bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverted base composition skews and discontinuous mitochondrial genome architecture evolution in the Enoplea (Nematoda)
Authors: Zou Hong , Chen Fang-Lin , Li Wen-Xiang , Li Ming , Lei Hong-Peng , Zhang Dong , Jakovlić Ivan , Wang Gui-Tang 
Published: May 2022

Abstract
Background
Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolving architecture of Dorylaimida and Mermithida. To better understand the evolution of mitogenomic architecture in this lineage, we sequenced the mitogenome of a fish parasite Pseudocapillaria tomentosa (Trichinellida: Capillariidae) and compared it to all available enoplean mitogenomes.

Results
P. tomentosa exhibited highly reduced noncoding regions (the largest was 98 bp), and a unique base composition among the Enoplea. We attributed the latter to the inverted GC skew (0.08) in comparison to the ancestral skew in Trichinellidae (-0.43 to -0.37). Capillariidae, Trichuridae and Longidoridae (Dorylaimida) generally exhibited low negative or low positive skews (-0.1 to 0.1), whereas Mermithidae exhibited fully inverted low skews (0 to 0.05). This is indicative of inversions in the strand replication order or otherwise disrupted replication mechanism in the lineages with reduced/inverted skews. Among the Trichinellida, Trichinellidae and Trichuridae have almost perfectly conserved architecture, whereas Capillariidae exhibit multiple rearrangements of tRNA genes. In contrast, Mermithidae (Mermithida) and Longidoridae (Dorylaimida) exhibit almost no similarity to the ancestral architecture.

Conclusions
Longidoridae exhibited more rearranged mitogenomic architecture than the hypervariable Mermithidae. Similar to the Chromadorea, the evolution of mitochondrial architecture in enoplean nematodes exhibits a strong discontinuity: lineages possessing a mostly conserved architecture over tens of millions of years are interspersed with lineages exhibiting architectural hypervariability. As Longidoridae also have some of the smallest metazoan mitochondrial genomes, they contradict the prediction that compact mitogenomes should be structurally stable. Lineages exhibiting inverted skews appear to represent the intermediate phase between the Trichinellidae (ancestral) and fully derived skews in Chromadorean mitogenomes (GC skews = 0.18 to 0.64). Multiple lines of evidence (CAT-GTR analysis in our study, a majority of previous mitogenomic results, and skew disruption scenarios) support the Dorylaimia split into two sister-clades: Dorylaimida + Mermithida and Trichinellida. However, skew inversions produce strong base composition biases, which can hamper phylogenetic and other evolutionary studies, so enoplean mitogenomes have to be used with utmost care in evolutionary studies.
Genome-wide identification and characterization of superoxide dismutases in four oyster species reveals functional differentiation in response to biotic and abiotic stress
Authors: Liu Youli , Bao Zhenmin , Lin Zhihua , Xue Qinggang 
Published: May 2022

Abstract
Background
Oysters inhabit in the intertidal zone and may be suffered from environmental stresses, which can increase the production of reactive oxygen species (ROS), resulting in mass mortality. Superoxide dismutases (SODs) protect oysters from ROS damage through different mechanisms compared with vertebrates. However, the molecular and functional differentiation in oyster SODs were rarely analyzed.

Result
In this study, a total of 13, 13, 10, and 8 candidate SODs were identified in the genome of Crassostrea gigas, Crassostrea virginica, Crassostrea hongkongensis, and Saccostrea glomerata respectively. The domain composition, gene structure, subcellular locations, conserved ligands, and cis-elements elucidated the SODs into five groups (Mn-SODs, Cu-only-SODs, Cu/Zn ion ligand Cu/Zn-SOD with enzyme activity, Zn-only-SODs, and no ligand metal ions Cu/Zn-SODs). For single domain Cu/Zn-SODs, only one cytosolic Cu/Zn-SOD (cg_XM_034479061.1) may conserve enzymatic activity while most extracellular Cu/Zn-SOD proteins appeared to lose SOD enzyme activity according to conserved ligand amino acid analysis and expression pattern under biotic and abiotic stress in C. gigas. Further, multi-domain-SODs were identified and some of them were expressed in response to biotic and abiotic stressors in C. gigas. Moreover, the expression patterns of these genes varied in response to different stressors, which may be due to the cis-elements in the gene promoter.

