bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides
Authors: Wan Yu , Wang Zhuo , Lee Tzong-Yi 
Published: May 2021

Abstract
Background
Cancer is one of the major causes of death worldwide. To treat cancer, the use of anticancer peptides (ACPs) has attracted increased attention in recent years. ACPs are a unique group of small molecules that can target and kill cancer cells fast and directly. However, identifying ACPs by wet-lab experiments is time-consuming and labor-intensive. Therefore, it is significant to develop computational tools for ACPs prediction. Though some ACP prediction tools have been developed recently, their performances are not well enough and most of them do not offer a function to distinguish ACPs from antimicrobial peptides (AMPs). Considering the fact that a growing number of studies have shown that some AMPs exhibit anticancer function, this work tries to build a model for distinguishing AMPs from ACPs in addition to a model that predicts ACPs from whole peptides.

Results
This study chooses amino acid composition, N5C5, k-space, position-specific scoring matrix (PSSM) as features, and analyzes them by machine learning methods, including support vector machine (SVM) and sequential minimal optimization (SMO) to build a model (model 2) for distinguishing ACPs from whole peptides. Another model (model 1) that distinguishes ACPs from AMPs is also developed. Comparing to previous models, models developed in this research show better performance (accuracy: 85.5% for model 1 and 95.2% for model 2).

Conclusions
This work utilizes a new feature, PSSM, which contributes to better performance than other features. In addition to SVM, SMO is used in this research for optimizing SVM and the SMO-optimized models show better performance than non-optimized models. Last but not least, this work provides two different functions, including distinguishing ACPs from AMPs and distinguishing ACPs from all peptides. The second SMO-optimized model, which utilizes PSSM as a feature, performs better than all other existing tools.
Two β-glucuronosyltransferases involved in the biosynthesis of type II arabinogalactans function in mucilage polysaccharide matrix organization in Arabidopsis thaliana
Authors: Ajayi Oyeyemi O. , Held Michael A. , Showalter Allan M. 
Published: May 2021

Abstract
Background
Arabinogalactan-proteins (AGPs) are heavily glycosylated with type II arabinogalactan (AG) polysaccharides attached to hydroxyproline residues in their protein backbone. Type II AGs are necessary for plant growth and critically important for the establishment of normal cellular functions. Despite the importance of type II AGs in plant development, our understanding of the underlying role of these glycans/sugar residues in mucilage formation and seed coat epidermal cell development is poorly understood and far from complete. One such sugar residue is the glucuronic acid residues of AGPs that are transferred onto AGP glycans by the action of β-glucuronosyltransferase genes/enzymes.

Results
Here, we have characterized two β-glucuronosyltransferase genes, GLCAT14A and GLCAT14C, that are involved in the transfer of β-glucuronic acid (GlcA) to type II AGs. Using a reverse genetics approach, we observed that glcat14a-1 mutants displayed subtle alterations in mucilage pectin homogalacturonan (HG) compared to wild type (WT), while glcat14a-1glcat14c-1 mutants displayed much more severe mucilage phenotypes, including loss of adherent mucilage and significant alterations in cellulose ray formation and seed coat morphology. Monosaccharide composition analysis showed significant alterations in the sugar amounts of glcat14a-1glcat14c-1 mutants relative to WT in the adherent and non-adherent seed mucilage. Also, a reduction in total mucilage content was observed in glcat14a-1glcat14c-1 mutants relative to WT. In addition, glcat14a-1glcat14c-1 mutants showed defects in pectin formation, calcium content and the degree of pectin methyl-esterification (DM) as well as reductions in crystalline cellulose content and seed size.

Conclusions
These results raise important questions regarding cell wall polymer interactions and organization during mucilage formation. We propose that the enzymatic activities of GLCAT14A and GLCAT14C play partially redundant roles and are required for the organization of the mucilage matrix and seed size in Arabidopsis thaliana. This work brings us a step closer towards identifying potential gene targets for engineering plant cell walls for industrial applications.
Comparative analysis of latex transcriptomes reveals the potential mechanisms underlying rubber molecular weight variations between the Hevea brasiliensis clones RRIM600 and Reyan7-33–97
Authors: Xin Shichao , Hua Yuwei , Li Ji , Dai Xuemei , Yang Xianfeng , Udayabhanu Jinu , Huang Huasun , Huang Tiandai 
Published: May 2021

Abstract
Background
The processabilities and mechanical properties of natural rubber depend greatly on its molecular weight (MW) and molecular weight distribution (MWD). However, the mechanisms underlying the regulation of molecular weight during rubber biosynthesis remain unclear.

