or rapid population losses.ConclusionsThe analysis of helminths of five central European aerial insectivores revealed component communities that heavily rely on completing host–parasite cycles at migration routes or wintering grounds. The composition of the analyzed component communities changed dynamically during the 60-year-long study period, but there was no evidence of large-scale declines in abundance or prevalence.Graphical Abstract
Leishmania tarentolae: a vaccine platform to target dendritic cells and a surrogate pathogen for next generation vaccine research in leishmaniases and viral infections
Authors: Bandi Claudio , Mendoza-Roldan Jairo Alfonso , Otranto Domenico , Alvaro Alessandro , Louzada-Flores Viviane Noll , Pajoro Massimo , Varotto-Boccazzi Ilaria , Brilli Matteo , Manenti Alessandro , Montomoli Emanuele , Zuccotti Gianvincenzo , Epis Sara 
Published: January 2023

AbstractParasites of the genus Leishmania are unusual unicellular microorganisms in that they are characterized by the capability to subvert in their favor the immune response of mammalian phagocytes, including dendritic cells. Thus, in overt leishmaniasis, dendritic cells and macrophages are converted into a niche for Leishmania spp. in which the parasite, rather than being inactivated and disassembled, survives and replicates. In addition, Leishmania parasites hitchhike onto phagocytic cells, exploiting them as a mode of transport to lymphoid tissues where other phagocytic cells are potentially amenable to parasite colonization. This propensity of Leishmania spp. to target dendritic cells has led some researchers to consider the possibility that the non-pathogenic, reptile-associated Leishmania tarentolae could be exploited as a vaccine platform and vehicle for the production of antigens from different viruses and for the delivery of the antigens to dendritic cells and lymph nodes. In addition, as L. tarentolae can also be regarded as a surrogate of pathogenic Leishmania parasites, this parasite of reptiles could possibly be developed into a vaccine against human and canine leishmaniases, exploiting its immunological cross-reactivity with other Leishmania species, or, after its engineering, for the expression of antigens from pathogenic species. In this article we review published studies on the use of L. tarentolae as a vaccine platform and vehicle, mainly in the areas of leishmaniases and viral infections. In addition, a short summary of available knowledge on the biology of L. tarentolae is presented, together with information on the use of this microorganism as a micro-factory to produce antigens suitable for the serodiagnosis of viral and parasitic infections.
Graphical Abstract
Wild deer (Pudu puda) from Chile harbor a novel ecotype of Anaplasma phagocytophilum
Authors: Santodomingo Adriana , Thomas Richard , Robbiano Sofía , Uribe Juan E. , Parragué-Migone Catalina , Cabello-Stom Javier , Vera-Otarola Frank , Valencia-Soto Carola , Moreira-Arce Darío , Hidalgo-Hermoso Ezequiel , Muñoz-Leal Sebastián 
Published: January 2023

Abstract
Background
Deer species play an important role in the enzootic cycles of several Anaplasma species. While in the Northern Hemisphere ticks of genus Ixodes are well recognized vectors of these intracellular bacteria, less is known regarding the biological cycles of Anaplasma spp. in South America.

Methods
Using PCR protocols and Sanger sequencing, we assessed the presence of Anaplasma spp. in blood and ticks collected on a native deer species (Pudupuda) from southern Chile.

Results
Based on phylogenetic analyses of the 16S rRNA, gltA and groEL genes and calculation of average sequence divergence for groEL, our results bring to light a novel genovariant of Anaplasmaphagocytophilum (named strain “Patagonia”). The strain represents a novel ecotype within the A. phagocytophilum species complex and was detected in both P.puda and their ticks. Using a larger matrix, denser taxon sampling and outgroup, our maximum-likelihood- and Bayesian-inferred phylogenies for groEL provide an accurate picture of the topology of A. phagocytophilum ecotypes and their evolutionary relationships.

Conclusions
This is the first report of an ecotype of A. phagocytophilum in South America. Our results provide novel insight into the genetic diversity and ecology of this complex of bacterial lineages. Further studies should elucidate the enzootic cycle of A. phagocytophilum strain “Patagonia” and assess its pathogenic potential for pudues, domestic animals and humans in the region.

Graphical Abstract
Reduced field-of-view DWI‑derived clinical–radiomics model for the prediction of stage in cervical cancer
Authors: Huang Qiuhan , Deng Baodi , Wang Yanchun , Shen Yaqi , Hu Xuemei , Feng Cui , Li Zhen 
Published: January 2023

Abstract
Background
Pretreatment prediction of stage in patients with cervical cancer (CC) is vital for tailoring treatment strategy. This study aimed to explore the feasibility of a model combining reduced field-of-view (rFOV) diffusion-weighted imaging (DWI)-derived radiomics with clinical features in staging CC.

