bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons
Authors: Barnes If Habib Ahmed , Ibarra-Soria Ximena , Fitzgerald Stephen , Gonzalez Jose Manuel , Davidson Claire , Hardy Matthew Philip , Manthravadi Deepa , Gerven Laura Van , Jorissen Mark , Zeng Zhen , Khan Mona , Mombaerts Peter , Harrow Jennifer , Logan Darren William , Frankish Adam 
Published: February 2020

Abstract
Background: Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. Results: Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.Conclusions: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.
DKK3 attenuates JNK and AP-1 induced inflammation via Kremen-1 and DVL-1 in mice following intracerebral hemorrhage
Authors: Xu Yang , Nowrangi Derek , Liang Hui , Wang Tian , Yu Lingyan , Lu Tai , Lu Zhengyang , Zhang John H. , Luo Benyan , Tang Jiping 
Published: February 2020

Abstract
Background: Intracerebral hemorrhage (ICH) is the most devastating stroke subtype, with a poor prognosis and few proven treatments. Neuroinﬂammation is associated with ICH-induced brain injury and unfavorable outcomes. There is growing evidence that Dickkopf (DKK) 3 plays a key role in the adaptive anti-inflammatory and neuroprotective responses following intracerebral hemorrhage. This study aimed to evaluate the protective effects of DKK3 against brain edema and neuroinflammation in a mice model of ICH. Methods: Male, adult CD1 mice were subjected to sham or ICH surgery using a collagenase injection model. ICH animals received either recombinant DKK3, Kremen-1 siRNA, or DVL-1 siRNA. The neurobehavioral deficits were evaluated at 24 h, 72 h, and 28 days after ICH induction. Western blot and immunofluorescence were employed to examine the expression and localization of DKK3, Kremen-1, Dishevelled-1 (DVL-1), c-JUN N-terminal kinase (JNK), Activator protein-1 (AP-1), cleaved caspase-1, NF-κB, and IL-1β in the brain. Results: The expression of endogenous DKK3 and DVL-1 was transiently decreased after ICH compared to that in the sham group. Compared to the mice of ICH, exogenous rDKK3 administration reduced the brain water content and affected the neurological functions in ICH mice. Moreover, DKK3 was colocalized with Kremen-1 in microglia. Using a Kremen-1 or DVL-1 siRNA-induced in vivo knockdown approach, we demonstrated that the effects of DKK3 against ICH were mediated , at least partly, by the Kremen-1 and DVL-1 pathways. Conclusions: DKK3 improves the neurological outcomes, potentially by decreasing JNK/AP-1 mediated inflammation, thereby ameliorating the short- and long-term sequelae after ICH.
Small intestinal microbiota composition and the prognosis of infants with ileostomy resulting from distinct primary diseases
Authors: Qian Tian , Zhu Haitao , Zhu Li , Chen Chao , Shen Chun , Zhang Rong 
Published: February 2020

Abstract
Background: Studies of microbiota composition of infants with small intestinal ostomy due to various etiologies are limited. Here, we characterized the intestinal microbiota of infants with ileostomy resulting from distinct primary diseases. Methods: Fifteen patients with necrotizing enterocolitis, eight patients with meconium peritonitis, and seven patients with Hirschsprung's disease were included in the study. The small intestinal microbiota composition in infants with ileostomy caused by these diseases was studied. Results: Microbial diversity in infantile ileostomy fluid was generally low, and was dominated by members of the Proteobacteria and Firmicutes phyla. At the genus level, the most abundant were Klebsiella, Escherichia-Shigella, Streptococcus, Clostridium sensu stricto 1, Enterococcus, and Lactobacillus. Streptococcus and Veillonella are related to carbohydrate metabolism and immunity, and breastfeeding can increase the proportion of these potentially beneficial bacteria. The proportion of Bifidobacterium in the breastfeeding group was higher than that in the non-breastfeeding group, and incidence of colitis and sepsis was significantly reduced in the breastfeeding group. The increase in body weight in the breastfeeding group was observed to be higher than in the non-breastfeeding group. Conclusions: Excessive Klebsiella and Escherichia-Shigella and low abundance of Streptococcus, Veillonella and Faecalibacterium suggests that the small intestinal microbiota is in an unhealthy state after ileostomy. However, Streptococcus, Faecalibacterium, and Veillonella species were frequently present, suggesting that expansion of these bacteria might assist the development of the immune system after surgery.
LIVE/DEAD™ Fixable Near-IR Cell Viability Assay
Authors: Faber Samantha C. , McCullough Shaun 
Published: February 2020