Results
In the present study, we determined the MW and particle size of latex from 1-year-old virgin trees and 30-year-old regularly tapped trees of the Hevea clones Reyan7-33–97 and RRIM600. The results showed that both the MW and the particle size of latex varied between these two clones and increased with tree age. Latex from RRIM600 trees had a smaller average particle size than that from Reyan7-33–97 trees of the same age. In 1-year-old trees, the Reyan7-33–97 latex displayed a slightly higher MW than that of RRIM600, whereas in 30-year-old trees, the RRIM600 latex had a significantly higher MW than the Reyan7-33–97 latex. Comparative analysis of the transcriptome profiles indicated that the average rubber particle size is negatively correlated with the expression levels of rubber particle associated proteins, and that the high-MW traits of latex are closely correlated with the enhanced expression of isopentenyl pyrophosphate (IPP) monomer-generating pathway genes and downstream allylic diphosphate (APP) initiator-consuming non-rubber pathways. By bioinformatics analysis, we further identified a group of transcription factors that potentially regulate the biosynthesis of IPP.

Conclusions
Altogether, our results revealed the potential regulatory mechanisms involving gene expression variations in IPP-generating pathways and the non-rubber isoprenoid pathways, which affect the ratios and contents of IPP and APP initiators, resulting in significant rubber MW variations among same-aged trees of the Hevea clones Reyan7-33–97 and RRIM600. Our findings provide a better understanding of rubber biosynthesis and lay the foundation for genetic improvement of rubber quality in H. brasiliensis.
Comparative transcriptomic analysis of seed coats with high and low lignin contents reveals lignin and flavonoid biosynthesis in Brassica napus
Authors: Ding Yiran , Yu Shizhou , Wang Jia , Li Maoteng , Qu Cunmin , Li Jiana , Liu Liezhao 
Published: May 2021

Abstract
Background
Brassica napus L. (2n = 38, AACC) is one of the most important oil crops and sources of protein for animal feed worldwide. Lignin is a large molecule aromatic polymer and a major cell wall component. However, lignin in the seed coat reduces the availability and restricts the development of rapeseed cake. Therefore, it is critical to reduce the lignin content of the seed coat. Here, high-lignin (H-lignin) and low-lignin (L-lignin) content recombinant inbred lines (RILs) were selected from an RIL population for analysis.

Results
The cross-section results indicated that the seed coat of the H-lignin lines was thicker than that of the L-lignin lines, especially the palisade layer. The seed coats and embryos at 35, 40 and 46 days after flowering (DAF) were subjected to RNA sequencing (RNA-Seq), and the expression of the BnPAL and BnC4H gene families in the lignin pathway was significantly higher in the H-lignin seed coat than in the L-lignin seed coat. The Bn4CL gene family also showed this trend. In addition, among the genes related to plant hormone synthesis, BnaC02g01710D was upregulated and BnaA07g11700D and BnaC09g00190D were downregulated in H-lignin lines. Some transcription factors were upregulated, such as BnNAC080, BnNAC083, BnMYB9, BnMYB9-1, BnMYB60 and BnMYB60-1, while BnMYB91 was downregulated in H-lignin lines. Moreover, most genes of the flavonoid pathway, such as BnCHS and BnDFR, were strongly expressed in H-lignin seed coat.

Conclusions
In Our study, some key genes such as hormone synthesis genes, transcription factors and miRNAs related to lignin and flavonoid biosynthesis were identified. A regulatory model of B. napus seed coat lignin was proposed. These results provide new insight into lignin and flavonoid biosynthesis in B. napus.
Reduced mechanical function of the left atrial predicts adverse outcome in pregnant women with clustering of metabolic risk factors
Authors: Ye Xiaoguang , Li Zhitian , Li Yidan , Cai Qizhe , Sun Lanlan , Zhu Weiwei , Ding Xueyan , Guo Dichen , Qin Yunyun , Lu Xiuzhang 
Published: May 2021

Abstract
Introduction
The left atrial (LA) strain and strain rate are sensitive indicators of LA function. However, they are not widely used for the evaluation of pregnant women with metabolic diseases. The aim of this study was to assess the LA strain and strain rate of pregnant women with clustering of metabolic risk factors and to explore its prognostic effect on adverse pregnancy outcomes.

