bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baicalin-loaded folic acid-modified albumin nanoparticles (FA-BSANPs/BA) induce autophagy in MCF-7 cells via ROS-mediated p38 MAPK and Akt/mTOR pathway
Authors: Liu Fengjie , Lan Meng , Ren Baoqi , Li Lihong , Zou Tengteng , Kong Zhaodi , Fan Dongmei , Cai Tiange , Cai Yu 
Published: January 2022

Abstract
Background
Breast cancer is the most frequently occurring cancer among women. Baicalin has been shown to inhibit breast cancer proliferation, but poor aqueous solubility and unknown mechanism of action limit its application. This study aimed to investigate the antiproliferative effects of baicalin-loaded folic acid-modified albumin nanoparticles (FA-BSANPs/BA) in breast cancer MCF-7 cells and its relationship with autophagy and ROS-mediated p38 MAPK and Akt/mTOR signaling pathways. Cell viability was detected by MTT assay. Flow cytometry and fluorescence microscopy were used to detect cell cycle, apoptosis and autophagy. Western blot was used to detect protein expression.

Results
Compared with the control and free baicalin groups, FA-BSANPs/BA inhibited viability of MCF-7 cells and increased cells in S phase, apoptotic bodies, pro-apoptotic proteins, autophagy markers and autophagosomes. These effects could be reversed when combined with the autophagy inhibitor 3-methyladenine. FA-BSANPs/BA increased the levels of phosphorylated p38 MAPK, inhibited the levels of phosphorylated Akt and mTOR, and increased the level of ROS in MCF-7 cells. The effects of FA-BSANPs/BA could be reversed or enhanced using inhibitors of Akt, mTOR, p38 MAPK and ROS scavengers.

Conclusions
Encapsulation in folate albumin nanoparticles improved the antiproliferative activity of baicalin. FA-BSANPs/BA induced autophagy and apoptosis via ROS-mediated p38 MAPK and Akt/mTOR signaling pathways in human breast cancer cells.
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families
Authors: Zhou Albert E. , Shah Zalak V. , Bradwell Katie R. , Munro James B. , Berry Andrea A. , Serre David , Takala-Harrison Shannon , O’Connor Timothy D. , Silva Joana C. , Travassos Mark A. 
Published: January 2022

Abstract
Background
RIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs, making their classification challenging using traditional bioinformatic methods.

Results
STRIDE (STevor and RIfin iDEntifier) is an HMM-based, command-line program that automates the identification and classification of RIFIN and STEVOR protein sequences in the malaria parasite Plasmodium falciparum. STRIDE is more sensitive in detecting RIFINs and STEVORs than available PFAM and TIGRFAM tools and reports RIFIN subtypes and the number of sequences with a FHEYDER amino acid motif, which has been associated with severe malaria pathogenesis.

Conclusions
STRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.
ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently
Authors: Tian Renmao , Imanian Behzad 
Published: January 2022

Abstract
Background
Amplicon sequencing of marker genes such as 16S rDNA have been widely used to survey and characterize microbial community. However, the complex data analyses have required many interfering manual steps often leading to inconsistencies in results.

Results
Here, we have developed a pipeline, amplicon sequence analysis pipeline 2 (ASAP 2), to automate and glide through the processes without the usual manual inspections and user’s interference, for instance, in the detection of barcode orientation, selection of high-quality region of reads, and determination of resampling depth and many more. The pipeline integrates all the analytical processes such as importing data, demultiplexing, summarizing read profiles, trimming quality, denoising, removing chimeric sequences and making the feature table among others. The pipeline accepts multiple file formats as input including multiplexed or demultiplexed, paired-end or single-end, barcode inside or outside and raw or intermediate data (e.g. feature table). The outputs include taxonomic classification, alpha/beta diversity, community composition, ordination analysis and statistical tests. ASAP 2 supports merging multiple sequencing runs which helps integrate and compare data from different sources (public databases and collaborators).