Abstract
This protocol is used to determine the viability of cells prior to the fixation and permeabilization required for intracellular antibody staining or prior to elimination of biohazardous materials using formaldehyde fixation. The attached methods document is a formal version of the information included here.Disclaimer: The contents of this article have been reviewed by the US Environmental Protection Agency and approved for publication and do not necessarily represent Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendations for use.
Isolation of Total RNA with the Life Technologies PureLink Kit
Authors: McNabb Nicole A. , McCullough Shaun D. 
Published: February 2020

Abstract
This protocol describes the use of the Life Technologies PureLink RNA isolation kit for the isolation and purification of total RNA from cells grown in culture. Notes describing specific modifications for use with the Trans-Epithelial Exposure Model are included.The attached methods document is a formal version of the information included hereDisclaimer: The contents of this article have been reviewed by the US Environmental Protection Agency and approved for publication and do not necessarily represent Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendations for use.
Autogeny in Culiseta longiareolata (Culicidae: Diptera) Mosquitoes in Laboratory Conditions in Iran
Authors: Khaligh Fereshteh Ghahvechi , Naghian Abdollah , Soltanbeiglou Shadiyeh , Gholizadeh Saber 
Published: February 2020

Abstract
Objectives Culiseta longiareolata is a cosmopolitan species and has implicated in the transmission of avian malaria, tularemia, and arboviruses. Despite the wide distribution of Cs. longiareolata in Iran, little is known about its biology and physiology. The current research was conducted to study the autogeny behavior in this potential vector. During 2018, larvae and pupae were collected from Nazloo region in Urmia City using standard methods. Mosquitoes were reared in cages and fed by 5% sugar in laboratory conditions and were then dissected in phosphate-buffered saline (PBS) under a stereo microscope.ResultsIn total, 230 adult female Cs. longiareolata mosquitoes were dissected. Egg rafts were observed in the ovary of only 10.86% unfed female mosquitoes. Autogeny behavior is a significant factor in the growth of population without a blood feeding. Therefore, it is necessary to study how autogenous reproduction affects mosquito-borne diseases.
The effectiveness of mindfulness on quality of life of women with premature menopause: a quasi-experimental study
Authors: Pyri Fatemeh , Abedi Parvin , Maraghi Elham , Jashreh Maryam Gholamzadeh 
Published: February 2020

Abstract
Background: Premature menopause may impair the quality of life and expose women to disorders such as cardiovascular disease, osteoporosis, and depression. This study aimed to evaluate the effectiveness of mindfulness on the quality of life of women with premature menopause. Methods: This was a quasi-experimental study in which 62 women were recruited and randomly allocated in two groups of mindfulness and control. The mindfulness group received eight sessions of training. A demographic questionnaire, Menopause-Specific Quality of Life (MENQOL) and a checklist (for assessing frequency and intensity of hot flashes) were used to collect data. The quality of life, frequency, and intensity of hot flashes measured at baseline, after eight weeks and in three months follow-up. The Independent t-test, the chi-square test, and the repeated measure test were used for analyzing data. Results: The score of quality of life was significantly improved after the intervention and in three months follow-up in the mindfulness group compared to the control group (p<0.001). The scores of vasomotor, psychological, physical, and sexual domains also improved significantly in the mindfulness group compared to the control group. The severity and the frequency of hot flashes were significantly reduced in the mindfulness group in comparison to the control group. Conclusion: The results of this study showed that eight weeks of mindfulness training could significantly improve the quality of life and also could reduce the frequency and intensity of hot flashes in women with premature menopause. Using mindfulness for women with premature menopause is recommended.
Observational Study Comparing Efficacy and Safety Between Preoperative Neoadjuvant Concurrent Chemoradiotherapy and Chemotherapy for Patients with Unresectable Locally Advanced or Metastatic Gastric Cancer
Authors: Yeh Yung-Sung , Huang Ming-Yii , Ma Cheng-Jen , Huang Ching-Wen , Tsai Hsiang-Lin , Chen Yen-Cheng , Li Ching-Chun , Yu Fang-Jung , Shih Hsiang-Yao , Wang Jaw-Yuan 
Published: February 2020