Materials and methods
Sixty-three pregnant women with a clustering of metabolic risk factors (CMR group), fifty-seven women with pregnancy-induced hypertension (PIH group), fifty-seven women with gestational diabetes mellitus (GDM group), and fifty matched healthy pregnant women (control group) were retrospectively evaluated. LA function was evaluated with two-dimensional speckle-tracking imaging. Iatrogenic preterm delivery caused by severe preeclampsia, placental abruption, and fetal distress was regarded as the primary adverse outcome.

Results
The CMR group showed the lowest LA strain during reservoir phase (LASr), strain during contraction phase (LASct) and peak strain rate during conduit phase (pLASRcd) among the three groups (P < 0.05). LA strain during conduit phase (LAScd) and peak strain rate during reservoir phase (pLASRr) in the CMR group were lower than those in the control and GDM groups (P < 0.05). Multivariable Cox regression analysis demonstrated systolic blood pressure (HR = 1.03, 95% CI 1.01–1.05, p = 0.001) and LASr (HR = 0.86, 95% CI 0.80–0.92, p < 0.0001) to be independent predictors of iatrogenic preterm delivery. An LASr cutoff value ≤ 38.35% predicted the occurrence of iatrogenic preterm delivery.

Conclusions
LA mechanical function in pregnant women with metabolic aggregation is deteriorated. An LASr value of 38.35% or less may indicate the occurrence of adverse pregnancy outcomes.
Changes in the proportion and severity of patients with fever or common cold symptoms utilizing an after-hours house call medical service during the COVID-19 pandemic in Tokyo, Japan: a retrospective cohort study
Authors: Inokuchi Ryota , Morita Kojiro , Iwagami Masao , Watanabe Taeko , Ishikawa Masatoshi , Tamiya Nanako 
Published: May 2021

Abstract
Background
Trends in the characteristics and disease severity of patients using an after-hours house call (AHHC) medical service changed during the coronavirus disease (COVID-19) pandemic. However, there have been no reports on this issue since the start of the COVID-19 pandemic. This study aimed to investigate patients’ tendencies to utilize an AHHC medical service for fever or common cold symptoms during the COVID-19 pandemic.

Methods
This retrospective cohort study compared the characteristics and disease severity of patients with fever or common cold symptoms utilizing an AHHC medical service offered by a single large company between the control period (December 1, 2018 to April 30, 2019) and the COVID-19 pandemic exposure period (December 1, 2019 to April 30, 2020). We also assessed the proportion of these patients in relation to all patients calling the service for any reason.

Results
During the control and COVID-19 pandemic exposure periods, a total of 6462 and 10,003 patients consulted the AHHC medical service, respectively. Of these, 5335 (82.6%) and 7423 (74.2%) patients had fever and common cold symptoms, respectively, during the control and COVID-19 pandemic exposure periods (P < 0.001). The corresponding median (interquartile range) ages were 8 (3–11) and 10 (4–33) years, respectively. The distribution of disease severity differed between the groups. The proportions of patients with mild, moderate, and severe illness were 71.1, 28.7, and 0.2% in the control period and 42.3, 56.7, and 0.9% in the COVID-19 pandemic exposure period, respectively (P < 0.001).

Conclusions
During the COVID-19 pandemic, the proportion of patients with fever or common cold symptoms was lower than that in the control period, but disease severity was significantly higher.
A preliminary study on the characteristics of Th1/Th2 immune response in cerebrospinal fluid of AIDS patients with cryptococcal meningitis
Authors: Li Aixin , Zhu Wenjiao , Yin Jiming , Huang Xiaojie , Sun Lijun , Hua Wei , Wang Wen , Zhang Tong , Dai Lili , Wu Hao 
Published: May 2021

Abstract
Background
Cryptococcal Meningitis (CM) is a common opportunistic infection in the late stage of acquired immunodeficiency syndrome (AIDS). Despite the wide use of effective antiretroviral and antifungal therapy in AIDS patients, CM is still a major morbidity and mortality cause. Understanding the immune response in cryptococcal infection may help to improve the treatment strategies.

Methods
We established a prospective cohort of twelve AIDS patients with CM (HIV + CM+) admitted to the hospital from 2019 to 2020. All patients were examined at the baseline, 2 weeks, and 4 weeks thereafter. The level of 19 cytokines in cerebrospinal fluid (CSF) were recorded to analyze the characteristics and dynamic changes of Th1/Th2 immune response. Meanwhile, six AIDS patients without CM (HIV + CM-) and seventeen healthy subjects (HIV-CM-) were included as control groups for CSF assessment.