Conclusions
Our pipeline minimizes hands-on interference and runs amplicon sequence variant (ASV)-based amplicon sequencing analysis automatically and consistently. Our web server assists researchers that have no access to high performance computer (HPC) or have limited bioinformatics skills. The pipeline and web server can be accessed at https://github.com/tianrenmaogithub/asap2 and https://hts.iit.edu/asap2, respectively.
Transcriptomics analysis reveals the signal transduction mechanism of brassinolides in tea leaves and its regulation on the growth and development of Camellia sinensis
Authors: Jin Qifang , Wang Zhong , Chen Yanni , Luo Yiping , Tian Na , Liu Zhonghua , Huang Jianan , Liu Shuoqian 
Published: January 2022

Abstract
Background
Brassinosteroids (BRs) are a type of sterol plant hormone that play an important role in various biochemical and physiological reactions such as promoting cell growth, increasing biomass, and improving stress resistance.

Results
To investigate the regulatory and molecular mechanism of BRs on the growth and development of tea plants (Camellia sinensis L.), changes in cell structure and gene expression levels of tea leaves treated with exogenous BRs were analyzed by electron microscopy and high-throughput Illumina RNA-Seq technology. The results showed that the number of starch granules in the chloroplasts and lipid globules increased and thylakoids expanded after BR treatment compared with the control. Transcriptome analysis showed that in the four BR treatments (CAA: BR treatment for 3 h, CAB: BR treatment for 9 h, CAC: BR treatment for 24 h, and CAD: BR treatment for 48 h), 3861 (1867 upregulated and 1994 downregulated), 5030 (2461 upregulated and 2569 downregulated), 1626 (815 upregulated and 811 downregulated), and 2050 (1004 upregulated and 1046 downregulated) differentially expressed genes were detected, respectively, compared with CAK (BR treatment for 0 h). Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, metabolic pathway enrichment analysis showed that the differentially expressed genes of CAA vs. CAK, CAB vs. CAK, CAC vs. CAK, and CAD vs. CAK significantly enriched the functional categories of signal transduction, cell cycle regulation, and starch, sucrose, and flavonoid biosynthesis and metabolism pathways. We also found that after spraying BR, the key genes for caffeine synthesis were downregulated. The results of qRT-PCR coincided with the findings of transcriptomic analysis.

Conclusions
The present study improved our understanding of the effects of BRs on the growth and development of tea leaves and laid the foundation for the in-depth analysis of signal transduction pathways of BRs in tea leaves.
Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration
Authors: Ochs Matthew E. , McWhirter Rebecca M. , Unckless Robert L. , Miller David M. , Lundquist Erik A. 
Published: January 2022

AbstractMigration of neuroblasts and neurons from their birthplace is central to the formation of neural circuits and networks. ETR-1 is the Caenorhabditis elegans homolog of the CELF1 (CUGBP, ELAV-like family 1) RNA-processing factor involved in neuromuscular disorders. etr-1 regulates body wall muscle differentiation. Our previous work showed that etr-1 in muscle has a non-autonomous role in neuronal migration, suggesting that ETR-1 is involved in the production of a signal emanating from body wall muscle that controls neuroblast migration and that interacts with Wnt signaling. etr-1 is extensively alternatively-spliced, and we identified the viable etr-1(lq61) mutant, caused by a stop codon in alternatively-spliced exon 8 and only affecting etr-1 isoforms containing exon 8. We took advantage of viable etr-1(lq61) to identify potential RNA targets of ETR-1 in body wall muscle using a combination of fluorescence activated cell sorting (FACS) of body wall muscles from wild-type and etr-1(lq61) and subsequent RNA-seq. This analysis revealed genes whose splicing and transcript levels were controlled by ETR-1 exon 8 isoforms, and represented a broad spectrum of genes involved in muscle differentiation, myofilament lattice structure, and physiology. Genes with transcripts underrepresented in etr-1(lq61) included those involved in ribosome function and translation, similar to potential CELF1 targets identified in chick cardiomyocytes. This suggests that at least some targets of ETR-1 might be conserved in vertebrates, and that ETR-1 might generally stimulate translation in muscles. As proof-of-principle, a functional analysis of a subset of ETR-1 targets revealed genes involved in AQR and PQR neuronal migration. One such gene, lev-11/tropomyosin, requires ETR-1 for alternative splicing, and another, unc-52/perlecan, requires ETR-1 for the production of long isoforms containing 3′ exons. In sum, these studies identified gene targets of ETR-1/CELF1 in muscles, which included genes involved in muscle development and physiology, and genes with novel roles in neuronal migration.
Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing
Authors: Guo Yaping , Huang Hetian , Zhang Zhenzhen , Ma Yanchao , Li Jianzeng , Tang Hehe , Ma Haoxiang , Li Zhuanjian , Li Wenting , Liu Xiaojun , Kang Xiangtao , Han Ruili 
Published: January 2022

