bluuebunny/crossref_metadata_2025_split huggingface dataset:
Qualitative and quantitative comparison of cell-free DNA and cell-free fetal DNA isolation by four (semi-)automated extraction methods: impact in two clinical applications: chimerism quantification and noninvasive prenatal diagnosis
Authors: Pedini Pascal , Graiet Hajer , Laget Laurine , Filosa Lugdivine , Chatron Jade , Cherouat Nicem , Chiaroni Jacques , Hubert Lucas , Frassati Coralie , Picard Christophe 
Published: January 2021

Abstract
Background
Non-invasive molecular analysis of cell-free DNA (cfDNA) became a sensitive biomarker for monitoring organ transplantation or for detection of fetal DNA (cffDNA) in noninvasive prenatal test. In this study, we compared the efficiencies of four (semi)-automated cfDNA isolation instruments using their respective isolation kit: MagNA Pure 24 (Roche®), IDEAL (IDSolution®), LABTurbo 24 (Taigen®) and Chemagic 360 (Perkin Elmer®). The cfDNA was isolated from 5 plasma samples and the Rhesus D (RhD)-cffDNA from 5 maternal plasmas. The cfDNA were quantified by digital droplet PCR (ddPCR), BIABooster system and QUBIT fluorometer. The cfDNA fragment size profiles were assessed by BIABooster system. Chimerism were quantified by home-made ddPCR and Devyser NGS kit. RhD-cffDNA in maternal plasma were detected between weeks 14 and 24 of amenorrhea using free DNA Fetal RHD Kit® (Biorad®).

Results
Statistical tests have shown differences in DNA yield depending on the isolation procedure and quantification method used. Magna Pure isolates smaller cfDNA fragment size than other extraction methods (90% ± 9% vs. 74% ± 8%; p = 0.009). Chimerism was only reliable from LABTurbo 24 extractions using the NGS but not with ddPCR whatever extraction methods. RhD-cffDNA were detected by all isolation methods, although IDEAL and LABTurbo 24 systems seemed more efficient.

Conclusions
This comparative study showed a dependency of cfDNA yield depending on isolation procedure and quantification method used. In total, these results suggest that the choice of pre-analytical isolation systems needs to be carefully validated in routine clinical practice.
A novel long intergenic non-coding RNA, Nostrill, regulates iNOS gene transcription and neurotoxicity in microglia
Authors: Mathy Nicholas W. , Burleigh Olivia , Kochvar Andrew , Whiteford Erin R. , Behrens Matthew , Marta Patrick , Tian Cong , Gong Ai-Yu , Drescher Kristen M. , Steyger Peter S. , Chen Xian-Ming , Shibata Annemarie 
Published: January 2021

Abstract
Background
Microglia are resident immunocompetent and phagocytic cells in the CNS. Pro-inflammatory microglia, stimulated by microbial signals such as bacterial lipopolysaccharide (LPS), viral RNAs, or inflammatory cytokines, are neurotoxic and associated with pathogenesis of several neurodegenerative diseases. Long non-coding RNAs (lncRNA) are emerging as important tissue-specific regulatory molecules directing cell differentiation and functional states and may help direct proinflammatory responses of microglia. Characterization of lncRNAs upregulated in proinflammatory microglia, such as NR_126553 or 2500002B13Rik, now termed Nostrill (iNOS Transcriptional Regulatory Intergenic LncRNA Locus) increases our understanding of molecular mechanisms in CNS innate immunity.

Methods
Microglial gene expression array analyses and qRT-PCR were used to identify a novel long intergenic non-coding RNA, Nostrill, upregulated in LPS-stimulated microglial cell lines, LPS-stimulated primary microglia, and LPS-injected mouse cortical tissue. Silencing and overexpression studies, RNA immunoprecipitation, chromatin immunoprecipitation, chromatin isolation by RNA purification assays, and qRT-PCR were used to study the function of this long non-coding RNA in microglia. In vitro assays were used to examine the effects of silencing the novel long non-coding RNA in LPS-stimulated microglia on neurotoxicity.