Methods
Patients with pathologically proven CC were enrolled in this retrospective study. The rFOV DWI with b values of 0 and 800 s/mm2 was acquired and the clinical characteristics of each patient were collected. Radiomics features were extracted from the apparent diffusion coefficient maps and key features were selected subsequently. A clinical–radiomics model combining radiomics with clinical features was constructed. The receiver operating characteristic curve was introduced to evaluate the predictive efficacy of the model, followed by comparisons with the MR-based subjective stage assessment (radiological model).

Results
Ninety-four patients were analyzed and divided into training (n = 61) and testing (n = 33) cohorts. In the training cohort, the area under the curve (AUC) of clinical–radiomics model (AUC = 0.877) for staging CC was similar to that of radiomics model (AUC = 0.867), but significantly higher than that of clinical model (AUC = 0.673). In the testing cohort, the clinical–radiomics model yielded the highest predictive performance (AUC = 0.887) of staging CC, even without a statistically significant difference when compared with the clinical model (AUC = 0.793), radiomics model (AUC = 0.846), or radiological model (AUC = 0.823).

Conclusions
The rFOV DWI-derived clinical–radiomics model has the potential for staging CC, thereby facilitating clinical decision-making.
The study of coefficient estimates and Fekete–Szegö inequalities for the new classes of m-fold symmetric bi-univalent functions defined using an operator
Authors: Breaz Daniel , Cotîrlă Luminiţa-Ioana 
Published: January 2023

AbstractThe objective of this paper is to introduce new classes of m-fold symmetric bi-univalent functions. We discuss estimates on the Taylor–Maclaurin coefficients$|a_{m+1}|$|am+1|and$|a_{2m+1}|$|a2m+1|, and the Fekete–Szegő problem is also considered for the new classes of functions introduced. We denote these classes by$MF-S_{\Sigma ,m}^{p,q}(h)$MF−SΣ,mp,q(h),$MF-S_{\Sigma , m}^{p,q}(s)$MF−SΣ,mp,q(s), and$MF-S_{\Sigma , m}^{b,d}$MF−SΣ,mb,d. Quantum calculus aspects are also considered in this study to enhance its novelty and to obtain more interesting results.
TRMT6 promotes hepatocellular carcinoma progression through the PI3K/AKT signaling pathway
Authors: Ye Yanqing , Liu Maosheng , Wu Fengfei , Ou Shiyu , Wang Weidong , Fei Jieying , Xie Fang , Bai Lan 
Published: January 2023

Abstract
Background
Hepatocellular carcinoma is one of the most common and deadly cancers. The aim of this study was to elucidate the role of tRNA methyltransferase 6 (TRMT6) during HCC progression.

Methods
The role of TRMT6 in the progression and prognosis of HCC was confirmed by analysis of online databases and clinical human samples. The effects of up-regulation or down-regulation of TRMT6 on HCC cell proliferation and PI3K/AKT pathway-related protein expressions were verified. The molecular mechanism was investigated in vivo by constructing subcutaneous xenograft tumor model.

Results
TRMT6 was overexpressed in HCC tissues and associated with Tumour-Node-Metastasis (TNM) stage, primary tumor (T) and regional lymph node (N) classification. TRMT6 expressions in HCC cell lines were higher than that in normal liver cell. TRMT6 overexpression can promote HCC cell proliferation, increase the number of S phase cells. Interference with TRMT6 reduced the PI3K/AKT pathway-related protein expressions, and was reversed by the addition of IGF1. Interference with TRMT6 inhibited tumor growth in vivo and was related to PI3K/AKT pathway.

Conclusions
Overexpression of TRMT6 promote HCC cell proliferation in vivo and in vitro through PI3K/AKT/mTOR axis, which provides a potential choice for the treatment of HCC in clinical practice.
Distribution characteristics and influencing factors of Intangible Cultural Heritage in Beijing-Tianjin-Hebei
Authors: Pang Ling , Wu Lina 
Published: January 2023

Abstract
The Beijing-Tianjin-Hebei region, with the capital Beijing as the core, carries a profound geo-culture and gathers numerous intangible cultural heritages. Studying the spatial distribution characteristics and influencing factors of intangible cultural heritage can help to propose positive suggestions for protection and development from the perspective of sustainable development. Taking 329 national intangible cultural heritages in Beijing-Tianjin—Hebei as the research objects, and using ArcGIS spatial analysis technology, combined with methods such as kernel density analysis, standard deviation ellipse and geographical detector, to visualize the spatial distribution of intangible cultural heritages and explore the influencing factors of their distribution. The results show that: (1) the distribution of intangible cultural heritage in Beijing-Tianjin-Hebei is not balanced, mainly concentrated in the central and southern regions, and three high-density core circles are formed in Beijing, Tianjin, and Handan-Xingtai in Hebei Province, showing large differences in spatial distribution density; (2) Traditional techniques, traditional arts, dramatic balladry, sports, music, and medicine show the characteristics of aggregated distribution. folkways, dance, and drama show the characteristics of random distribution. Folk literature shows the characteristics of uniform distribution; (3) The Cultural Development Period is an important evolutionary turning point in the spatial and temporal distribution of intangible cultural heritage in Beijing-Tianjin-Hebei, as well as an accelerating period in the development of intangible cultural heritage, and completes the transformation from decentralized distribution to localized aggregation distribution. In The Period of Regional Cultural Integration, the peak value is reached; (4) Economic development and social culture have the greatest influence on the spatial distribution of intangible cultural heritage in Beijing-Tianjin-Hebei, while the influence of physical environment is relatively small.
Identification of a novel transcription factor under long-term drought resistance in highland barley: a DNA affinity purification sequencing-based transcriptomic analysis
Authors: Wang Yulin , Li Heng , Zhao Chuansen , Yang Chunbao , Xu Qijun , Yuan Hongjun , Yang Haizhen , Zeng Xingquan 
Published: January 2023