Results
The HIV+ CM+ group had higher CSF IFN-γ, TNF-α, IL-6, IL-7, IL-8, IL-10, IL-12 (P40), IL-15, IL-18, CCL2 levels but lower IL-4 when compared with the HIV-CM- group at baseline. And they also had a higher level of IL-12 (P40) and IL-17A compared with HIV + CM- patients. Except one patient dropped out of the study, eleven HIV + CM+ patients received induction antifungal therapy and regular CSF testing, and the mortality rate was 9.1% (1/11) and 18.2% (2/11) respectively at week 2 and week 4. Compared with baseline CSF cytokines, IL-2, IL-13, IL-17A, and VEGF-A decreased in week 2, and the VEGF-A levels further decreased in week 4. But there was no difference in the levels of all cytokines between survivors and the dead.

Conclusion
No evidence of Th1/Th2 imbalance was found in AIDS patients with CM. However, the CSF cytokine network may provide new clues for the treatment of AIDS patients with CM.

Trial registration
This trial was prospectively registered in 2019.7.16. The registered number is ChiCTR1900024565.
Primary meningococcal arthritis in a COVID-19 18-year-old man: a case report and review of the literature
Authors: Ducatez Norman , Chancel Marine , Douadi Youcef , Dayen Charles , Suguenot Rémi , Lecuyer Emmanuelle , Brihaye Benoit , Bentayeb Houcine 
Published: May 2021

Abstract
Background
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is associated with various complications. PMA (primary meningococcal arthritis) is a rare meningococcus-associated disease causing arthritis of the knee usually, without any signs of invasive meningococcal disease. No case of PMA in a COVID-19 (coronavirus disease, 2019) patient has yet been described. PMA mainly strikes young adults. PMA is not associated with any immunocompromising condition. It has a better outcome than usual septic arthritis

Case presentation
Herein, we report an 18-year-old man diagnosed with COVID-19, later admitted with persistent fever, right knee arthralgia and maculopapular rash. Due to family history, psoriasis and Henoch-Schönlein purpura were hypothesized and ruled out. Finally, synovial fluid culture confirmed Neisseria meningitidis serogroup B arthritis without any other symptoms of invasive meningococcal disease. Healing was achieved quickly with surgery and antibiotics. We concluded in a PMA.

Conclusion
We describe here the first primary meningococcal arthritis in a COVID-19 patient and we hope to shine a light on this rare but serious complication.
Maternal region of origin and Small for gestational age: a cross-sectional analysis of Victorian perinatal data
Authors: Grundy Sarah , Lee Patricia , Small Kirsten , Ahmed Faruk 
Published: May 2021

Abstract
Background
Being born small for gestational age is a strong predictor of the short- and long-term health of the neonate, child, and adult. Variation in the rates of small for gestational age have been identified across population groups in high income countries, including Australia. Understanding the factors contributing to this variation may assist clinicians to reduce the morbidity and mortality associated with being born small. Victoria, in addition to New South Wales, accounts for the largest proportion of net overseas migration and births in Australia. The aim of this research was to analyse how migration was associated with small for gestational age in Victoria.

Methods
This was a cross sectional population health study of singleton births in Victoria from 2009 to 2018 (n = 708,475). The prevalence of being born small for gestational age (SGA; <10th centile) was determined for maternal region of origin groups. Multivariate logistic regression analysis was used to analyse the association between maternal region of origin and SGA.

Results
Maternal region of origin was an independent risk factor for SGA in Victoria (p < .001), with a prevalence of SGA for migrant women of 11.3% (n = 27,815) and 7.3% for Australian born women (n = 33,749). Women from the Americas (aOR1.24, 95%CI:1.14 to 1.36), North Africa, North East Africa, and the Middle East (aOR1.57, 95%CI:1.52 to 1.63); Southern Central Asia (aOR2.58, 95%CI:2.50 to 2.66); South East Asia (aOR2.02, 95%CI: 1.95 to 2.01); and sub-Saharan Africa (aOR1.80, 95%CI:1.69 to 1.92) were more likely to birth an SGA child in comparison to women born in Australia.