Conclusion
These findings revealed the most extracellular Cu/Zn-SOD proteins appeared to lose SOD enzyme activity in oysters. Further, our study revealed that only one cytosolic Cu/Zn-SOD (cg_XM_034479061.1) may conserve enzymatic activity of SOD. Moreover, the expression patterns of these genes varied in response to different stressors, which may be due to the cis-elements in the promoter. This study provides important insights into the mechanisms through which oysters adapt to harsh intertidal conditions, as well as potential biomarkers of stress response in related species.
Genome-wide identification of sugar transporter gene family in Brassicaceae crops and an expression analysis in the radish
Authors: Liu Tongjin , Bao Chonglai , Ban Qiuyan , Wang Changyi , Hu Tianhua , Wang Jinglei 
Published: May 2022

Abstract
Background
Sugar not only is an important biomacromolecule that plays important roles in plant growth, development, and biotic and abiotic stress tolerance but also provides a skeleton for other macromolecules, such as proteins and nucleic acids. Sugar transporter proteins (STPs) play essential roles in plant sugar transport and ultimately affect the abovementioned life processes. However, the evolutionary dynamics of this important gene family in Brassicaceae crops are still largely unknown, and the functional differentiation of radish STP genes remains unclear.

Results
In the present study, a comparative genomic study of STP genes in five representative Brassicaceae crops was conducted, and a total of 25, 25, 28, 36 and 49 STP genes were individually identified in Raphanus sativus (Rs), Brassica oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj), which were divided into four clades by phylogenetic analysis. The number of STP genes was no direct correlation with genome size and the total number of coding genes in Brassicaceae crops, and their physical and chemical properties showed no significant difference. Expression analysis showed that radish STP genes play vital roles not only in flower and seedpod development but also under heavy metal (cadmium, chromium and lead), NaCl and PEG-6000 stresses, Agrobacterium tumefaciens infection, and exogenous sugar treatment. RsSTP13.2 was significantly upregulated in the resistant radish cultivar by A. tumefaciens infection and induced by heavy metal, NaCl and PEG-6000 stress, indicating that it is involved in resistance to both biotic and abiotic stress in radish.

Conclusions
The present study provides insights into the evolutionary patterns of the STP gene family in Brassicaceae genomes and provides a theoretical basis for future functional analysis of STP genes in Brassicaceae crops.
Age- and sex-related differences of muscle cross-sectional area in iliocapsularis: a cross-sectional study
Authors: Yagi Masahide , Taniguchi Masashi , Tateuchi Hiroshige , Hirono Tetsuya , Fukumoto Yoshihiro , Yamagata Momoko , Nakai Ryusuke , Yamada Yosuke , Kimura Misaka , Ichihashi Noriaki 
Published: May 2022

Abstract
Background
This study aimed to determine in how many individuals the iliocapsularis muscle (IC) could be identified on magnetic resonance imaging (MRI) and whether age and sex are associated with the cross-sectional area (CSA) of the IC.

Methods
Thirty-seven healthy younger adults and 40 healthy older adults were assigned to four groups: 1) 20 younger men; 2) 17 younger women; 3) 20 older men; and 4) 20 older women. The CSAs of the IC, IP, the rectus femoris (RF) and the quadriceps (QUAD) were quantified on an axial MRI.

Results
The number of individuals with the identified IC was n = 17 (85.0%) of 20 younger men, n = 15 (88.2%) of 17 younger women, n = 18 (90.0%) of 20 older men, and 19 (95.0%) of 20 older women. Our results showed the main effect of sex, but not age, in the CSA of the IC. The men-groups had larger CSA of the IC than the women-groups; however, no difference in CSA of the IC was found between the younger and older groups. Meanwhile, the main effects of age and sex were found for the IP, RF, and QUAD; thus, younger or men groups have larger CSAs of the three muscles than the older or women groups. The IC muscle can be discriminated in 85% – 95% of healthy individuals.

Conclusion
Although sex and age are associated with the CSA of lower-limb muscles other than the IC, only sex is associated with the CSA of the IC.
Diagnostic gene biomarkers for predicting immune infiltration in endometriosis
Authors: Xie Chengmao , Lu Chang , Liu Yong , Liu Zhaohui 
Published: May 2022

Abstract
Objective
To determine the potential diagnostic markers and extent of immune cell infiltration in endometriosis (EMS).

Methods
Two published profiles (GSE7305 and GSE25628 datasets) were downloaded, and the candidate biomarkers were identified by support vector machine recursive feature elimination analysis and a Lasso regression model. The diagnostic value and expression levels of biomarkers in EMS were verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blotting, then further validated in the GSE5108 dataset. CIBERSORT was used to estimate the composition pattern of immune cell components in EMS.

Results
One hundred and fifty-three differential expression genes (DEGs) were identified between EMS and endometrial with 83 upregulated and 51 downregulated genes. Gene sets related to arachidonic acid metabolism, cytokine–cytokine receptor interactions, complement and coagulation cascades, chemokine signaling pathways, and systemic lupus erythematosus were differentially activated in EMS compared with endometrial samples. Aquaporin 1 (AQP1) and ZW10 binding protein (ZWINT) were identified as diagnostic markers of EMS, which were verified using qRT-PCR and western blotting and validated in the GSE5108 dataset. Immune cell infiltrate analysis showed that AQP1 and ZWINT were correlated with M2 macrophages, NK cells, activated dendritic cells, T follicular helper cells, regulatory T cells, memory B cells, activated mast cells, and plasma cells.