AbstractStress emanating from drought condition is one of the inevitable conditions that occurs in many environments and spread across borders and results in severe hindrance to the morphology, physiology, biochemistry and molecular attributes of plants. Highland barley drought tolerance has been demonstrated to be a polygenic related characteristic and genetic composition that can assist in dissecting the gene network(s) controlling the drought tolerance needs to be adequately understood. DNA affinity purification sequencing (DAP-seq) has been shown to contribute to ways of making pure some of the protein with rare sequence-specific DNA binding and can help understand the molecular dynamics in barley under varying exposure time to drought. The present study aimed at identifying novel transcription factors (TFs) in highland barley that are key in drought resistance through DAP-seq-based transcriptomic analysis. The experimental design included two hulless barley accessions; drought-resistant Sheera 10 (X) and drought-sensitive 5171–7 (W), that were both subjected to short-term (4 h) and long-term (48 h) exposure to drought (T1 and T5, respectively), with the control group (CK) involving not subjecting the two accessions to any treatment. Through transcriptome analysis, one candidate transcription factor (GATA family; (bHLH, MYB-related, GARP-G2-like, bZIP, HB-HD-ZIP, C2H2, SET, mTERF, AP2/ERF-ERF, ARID, NAC, GARP-ARR-B, C2C2-GATA, FAR1, Trihelix, NF-YB, B3 and AUX/IAA) was found. The motif obtained was found to be consistent with GATA transcription factor. The DAP-seq highlighted the differential expression target gene which were verified by RT-qPCR. The associated genes were found to be a cluster of structural gene IP_HOR_1, IP_HOR_2 and In_HOR locus. Through RT-qPCR, it was also proved that the gene expressions were indeed upregulated. The TF HOVUSG2784400 was confirmed to be responsible to drought stress under long-term exposure, which regulates the differential expression of the genes, thereby improving the drought resistance of barley.
Graphical Abstract
Innate immune recognition against SARS-CoV-2
Authors: Yamada Taisho , Takaoka Akinori 
Published: January 2023

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative virus of pandemic acute respiratory disease called coronavirus disease 2019 (COVID-19). Most of the infected individuals have asymptomatic or mild symptoms, but some patients show severe and critical systemic inflammation including tissue damage and multi-organ failures. Immune responses to the pathogen determine clinical course. In general, the activation of innate immune responses is mediated by host pattern-recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) as well as host damage-associated molecular patterns (DAMPs), which results in the activation of the downstream gene induction programs of types I and III interferons (IFNs) and proinflammatory cytokines for inducing antiviral activity. However, the excessive activation of these responses may lead to deleterious inflammation. Here, we review the recent advances in our understanding of innate immune responses to SARS-CoV-2 infection, particularly in terms of innate recognition and the subsequent inflammation underlying COVID-19 immunopathology.
Accelerating corneal wound healing using exosome-mediated targeting of NF-κB c-Rel
Authors: Zhao Wenbo , He Xiaozhen , Liu Ruiling , Ruan Qingguo 
Published: January 2023

AbstractThe integrity of the corneal epithelium is essential for the maintenance of the physiological function of the cornea. Studies have found that inflammation greatly delays corneal wound healing. NF-κB c-Rel is preferentially expressed by immune cells and promotes the expression of inflammatory cytokines. In the current study, we sought to investigate whether c-Rel could be used as a potential therapeutic target for treating a corneal injury. Our studies reveal that expressions of c-Rel and its inflammatory targets are significantly increased in the cornea of mice with corneal injury. In addition, we find that c-Rel-deficient mice exhibit accelerated corneal wound healing and reduced expression of inflammatory cytokines. Further studies show that topical treatment on the corneal surface using nano-polymers or exosomes loaded with c-Rel-specific siRNA (siRel) can effectively accelerate regular and diabetic corneal wound healing. More importantly, we find that exosomes, as carriers of siRel, showed better efficacy than nano-polymers in treating corneal injury. We further demonstrate that exosomes secreted by mesenchymal stem cells can efficiently transfer siRNA into macrophages and dendritic cells but not T cells. Taken together, these results indicate that blocking c-Rel may represent an attracting strategy for the treatment of both regular and diabetic corneal injury.