Abstract
Background
Valgus-varus deformity (VVD) is a lateral or middle deviation of the tibiotarsus or tarsometatarsus, which is associated with compromised growth, worse bone quality and abnormal changes in serum indicators in broilers. To investigate the genetic basis of VVD, a genome wide association study (GWAS) was performed to identify candidate genes and pathways that are responsible for VVD leg disease, serum indicators and growth performance in broilers.

Results
In total, VVD phenotype, seven serum indicators and three growth traits were measured for 126 VVD broilers (case group) and 122 sound broilers (control group) based on a high throughput genome wide genotyping-by-sequencing (GBS) method. After quality control 233 samples (113 sound broilers and 120 VVD birds) and 256,599 single nucleotide polymorphisms (SNPs) markers were used for further analysis. As a result, a total of 5 SNPs were detected suggestively significantly associated with VVD and 70 candidate genes were identified that included or adjacent to these significant SNPs. In addition, 43 SNPs located on Chr24 (0.22 Mb - 1.79 Mb) were genome-wide significantly associated with serum alkaline phosphatase (ALP) and 38 candidate genes were identified. Functional enrichment analysis showed that these genes are involved in two Gene Ontology (GO) terms related to bone development (cartilage development and cartilage condensation) and two pathways related to skeletal development (Toll−like receptor signaling pathway and p53 signaling pathway). BARX2 (BARX homeobox 2) and Panx3 (Pannexin 3) related to skeleton diseases and bone quality were obtained according to functional analysis. According to the integration of GWAS with transcriptome analysis, HYLS1 (HYLS1 centriolar and ciliogenesis associated) was an important susceptibility gene.

Conclusions
The results provide some reference for understanding the relationship between metabolic mechanism of ALP and pathogenesis of VVD, which will provide a theoretical basis for disease-resistant breeding of chicken leg soundness.
Diversity of bacterium communities in saline-alkali soil in arid regions of Northwest China
Authors: Nan Lili , Guo Quanen , Cao Shiyu , Zhan Zongbing 
Published: January 2022

Abstract
Background
The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources.

Results
The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks.

Conclusions
The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%).
The identification of type I MADS box genes as the upstream activators of an endosperm-specific invertase inhibitor in Arabidopsis
Authors: Hoffmann Tobias , Shi Xiuling , Hsu Chuan-Yu , Brown Aakilah , Knight Quintera , Courtney La’ Shyra , Mukarram Ruqiyah J. , Wang Dongfang 
Published: January 2022

Abstract
Background
Nuclear endosperm development is a common mechanism among Angiosperms, including Arabidopsis. During nuclear development, the endosperm nuclei divide rapidly after fertilization without cytokinesis to enter the syncytial phase, which is then followed by the cellularized phase. The endosperm can be divided into three spatial domains with distinct functions: the micropylar, peripheral, and chalazal domains. Previously, we identified two putative small invertase inhibitors, InvINH1 and InvINH2, that are specifically expressed in the micropylar region of the syncytial endosperm. In addition, ectopically expressing InvINH1 in the cellularized endosperm led to a reduction in embryo growth rate. However, it is not clear what are the upstream regulators responsible for the specific expression of InvINHs in the syncytial endosperm.