Results
We report here characterization of intergenic lncRNA, NR_126553, or 2500002B13Rik now termed Nostrill (iNOS Transcriptional Regulatory Intergenic LncRNA Locus). Nostrill is induced by LPS stimulation in BV2 cells, primary murine microglia, and in cortical tissue of LPS-injected mice. Induction of Nostrill is NF-κB dependent and silencing of Nostrill decreased inducible nitric oxide synthase (iNOS) expression and nitric oxide (NO) production in BV2 and primary microglial cells. Overexpression of Nostrill increased iNOS expression and NO production. RNA immunoprecipitation assays demonstrated that Nostrill is physically associated with NF-κB subunit p65 following LPS stimulation. Silencing of Nostrill significantly reduced NF-κB p65 and RNA polymerase II recruitment to the iNOS promoter and decreased H3K4me3 activating histone modifications at iNOS gene loci. In vitro studies demonstrated that silencing of Nostrill in microglia reduced LPS-stimulated microglial neurotoxicity.

Conclusions
Our data indicate a new regulatory role of the NF-κB-induced Nostrill and suggest that Nostrill acts as a co-activator of transcription of iNOS resulting in the production of nitric oxide by microglia through modulation of epigenetic chromatin remodeling. Nostrill may be a target for reducing the neurotoxicity associated with iNOS-mediated inflammatory processes in microglia during neurodegeneration.
Clinical evaluation of neuroinflammation in child-onset focal epilepsy: a translocator protein PET study
Authors: Kagitani-Shimono Kuriko , Kato Hiroki , Kuwayama Ryoko , Tominaga Koji , Nabatame Shin , Kishima Haruhiko , Hatazawa Jun , Taniike Masako 
Published: January 2021

AbstractBackgroundNeuroinflammation is associated with various chronic neurological diseases, including epilepsy; however, neuroimaging approaches for visualizing neuroinflammation have not been used in the clinical routine yet. In this study, we used the translocator protein positron emission tomography (PET) with [11C] DPA713 to investigate neuroinflammation in the epileptogenic zone in patients with child-onset focal epilepsy.MethodsPatients with intractable focal epilepsy were recruited at the Epilepsy Center of Osaka University; those who were taking any immunosuppressants or steroids were excluded. PET images were acquired for 60 min after intravenous administration of [11C] DPA713. The PET image of [11C] DPA713 was co-registered to individual’s magnetic resonance imaging (MRI), and the standardized uptake value ratio (SUVr) in regions of interest, which were created in non-lesions and lesions, was calculated using the cerebellum as a pseudo-reference region. In the case of epilepsy surgery, the correlation between SUVr in lesions and pathological findings was analyzed.ResultsTwenty-seven patients (mean age: 11.3 ± 6.2 years, male/female: 17/10) were included in this study. Of these, 85.1% showed increased uptake of [11C] DPA713 in the focal epileptic lesion. Three patients showed epileptic spasms, suggesting partial seizure onset, and all 18 patients with abnormal lesions on MRI were similarly highlighted by significant uptake of [11C] DPA713. DPA713-positive patients had a broad range of etiologies, including focal cortical dysplasia, tumors, infarction, and hippocampal sclerosis. Five out of nine MRI-negative patients showed abnormal [11C] DPA713 uptake. The SUVr of [11C] DPA713 in lesions was significantly higher than that in non-lesions. In seven patients who underwent epilepsy surgery, increased [11C] DPA713 uptake was associated with microglial activation.ConclusionsThis study indicates that [11C] DPA713 uptake has valuable sensitivity in the identification of epileptic foci in child-onset focal epilepsy, and inflammation is implicated in the pathophysiology in the epileptic foci caused by various etiologies. Further research is required to establish diagnostic tools for identifying focal epileptogenic zones.
Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya
Authors: Avedi Edith Khamonya , Adediji Adedapo Olutola , Kilalo Dora Chao , Olubayo Florence Mmogi , Macharia Isaac , Ateka Elijah Miinda , Machuka Eunice Magoma , Mutuku Josiah Musembi 
Published: January 2021

AbstractBackgroundTomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya.MethodsTomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated.ResultsTwelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with aTomato leaf curl virus Arusha virus(ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences.ConclusionsThe begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.
Ever-increasing viral diversity associated with the red imported fire ant Solenopsis invicta (Formicidae: Hymenoptera)
Authors: Xavier César Augusto Diniz , Allen Margaret Louise , Whitfield Anna Elizabeth 
Published: January 2021

Abstract
Background
Advances in sequencing and analysis tools have facilitated discovery of many new viruses from invertebrates, including ants. Solenopsis invicta is an invasive ant that has quickly spread worldwide causing significant ecological and economic impacts. Its virome has begun to be characterized pertaining to potential use of viruses as natural enemies. Although the S. invicta virome is the best characterized among ants, most studies have been performed in its native range, with less information from invaded areas.

Methods
Using a metatranscriptome approach, we further identified and molecularly characterized virus sequences associated with S. invicta, in two introduced areas, U.S and Taiwan. The data set used here was obtained from different stages (larvae, pupa, and adults) of S. invicta life cycle. Publicly available RNA sequences from GenBank’s Sequence Read Archive were downloaded and de novo assembled using CLC Genomics Workbench 20.0.1. Contigs were compared against the non-redundant protein sequences and those showing similarity to viral sequences were further analyzed.

Results
We characterized five putative new viruses associated with S. invicta transcriptomes. Sequence comparisons revealed extensive divergence across ORFs and genomic regions with most of them sharing less than 40% amino acid identity with those closest homologous sequences previously characterized. The first negative-sense single-stranded RNA virus genomic sequences included in the orders Bunyavirales and Mononegavirales are reported. In addition, two positive single-strand virus genome sequences and one single strand DNA virus genome sequence were also identified. While the presence of a putative tenuivirus associated with S. invicta was previously suggested to be a contamination, here we characterized and present strong evidence that Solenopsis invicta virus 14 (SINV-14) is a tenui-like virus that has a long-term association with the ant. Furthermore, based on virus sequence abundance compared to housekeeping genes, phylogenetic relationships, and completeness of viral coding sequences, our results suggest that four of five virus sequences reported, those being SINV-14, SINV-15, SINV-16 and SINV-17, may be associated to viruses actively replicating in the ant S. invicta.

Conclusions
The present study expands our knowledge about viral diversity associated with S. invicta in introduced areas with potential to be used as biological control agents, which will require further biological characterization.
HEV prevalence and potential risk factors in a large multi-ethnic youth cohort in China
Authors: Li Huixia , Zhang Yinxia , Ma Zhongren , Liu Zewen , Ikram Aqsa , Liu Lijiang , Zhao Guoqin , Pan Qiuwei , Baloch Zulqarnain 
Published: January 2021

Abstract
Background
This cohort study was designed to investigate the prevalence of and potential risk factors of HEV infection in a large multi-ethnic youth cohort in China.

Methods
Blood samples were collected from participants (n = 6269) and serum was isolated. All serum samples were tested for anti-HEV IgG, anti-HEV IgM antibodies using commercial enzyme immunoassay kits (Wantai Biological Pharmacy Enterprise, Beijing, China).

Results
The overall rate of anti-HEV IgG and anti-HEV IgM prevalence was 4.78% and 0.14%, 0.03% were positive for both anti-HEV IgG and anti-HEV IgM antibodies. Anti-HEV IgG positivity is significantly higher in females (5.27%) compared to males (4.14%) (P = 0.028). Anti-HEV IgG prevalence is significantly (P = 0.0001) higher in Dong (17.57%), Miao (12.23%), Yi (11.04%), Gelao (9.76%), and Bai (10.00%) compared to other ethnic groups. It is significantly higher in Guizhou (11.4%), Sichuan (10.1%), Yunnan (9.3%), and Guangxi (6.9%) than that other province. We found that ethnicity and provincial background are significantly associated with HEV infection in this cohort.