Conclusion
AQP1 and ZWINT could be regarded as diagnostic markers of EMS and may provide a new direction for the study of EMS pathogenesis in the future.
Standardization of the ethanolic extract of Crinum latifolium leaves by two bioactive markers with antiproliferative activity against TGF-β-promoted prostate stromal cells (WPMY-1)
Authors: Thongphichai Wisuwat , Uttarawichien Tamonwan , Chanvorachote Pithi , Pitiporn Supaporn , Charoen-ame Todsaphol , Kwankhao Pakakrong , Towiwat Pasarapa , Sukrong Suchada 
Published: May 2022

Abstract
Background
Crinum latifolium L. (Amaryllidaceae) has been used in Southeast Asian traditional medicine to alleviate the symptoms of benign prostatic hyperplasia (BPH). The pathological mechanism of BPH is associated with the induction of prostate stromal cell proliferation through transforming growth factor-beta (TGF-β). Standardization as well as investigation of the potential anti-BPH activity of C. latifolium extract could benefit the further development of BPH-related analyses and provide evidence to support the application of this extract for BPH treatment. This study aimed to standardize and investigate the antiproliferative activity of the ethanolic extract of C. latifolium leaves. The major alkaloids isolated from C. latifolium were also explored for their potential use as bioactive markers.

Methods
Two major alkaloids were isolated from the ethanolic extract of C. latifolium leaves by chromatographic techniques, identified by NMR and MS, and quantified by a validated UHPLC method. Their antiproliferative activity was studied in human prostate stromal cells (WPMY-1) induced by TGF-β. The synergistic effect of combining the two major isolated alkaloids was analyzed by the zero interaction potency (ZIP) model.

Results
Two alkaloids, lycorine (1) and 6α-hydroxybuphanidrine (2), were isolated from the ethanolic leaf extract of C. latifolium. A UHPLC method for the quantification of (1) and (2) was developed and validated in terms of linearity, precision, and accuracy. The C. latifolium leaf extract contained 0.279 ± 0.003% (1) and 0.232 ± 0.004% (2). The crude extract was more potent than either (1) and (2) alone against TGF-β-treated WPMY-1 cell proliferation. The drug combination study revealed that the greatest synergistic effect of (1) and (2) was achieved at a 1:1 ratio.

Conclusions
The results of this study support the anti-BPH activity of C. latifolium in traditional medicine and suggest that these the two isolated alkaloids may promote the efficacy of the C. latifolium extract. Additionally, major alkaloids (1) and (2) can be used as bioactive markers for the standardization of C. latifolium extracts.
Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Authors: Petrosino Giuseppe , Ponte Giovanna , Volpe Massimiliano , Zarrella Ilaria , Ansaloni Federico , Langella Concetta , Di Cristina Giulia , Finaurini Sara , Russo Monia T. , Basu Swaraj , Musacchia Francesco , Ristoratore Filomena , Pavlinic Dinko , Benes Vladimir , Ferrante Maria I. , Albertin Caroline , Simakov Oleg , Gustincich Stefano , Fiorito Graziano , Sanges Remo 
Published: May 2022

Abstract
Background
Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus.

Results
Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes.

Conclusions
The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.
Unplanned reoperation after resection of retroperitoneal sarcoma: experience based on a high-volume sarcoma center
Authors: Zhuang Aobo , Zhao Mingkun , Fang Yuan , Ma Lijie , Lu Weiqi , Zhou Yuhong , Zhang Yong , Tong Hanxing 
Published: May 2022