Results
Using protoplast transient expression system, we discovered that a group of type I MADS box transcription factors can form dimers to activate InvINH1 promoter. Promoter deletion assays carried out in the protoplast system revealed the presence of an enhancer region in InvINH1 promoter, which contains several consensus cis-elements for the MADS box proteins. Using promoter deletion assay in planta, we further demonstrated that this enhancer region is required for InvINH1 expression in the syncytial endosperm. One of the MADS box genes, AGL62, is a key transcription factor required for syncytial endosperm development. Using promoter-GFP reporter assay, we demonstrated that InvINH1 and InvINH2 are not expressed in agl62 mutant seeds. Collectively, our data supports the role of AGL62 and other type I MADS box genes as the upstream activators of InvINHs expression in the syncytial endosperm.

Conclusions
Our findings revealed several type I MADS box genes that are responsible for activating InvINH1 in the syncytial endosperm, which in turn regulates embryo growth rate during early stage of seed development.
Incidence of emergency neurosurgical TBI procedures: a population-based study
Authors: Tverdal Cathrine , Aarhus Mads , Rønning Pål , Skaansar Ola , Skogen Karoline , Andelic Nada , Helseth Eirik 
Published: January 2022

Abstract
Background
The rates of emergency neurosurgery in traumatic brain injury (TBI) patients vary between populations and trauma centers. In planning acute TBI treatment, knowledge about rates and incidence of emergency neurosurgery at the population level is of importance for organization and planning of specialized health care services. This study aimed to present incidence rates and patient characteristics for the most common TBI-related emergency neurosurgical procedures.

Methods
Oslo University Hospital is the only trauma center with neurosurgical services in Southeast Norway, which has a population of 3 million. We extracted prospectively collected registry data from the Oslo TBI Registry – Neurosurgery over a five-year period (2015–2019). Incidence was calculated in person-pears (crude) and age-adjusted for standard population. We conducted multivariate multivariable logistic regression models to assess variables associated with emergency neurosurgical procedures.

Results
A total of 2151 patients with pathological head CT scans were included. One or more emergency neurosurgical procedure was performed in 27% of patients. The crude incidence was 3.9/100,000 person-years. The age-adjusted incidences in the standard population for Europe and the world were 4.0/100,000 and 3.3/100,000, respectively. The most frequent emergency neurosurgical procedure was the insertion of an intracranial pressure monitor, followed by evacuation of the mass lesion. Male sex, road traffic accidents, severe injury (low Glasgow coma score) and CT characteristics such as midline shift and compressed/absent basal cisterns were significantly associated with an increased probability of emergency neurosurgery, while older age was associated with a decreased probability.

Conclusions
The incidence of emergency neurosurgery in the general population is low and reflects neurosurgery procedures performed in patients with severe injuries. Hence, emergency neurosurgery for TBIs should be centralized to major trauma centers.
Uncommon cause of respiratory failure due to a bezoar in the hypopharynx: a case report
Authors: Adeli Seyed-Hasan , Sehat Malihe , Azarnia Samarin Gholamreza , Vafaeimanesh Jamshid , Ahmadpour Sajjad , Nasiri Sara 
Published: January 2022

AbstractBackgroundTrichotillomania and trichophagia cause trichobezoars, which are masses made of hair. The main presentation of this condition is abdominal pain. However, other complications include gastric outlet obstruction, nausea, vomiting, weight loss, malnutrition, hematemesis, diarrhea, and constipation.Case presentationA 57-year-old woman with trichotillomania was admitted to the Emergency Department with the chief complaints of dyspnea on exertion, shortness of breath, dysphagia, generalized weakness, and hoarseness. Spiral chest computed tomography (CT) scan did not reveal any parenchymal lesions Pulmonary CT angiography did not reveal pulmonary embolism. The patient was admitted to the Surgery Department for hand fasciotomy due to contrast leakage, and during laryngoscopy, a trichobezoar was detected that was removed with Magill forceps.ConclusionsRare cases of trichobezoars can be observed in humans with gastrointestinal and respiratory symptoms. Precise and timely diagnosis are key for the prevention of more invasive diagnostic procedures.
Multi-loop traction device facilitates gastric endoscopic submucosal dissection: ex vivo pilot study and an inaugural clinical experience
Authors: Matsui Hiroaki , Tamai Naoto , Futakuchi Toshiki , Kamba Shunsuke , Dobashi Akira , Sumiyama Kazuki 
Published: January 2022