Conclusions
Victorian woman’s region of origin was an independent risk factor for SGA. Variation in the rates of SGA between maternal regions of origin suggests additional factors such as a woman’s pre-migration exposures, the context of the migration journey, settlement conditions and social environment post migration might impact the potential for SGA. These findings highlight the importance of intergenerational improvements to the wellbeing of migrant women and their children. Further research to identify modifiable elements that contribute to birthweight differences across population groups would help enable appropriate healthcare responses aimed at reducing the rate of being SGA.
Extending screening intervals for women at low risk of breast cancer: do they find it acceptable?
Authors: McWilliams Lorna , Woof Victoria G. , Donnelly Louise S. , Howell Anthony , Evans D. Gareth , French David P. 
Published: May 2021

Abstract
Background
Trials of risk estimation in breast cancer screening programmes, in order to identify women at higher risk and offer extra screening/preventive measures, are ongoing. It may also be feasible to introduce less frequent screening for women at low-risk of breast cancer. This study aimed to establish views of women at low-risk of breast cancer regarding the acceptability of extending breast screening intervals for low-risk women beyond 3 y.

Methods
Semi-structured interviews were used to explore views of low-risk women, where “low-risk” was defined as less than 2% estimated 10-year risk of breast cancer aged > 46 years. Low-risk women were identified via the BC-Predict study, where following routine screening, women were given their 10-year risk of breast cancer by letter, along with additional information explaining breast cancer risk factors. To gain diversity of views, purposive sampling by ethnicity and socioeconomic background was used to recruit women. Data were analysed using thematic analysis.

Results
Twenty-three women participated in individual interviews. Three themes are reported: (1) A good opportunity to receive risk estimation, where women found it worthwhile to receive a low-risk result although some were surprised if expecting a higher risk result; (2) Multi-faceted acceptability of extended screening intervals, with reactions to less frequent screening dependent on whether women were confident in being low-risk status and current safety evidence, (3) Passive approval versus informed choice, highlighting that women found it difficult to consider choosing less frequent screening without professionals’ recommendations, as they generally viewed attending breast screening as positive.

Conclusions
Risk assessment and receiving a low-risk of breast cancer is acceptable although, further research is required with more diverse samples of women. Any recommendation of less frequent screening in this risk group should be evidence-based in order to be acceptable. Communication needs to be carefully developed, with a focus on ensuring informed choice, prior to trialling any extended screening recommendations in future studies.
Genetic analysis of sinonasal undifferentiated carcinoma discovers recurrent SWI/SNF alterations and a novel PGAP3-SRPK1 fusion gene
Authors: Heft Neal Molly E. , Birkeland Andrew C. , Bhangale Apurva D. , Zhai Jingyi , Kulkarni Aditi , Foltin Susan K. , Jewell Brittany M. , Ludwig Megan L. , Pinatti Lisa , Jiang Hui , McHugh Jonathan B. , Marentette Lawence , McKean Erin L. , Brenner J. Chad 
Published: May 2021

Abstract
Background
Sinonasal Undifferentiated Carcinoma (SNUC) is a rare and aggressive skull base tumor with poor survival and limited treatment options. To date, targeted sequencing studies have identified IDH2 and SMARCB1 as potential driver alterations, but the molecular alterations found in SMARCB1 wild type tumors are unknown.

Methods
We evaluated survival outcomes in a cohort of 46 SNUC patients treated at an NCI designated cancer center and identify clinical and disease variables associated with survival on Kaplan-Meier and Cox multivariate survival analysis. We performed exome sequencing to characterize a series of SNUC tumors (n = 5) and cell line (MDA8788–6) to identify high confidence mutations, copy number alterations, microsatellite instability, and fusions. Knockdown studies using siRNA were utilized for validation of a novel PGAP3-SRPK1 gene fusion.

Results
Overall survival analysis revealed no significant difference in outcomes between patients treated with surgery +/− CRT and CRT alone. Tobacco use was the only significant predictor of survival. We also confirmed previously published findings on IDH and SMARC family mutations and identified novel recurrent aberrations in the JAK/STAT and PI3K pathways. We also validated a novel PGAP3-SRPK1 gene fusion in the SNUC cell line, and show that knockdown of the fusion is negatively associated with EGFR, E2F and MYC signaling.

Conclusion
Collectively, these data demonstrate recurrent alterations in the SWI/SNF family as well as IDH, JAK/STAT, and PI3K pathways and discover a novel fusion gene (PGAP3-SRPK1). These data aim to improve understanding of possible driver mutations and guide future therapeutic strategies for this disease.