Conclusion
This study provides comprehensive information on HEV prevalence in multi-ethnic populations in China. However, our study only focused on a youth population from different provinces of China. Future studies are recommended to investigate HEV prevalence in other age groups of the ethnic populations.
Sialylated human milk oligosaccharides prevent intestinal inflammation by inhibiting toll like receptor 4/NLRP3 inflammasome pathway in necrotizing enterocolitis rats
Authors: Zhang Wenting , He-Yang Jingqiu , Tu Wenjuan , Zhou Xiaoying 
Published: January 2021

Abstract
Background
Necrotizing enterocolitis (NEC) remains a fatal gastrointestinal disorder in neonates and has very limited therapeutic options. Sialylated human milk oligosaccharides (SHMOs) improve pathological changes in experimental NEC models. The objectives of this study were to investigate the involvement of NLRP3 inflammasome in NEC pathology and to explore the effects of SHMOs on toll-like receptor 4 (TLR4)/nuclear factor κB (NF-κB)/NLRP3 inflammatory pathway in experimental NEC.

Methods
The intestinal-tissue segments were collected from NEC infants, NLRP3 and caspase-1 positive cell were examined by immunohistochemistry. Newborn rats were hand-fed with formula containing or non-containing SHMOs (1500 mg/L) and exposed to hypoxia/cold stress to induce experimental NEC. The NEC pathological scores were evaluated; ileum protein expression of membrane TLR4 (mTLR4), inhibitor κB-α (IκB-α), NF-κB p65 subunit and phospho-NF-κB p65, as well as NLRP3 and caspase-1 were analyzed; ileum concentrations of interleukin-1β, interleukin-6, tumor necrosis factor-α (TNF-α) were also measured. Human colon epithelial Caco-2 cells were pre-treated with or without SHMOs and stimulated with TLR4 activator, lipopolysaccharide. Cell viabilities, mitochondrial membrane potential and supernatant matrix metalloprotease 2 (MMP-2) activities were analyzed.

Results
Increased frequencies of NLRP3 and caspase-1 positive cells were found in the lamina propria of damaged intestinal area of NEC neonates. SHMOs supplementation reduced NEC incidence and pathological damage scores of rats challenged with hypoxia/cold stress. Accumulation of interleukin-1β, interleukin-6 and TNF-α in NEC group were attenuated in SHMOs + NEC group. Protein expression of mTLR4, NLRP3 and caspase-1 were elevated, cytoplasmic IκB-α were reduced, nuclear phospho-NF-κB p65 were increased in the ileum of NEC rats. SHMOs supplementation ameliorated the elevation of mTLR4, NLRP3 and caspase-1, restored IκB-α in the cytoplasmic fraction and reduced phospho-NF-κB p65 in the nuclear fraction in the ileum of NEC rats. SHMOs pre-treatment improved Caco-2 cell viability, mitigated loss of mitochondrial membrane potential and modulated MMP-2 activities in the presence of lipopolysaccharide in-vitro.

Conclusions
This study provided clinical evidence of involvement of NLRP3 inflammasome in NEC pathology, and demonstrated the protective actions of SHMOs might be owing to the suppression of TLR4/NF-κB/NLRP3-mediated inflammation in NEC.
Association between breastfeeding and new mothers’ sleep: a unique Australian time use study
Authors: Smith Julie P. , Forrester Robert I. 
Published: January 2021

Abstract
Background
Infant sleep is of great interest to new parents. There is ongoing debate about whether infants fed with breastmilk substitutes sleep longer than those exclusively or partially breastfed, but what does this mean for the mother? What expectations are realistic for mothers desiring to exclusively breastfeed as recommended by health authorities?
There are both biological and social influences on infant and maternal sleep. More accurate information on average maternal sleep hours for diverse feeding practices may help guide realistic expectations and better outcomes for mothers, infants and families.