Abstract
Background
Endoscopic submucosal dissection (ESD) is technically difficult and requires considerable training. The authors have developed a multi-loop traction device (MLTD), a new traction device that offers easy attachment and detachment. We aimed to evaluate the utility of MLTD in ESD.

Methods
This ex vivo pilot study was a prospective, block-randomized, comparative study of a porcine stomach model. Twenty-four lesions were assigned to a group that undertook ESD using the MLTD (M-ESD group) and a group that undertook conventional ESD (C-ESD group) to compare the speed of submucosal dissection. In addition, the data of consecutive 10 patients with eleven gastric lesions was collected using electronic medical records to clarify the inaugural clinical outcomes of gastric ESD using MLTD.

Results
The median (interquartile range) speed of submucosal dissection in the M-ESD and C-ESD groups were 141.5 (60.9–177.6) mm2/min and 35.5 (20.8–52.3) mm2/min, respectively; submucosal dissection was significantly faster in the M-ESD group (p < 0.05). The rate of en bloc resection and R0 resection was 100% in both groups, and there were no perforation in either group. The MLTD attachment time was 2.5 ± 0.9 min and the MLTD extraction time was 1.0 ± 1.1 min. Clinical outcomes of MLTD in gastric ESD were almost the same as those of ex vivo pilot study.

Conclusions
MLTD increased the speed of submucosal dissection in ESD and was similarly effective when used by expert and trainee endoscopists without perforation. MLTD can potentially ensure a safer and faster ESD.
Known in the nursing home: development and evaluation of a digital person-centered artistic photo-activity intervention to promote social interaction between residents with dementia, and their formal and informal carers
Authors: Tan Josephine Rose Orejana , Boersma Petra , Ettema Teake P. , Aëgerter Laurence , Gobbens Robbert , Stek Max L. , Dröes Rose-Marie 
Published: January 2022

AbstractBackgroundTo address the lack of social interaction and meaningful activities for persons with dementia (PWD) in nursing homes an artistic Photo-Activity was designed. The present study aims to develop a digital version of the Photo-Activity and to investigate its implementation and impact on nursing home residents with advanced dementia, and their (in)formal carers.MethodsFirst, within a user-participatory design, a digital-app version of the Photo-Activity will be developed and pilot-tested, in co-creation with (in)formal carers and PWD.Next, the feasibility and effectiveness of the Photo-Activity versus a control activity will be explored in a randomized controlled trial with nursing home residents (N=90), and their (in)formal carers. Residents will be offered the Photo-Activity or the control activity by (in)formal carers during one month. Measurements will be conducted by independent assessors at baseline (T0), after one month (T1) and at follow up, two weeks after T1 (T2). Qualitative and quantitative methods will be used to investigate the effects of the intervention on mood, social interaction and quality of life of the PWD, sense of competence of informal carers, empathy and personal attitude of the formal carers, and quality of the relationship between the PWD, and their (in)formal carers. In addition, a process evaluation will be carried out by means of semi-structured interviews with the participating residents and (in)formal carers.Finally, an implementation package based on the process evaluation will be developed, allowing the scaling up of the intervention to other care institutions.DiscussionResults of the trial will be available for dissemination by Spring 2023. The digital Photo-Activity is expected to promote meaningful connections between the resident with dementia, and their (in)formal carers through the facilitation of person-centered conversations.Trial registrationNetherlands Trial Register:NL9219; registered (21 January 2021); NTR (trialregister.nl)