Abstract
Background Dismal outcomes in patients with locally advanced or metastatic gastric cancer (GC) highlights the need for effective systemic neoadjuvant treatment strategies to improve clinical results. Neoadjuvant multimodality strategies vary widely. This study compared the efficacy, safety, and clinical outcomes of preoperative neoadjuvant CCRT and chemotherapy for such patients. Methods Sixty-five patients with histologically confirmed locally advanced or metastatic GC following neoadjuvant CCRT or computed tomography (CT) were retrospectively enrolled between January 2010 and April 2019. Clinical outcomes included response, progression-free survival (PFS), and overall survival (OS), and toxicity was compared between the two groups. Results Of the 65 patients, 18 (27.7%) were in the response group (2 patients with complete response and 16 with partial response) and 47 (72.3%) in the nonresponse group (29 patients with stable disease and 18 with progressive disease). Multivariate analysis revealed no independent response predictor between CCRT and CT groups (all P > 0.05). Furthermore, results revealed no statistical differences in toxicity between the two groups (all P > 0.05). With a follow-up median of 12 months (ranging 6–48 months), 12-month OS and PFS were 39.7% and 20.4% in the CCRT group and 30.3% and 13.2% in the chemotherapy group, respectively. The median OS and PFS were 14.0 months (95% CI 9.661–18.339) and 9.0 months (95% CI 6.805–11.195) in the CCRT group and 10.0 months (95% CI 6.523–13.477) and 8.0 months (95% CI 6.927–9.073) in the CT group, respectively. Both OS (P = 0.011) and PFS (P = 0.008) in patients with CCRT were significantly better than those in patients with chemotherapy alone. Conclusions Neoadjuvant CCRT achieved more favorable OS and PFS than did neoadjuvant chemotherapy alone, without significant increases of toxicity in patients. However, prospective randomized trials comparing treatment modalities are necessary to confirm potential advantages of preoperative neoadjuvant CCRT.
Association between serum vitamin D and uric acid in the eastern Chinese population: a population-based cross-sectional study
Authors: Chen Yingchao , Cheng Jing , Chen Yi , Wang Ningjian , Xia Fangzhen , Chen Chi , Han Bing , Lu Yingli 
Published: February 2020

Abstract
Background Uric acid (UA) is the end product of purine metabolism, which is thought to be related to many human diseases, such as nephrolithiasis, gout, cardiovascular disease (CVD), type 2 diabetes mellitus, metabolic syndrome. However, the relationship between serum UA (SUA) and 25(OH)D is still unclear in the eastern Chinese population. Methods We did a population-based observational investigation, which included 12,770 residents living in eastern China. Ultimately, data from 9,220 subjects were analyzed. Serum 25(OH)D, SUA, fasting plasma glucose(FPG), fasting insulin, HbA1c and other metabolic parameters were tested. Waist circumference (WC), weight and height were also measured. Questionnaires were collected from these subjects for information on smoking and drinking status. Results We enrolled 9,220 Chinese adults, including 3,681 males (age 55.57±13.23 years) and 5,539 females (age 54.31±12.83 years). The levels of SUA were 352.07±79.25 nmol/L and 269.29±64.68 nmol/L in males and females, respectively. The proportion of adults with hyperuricemia (HUA) was 12.26% in the total population. Levels of SUA were positively associated with 25(OH)D, and the incidence of HUA increased 9.4% for every 10 nmol/L increase in 25(OH)D (P<0.001). Conclusions SUA was positively associated with 25(OH)D in the eastern Chinese population. Higher levels of serum 25(OH)D may be a potential predictor of HUA.
Body mass index affects adaptive immune cells in the human bone marrow
Authors: Pangrazzi Luca , Naismith Erin , Miggitsch Carina , Arana Jose’ Antonio Carmona , Keller Michael , Grubeck-Loebenstein Beatrix , Weinberger Birgit 
Published: February 2020

Abstract
Background. Obesity has been associated with chronic inflammation and oxidative stress. Both conditions play a determinant role in the pathogenesis of age-related diseases, such as immunosenescence. Adipose tissue can modulate the function of the immune system with the secretion of molecules influencing the phenotype of immune cells. Recently, the importance of the bone marrow (BM) in the maintenance of antigen-experienced adaptive immune cells has been documented. Despite this, whether high body mass index (BMI) may affect immune cells in the BM and the production of molecules supporting the maintenance of these cells it is unknown. Methods. Using flow cytometry, the frequency and the phenotype of immune cell populations were measured in paired BM and PB samples obtained from persons with different BMI. Furthermore, the expression of BM cytokines was assessed. The influence of cytomegalovirus (CMV) on T cell subsets was additionally considered, dividing the donors into the CMV - and CMV + groups. Results. Our study suggests that increased BMI may affect both the maintenance and the phenotype of adaptive immune cells in the BM. While the BM levels of IL-15 and IL-6, supporting the survival of highly differentiated T cells, and oxygen radicals increased in overweight persons, the production of IFNγ and TNF by CD8 + T cells was reduced. In addition, the frequency of B cells and CD4 + T cells positively correlated with BMI in the BM of CMV - persons. Finally, the frequency of several T cell subsets, and the expression of senescence/exhaustion markers within these subpopulations, were affected by BMI. In particular, the levels of bona fide memory T cells may be reduced in overweight persons. Conclusion. Our work suggests that obesity may represent an independent risk factor supporting immunosenescence, in addition to aging and CMV. Metabolic interventions may help in improving the fitness of the immune system in the elderly.
Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling
Authors: Li Xizhi , Li Min , Zhou Beibei , Bao Jinlin , Zhu Liang , Xue Pengbo , Wang Jun , Jin Jian 
Published: February 2020