Methods
Using a unique time use dataset purposefully designed to study the time use of new mothers, this study investigated whether the weekly duration of maternal sleep, sleep disturbance, unpaid housework, and free time activities differed by detailed feeding method. The study collected 24/7 time use data from 156 mothers of infants aged 3, 6 and/or 9 months between April 2005 and April 2006, recruited via mother’s groups, infant health clinics, and childcare services throughout Australia. Sociodemographic and feeding status data were collected by questionnaire. Statistical analysis used linear mixed modelling and residual maximum likelihood analysis to compare effects of different infant feeding practices on maternal time use.

Results
There were no significant differences in time spent asleep between lactating and non lactating mothers, though lactating mothers had more time awake at night. Lactating mothers spent more time (8.5 h weekly) in childcaring activity (p = 0.007), and in employment (2.7 vs. 1.2 h, p < 0.01), but there were no significant differences in free time. Those not breastfeeding spent more time in unpaid domestic work.
Exclusive breastfeeding was associated with reduced maternal sleep hours (average 7.08 h daily). Again, free time did not differ significantly between feeding groups. Exclusively breastfeeding mothers experienced reduced sleep hours, but maintained comparable leisure time to other mothers by allocating their time differently. Domestic work hours differed, interacting in complex ways with infant age and feeding practice.

Conclusions
Optimal breastfeeding may require realistic maternal sleep expectations and equitable sharing of paid and unpaid work burdens with other household members in the months after the birth of an infant.
Comparing breastfeeding experiences between mothers spending the traditional Chinese confinement period in a confinement centre and those staying at home: a cohort study
Authors: Foong Siew Cheng , Tan May Loong , Foong Wai Cheng , Ho Jacqueline J. , Rahim Fairuz Fadzilah 
Published: January 2021

AbstractBackgroundEthnic Chinese mothers in Malaysia adhere to 30 days of traditional postpartum practices (the “confinement period”) aimed at recuperation after delivery. Recently there has been an emergence of confinement centres (CCs) where mothers stay and receive traditional confinement care. Ethnic Chinese mothers have low breastfeeding rates. There are concerns that practices in CCs could contribute to this but no data exists. We described mothers’ breastfeeding experiences at CCs and identified areas for potential improvement in breastfeeding support.MethodsEthnic Chinese mothers intending to breastfeed their healthy infants were recruited post-delivery between August and October 2017 then, at 1 and 6 months, they were telephone interviewed about their experience. For every participant going to a CC after the birth, another mother going home (“home”) for her confinement was recruited. Chi-square test was used to compare groups and multiple logistic regression was used to assess the effect of confinement place on exclusive breastfeeding.ResultsOf 187 mothers, 88 (47%) went to CCs. Significantly more were primipara and fewer had previous breastfeeding experience. Response rates for the 1- and 6- month interviews were 88% (CC) versus 97% (home); and 77% (CC) versus 87% (home) respectively.Exclusive breastfeeding rates were similar between the groups: 62% (CC) versus 56% (home) at 1 month (p = 0.4); and 37% (CC) versus 42% (home) at 6 months (p = 0.5). Multiple logistic regression did not show that CCs were a factor affecting exclusive breastfeeding rates at 1 month, (adjusted odds ratio [aOR] 1.7, 95% confidence interval [CI] 0.9, 3.3), or 6 months (aOR 0.9, 95% CI 0.4, 1.7). However, significantly more CC participants only fed expressed breast milk. Despite 66% of CC participants reporting that their centre supported breastfeeding, only 6 (8%) CC participants compared to 66 (69%) of home participants roomed-in with their baby (p < 0.001). The proportion encountering breastfeeding difficulties were similar between groups. CC participants sought help for breastfeeding problems mainly from CC staff and support groups while home participants obtained help from friends and healthcare professionals.ConclusionsBreastfeeding rates appeared to be similar at CCs and at home during the confinement period, but there were gaps in how CCs supported breastfeeding. Targeted training to CC staff to support breastfeeding may result in better outcomes for mothers staying in CCs.