AbstractBackgroundMost retroperitoneal sarcoma (RPS) operations require combined multi-organ resection, and the proportion of unplanned reoperation is high. However, there are no relevant studies on reoperation for RPS.MethodsPatients who underwent at least once unplanned reoperation at Shanghai Public Health Clinical Center, Fudan University, China, from August 2009 to December 2021 were retrospectively analyzed. The baseline characteristics, primary surgery, and reoperation information, postoperative complications, and survival were analyzed.ResultsA total of 51 patients were included. Among them, 21 (41.2%) were male and 30 (58.8%) were female. The median age was 51 (interquartile range [IQR], 49-63) years. Most (88.3%) had a history of abdominal surgery. Dedifferentiated liposarcoma, well-differentiated liposarcoma, leiomyosarcoma, and others accounted for 50.9%, 21.6%, 15.7%, and 11.8%, respectively. The conditions of the primary operation were as follows: 35 (68.6%) patients achieved complete surgical resection, 48 patients had combined organ resection, and a median of 3 (IQR, 2–4) organs was removed, of which 5 (9.9%) were combined with pancreaticoduodenectomy. The median operative time was 330 (IQR, 245–440) min, and the median estimated blood loss was 1500 (IQR, 500–2600) ml. The median postoperative hospital stay was 42 (IQR, 23–82) days. For reoperation, the most common reasons were bleeding (31.3%), complications related to intestinal anastomosis (27.4%), and intestinal perforation (19.9%). The mortality rate after reoperation was 39.2% (20/51). Twelve (23.5%) patients underwent reoperation at least twice.ConclusionsUnplanned reoperation among retroperitoneal sarcoma correlates with established measures of surgical quality.
Banana plant counting and morphological parameters measurement based on terrestrial laser scanning
Authors: Miao Yanlong , Wang Liuyang , Peng Cheng , Li Han , Li Xiuhua , Zhang Man 
Published: May 2022

AbstractBackgroundThe number of banana plants is closely related to banana yield. The diameter and height of the pseudo-stem are important morphological parameters of banana plants, which can reflect the growth status and vitality. To address the problems of high labor intensity and subjectivity in traditional measurement methods, a fast measurement method for banana plant count, pseudo-stem diameter, and height based on terrestrial laser scanning (TLS) was proposed.ResultsFirst, during the nutritional growth period of banana, three-dimensional (3D) point cloud data of two measured fields were obtained by TLS. Second, the point cloud data was preprocessed. And the single plant segmentation of the canopy closed banana plant point cloud was realized furtherly. Finally, the number of banana plants was obtained by counting the number of pseudo-stems, and the diameter of pseudo-stems was measured using a cylindrical segmentation algorithm. A sliding window recognition method was proposed to determine the junction position between leaves and pseudo-stems, and the height of the pseudo-stems was measured. Compared with the measured value of artificial point cloud, when counting the number of banana plants, the precision,recall and percentage error of field 1 were 93.51%, 94.02%, and 0.54% respectively; the precision,recall and percentage error of field 2 were 96.34%, 92.00%, and 4.5% respectively; In the measurement of pseudo-stem diameter and height of banana, the root mean square error (RMSE) of pseudo-stem diameter and height of banana plant in field 1 were 0.38 cm and 0.2014 m respectively, and the mean absolute percentage error (MAPE) were 1.30% and 5.11% respectively; the RMSE of pseudo-stem diameter and height of banana plant in field 2 were 0.39 cm and 0.2788 m respectively, and the MAPE were 1.04% and 9.40% respectively.ConclusionThe results show that the method proposed in this paper is suitable for the field measurement of banana count, pseudo-stem diameter, and height and can provide a fast field measurement method for banana plantation management.
Determination of protoplast growth properties using quantitative single-cell tracking analysis
Authors: Dawson Jonathan , Pandey Saurabh , Yu Qiuju , Schaub Patrick , Wüst Florian , Moradi Amir Bahram , Dovzhenko Oleksandr , Palme Klaus , Welsch Ralf 
Published: May 2022

Abstract
Background
Although quantitative single-cell analysis is frequently applied in animal systems, e.g. to identify novel drugs, similar applications on plant single cells are largely missing. We have exploited the applicability of high-throughput microscopic image analysis on plant single cells using tobacco leaf protoplasts, cell-wall free single cells isolated by lytic digestion. Protoplasts regenerate their cell wall within several days after isolation and have the potential to expand and proliferate, generating microcalli and finally whole plants after the application of suitable regeneration conditions.

Results
High-throughput automated microscopy coupled with the development of image processing pipelines allowed to quantify various developmental properties of thousands of protoplasts during the initial days following cultivation by immobilization in multi-well-plates. The focus on early protoplast responses allowed to study cell expansion prior to the initiation of proliferation and without the effects of shape-compromising cell walls. We compared growth parameters of wild-type tobacco cells with cells expressing the antiapoptotic protein Bcl2-associated athanogene 4 from Arabidopsis (AtBAG4).

Conclusions
AtBAG4-expressing protoplasts showed a higher proportion of cells responding with positive area increases than the wild type and showed increased growth rates as well as increased proliferation rates upon continued cultivation. These features are associated with reported observations on a BAG4-mediated increased resilience to various stress responses and improved cellular survival rates following transformation approaches. Moreover, our single-cell expansion results suggest a BAG4-mediated, cell-independent increase of potassium channel abundance which was hitherto reported for guard cells only. The possibility to explain plant phenotypes with single-cell properties, extracted with the single-cell processing and analysis pipeline developed, allows to envision novel biotechnological screening strategies able to determine improved plant properties via single-cell analysis.