Abstract
Background SRL1 (SEMI-ROLLED LEAF 1) also named as CLD1 (CURLED LEAF AND DWARF 1), encoding a putative glyphopholipidininol-anchored membrane protein, has been characterized as a gene involved in the regulation of leaf morphology in rice. Mutants of srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit defects in leaf development resulting in a phenotype with adaxially rolled leaves. Results To explore the gene regulatory network of leaf development that controlled by SRL1 in rice, we created a homozygous SRL1 knock out (KO) line by CRISPR/Cas9, which showed defects in leaf development with adaxially rolling. By comparing the leaf transcriptome of a homozygous SRL1 KO line (srl1-KO) with the control, a total number of 3,178 genes were identified as differentially expressed genes, of which 1,216 genes were significantly up regulated, while 1,962 genes were down regulated. Further analyses indicated that, a group of known leaf rolling related genes, which involved in bulliform cells and cuticle development such as OsZHD1, OsLBD3-7, RFS, ACL1, CFL1, SND1, OsCESA5 and OsCESA6 were up or down regulated in the srl1-KO. Conclusions SRL1 might control leaf rolling by regulating a couple of genes that affecting cytological architecture of leaf cells such as bulliforms and cuticle of leaves.
Feature-driven classification reveals potential comorbid subtypes within childhood apraxia of speech
Authors: Stein Catherine , Benchek Penelope , Miller Gabrielle , Hall Noémi B. , Menon Dhanya , Freebairn Lisa , Tag Jessica , Vick Jennell , Taylor H. Gerry , Lewis Barbara A. , Iyengar Sudha K. 
Published: February 2020

Abstract
Background

Childhood apraxia of speech (CAS) is a neurodevelopmental disorder with heterogeneous communication and other comorbid manifestations. While previous studies have characterized speech deficits associated with CAS, few studies have examined variability in reading and language and/or other developmental comorbidities. We sought to identify comorbid subgroups within CAS that could be clinically relevant as well as genetically distinctive.

Methods

In a group of 31 children with CAS and 8 controls, we performed hierarchical cluster analysis utilizing measures of articulation, vocabulary, and reading. We also conducted a chart review of the children with CAS to examine other clinical characteristics in these children and their association with subgroup membership.

Results

We identified 3 comorbid subgroups within CAS of varying severity. The high severity subgroup was characterized by poor reading and vocabulary, and the moderate severity subgroup by poor reading and non-word repetition but average vocabulary, compared to the mild severity subgroup. Subgroups were indistinguishable with respect to speech sound production, the hallmark of CAS, all demonstrating poor articulation. Children in the most severe subgroup were more likely to have early problems feeding (p=0.036).

Conclusions

Children with CAS may potentially be classified into comorbidity groups based on performance on vocabulary and reading measures, providing additional insight into the heterogeneity within CAS with implications for educational interventions.
Long non-coding RNA SNHG16 activates USP22 expression to regulate colorectal cancer progression by sponging miR-132-3p
Authors: He Xiaowen , Ma Jun , Zhang Mingming , Cui Jianhua , Yang Hao 
Published: February 2020

Abstract
Colorectal cancer (CRC) is the most common cause of cancer-related mortality in the world. Long non-coding RNAs (lncRNAs) were involved in the development of many cancers. However, studies on the effect of lncRNA small nucleolar RNA host gene 16 (SNHG16) on the proliferation, metastasis and apoptosis of CRC cells were still few. SNHG16 was highly expressed in CRC tissues and cells. Knockdown of SNHG16 reduced the proliferation, migration, invasion, and promoted the apoptosis of CRC cells. MiR-132-3p could interact with SNHG16, and its inhibitor recovered the suppression effects of silenced-SNHG16 on CRC cell progression. Besides, USP22 was a target of miR-132-3p, and its overexpression restored the inhibition effects of miR-132-3p mimic on CRC cell progression. Interference of SNHG16 reduced the tumor growth in vivo. LncRNA SNHG16 played an oncogene in CRC progression. The discovery of SNHG16/ miR-132-3p/ USP22 pathway provided new thinking for the treatment of CRC.