bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain
Authors: Liu Ailing , Zhou Zhibo , Yi Yake , Chen Guanghui 
Published: February 2020

Abstract
Background
Node is the central organ of transferring nutrients and ions in plants. Cadmium (Cd) induced crop pollution threatens the food safety. Breeding of low Cd accumulation cultivar is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 (low Cd accumulation cultivar) and Yuzhenxiang (high Cd accumulation cultivar). RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs.

Results
Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node I had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4535 DEGs and 70 miRNAs between the two cultivars. Most genesrelated to the “transporter activity”, such as OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1, play roles in blocking the upward transport of Cd. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) in Xiangwanxian No. 12 played a potent role in lowering Cd accumulation via down regulating the expression of candidate genes, such as bZIP, ERF, MYB, SnRK1 and HSPs.

Conclusions
Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in Cd stress response.
Genome-wide identification of cold responsive transcription factors in Brassica napus L
Authors: Ke Liping , Lei Weixia , Yang Weiguang , Wang Jinyu , Gao Janfang , Cheng Jinhua , Sun Yuqiang , Fan Zhixiong , Yu Dongliang 
Published: February 2020

Abstract
Background
Cold stress is one of the primary environmental factors that affect plant growth and productivity, especially for crops like Brassica napus that live through cold seasons. Till recently, although a number of genes and pathways involved in B. napus cold response have been revealed by independent studies, a genome-wide identification of the key regulators and the regulatory networks is still lack. In this study, we investigated the transcriptomes of cold stressed semi-winter and winter type rapeseeds in short day condition, mainly with the purpose to systematically identify the functional conserved transcription factors (TFs) in cold response of B. napus.

Results
Global modulation of gene expression was observed in both the semi-winter type line (158A) and the winter type line (SGDH284) rapeseeds, in response to a seven-day chilling stress in short-day condition. Function analysis of differentially expressed genes (DEGs) revealed enhanced stresses response mechanisms and inhibited photosynthesis in both lines, as well as a more extensive inhibition of some primary biological processes in the semi-winter type line. Over 400 TFs were differentially expressed in response to cold stress, including 56 of them showed high similarity to the known cold response TFs and were consistently regulated in 158A and SGDH284, as well as 25 TFs which targets were over-represented in the total DEGs. A further investigation based on their interactions indicated the critical roles of several TFs in cold response of B. napus.

Conclusion
In summary, our results revealed the alteration of gene expression in cold stressed semi-winter and winter ecotype B. napus lines and provided a valuable collection of candidate key regulators involved in B. napus response to cold stress, which could expand our understanding of plant stress response and benefit the future improvement of the breed of rapeseeds.
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites
Authors: Yang Xiaodi , Yang Shiping , Qi Huan , Wang Tianpeng , Li Hong , Zhang Ziding 
Published: February 2020

AbstractBackgroundProtein-protein interactions (PPIs) play very important roles in diverse biological processes. Experimentally validated or predicted PPI data have become increasingly available in diverse plant species. To further explore the biological functions of PPIs, understanding the interaction details of plant PPIs (e.g., the 3D structural contexts of interaction sites) is necessary. By integrating bioinformatics algorithms, interaction details can be annotated at different levels and then compiled into user-friendly databases. In our previous study, we developed AraPPISite, which aimed to provide interaction site information for PPIs in the model plantArabidopsis thaliana. Considering that the application of AraPPISite is limited to one species, it is very natural that AraPPISite should be evolved into a new database that can provide interaction details of PPIs in multiple plants.DescriptionPlaPPISite (http://zzdlab.com/plappisite/index.php) is a comprehensive, high-coverage and interaction details-oriented database for 13 plant interactomes. In addition to collecting 121 experimentally verified structures of protein complexes, the complex structures of experimental/predicted PPIs in the 13 plants were also constructed, and the corresponding interaction sites were annotated. For the PPIs whose 3D structures could not be modelled, the associated domain-domain interactions (DDIs) and domain-motif interactions (DMIs) were inferred. To facilitate the reliability assessment of predicted PPIs, the source species of interolog templates, GO annotations, subcellular localizations and gene expression similarities are also provided. JavaScript packages were employed to visualize structures of protein complexes, protein interaction sites and protein interaction networks. We also developed an online tool for homology modelling and protein interaction site annotation of protein complexes. All data contained in PlaPPISite are also freely available on the Download page.ConclusionPlaPPISite provides the plant research community with an easy-to-use and comprehensive data resource for the search and analysis of protein interaction details from the 13 important plant species.
The endophytic bacterium Sphingomonas SaMR12 alleviates Cd stress in oilseed rape through regulation of the GSH-AsA cycle and antioxidative enzymes
Authors: Wang Qiong , Ge Chaofeng , Xu Shun’an , Wu Yingjie , Sahito Zulfiqar Ali , Ma Luyao , Pan Fengshan , Zhou Qiyao , Huang Lukuan , Feng Ying , Yang Xiaoe 
Published: February 2020

Abstract
Background
Microbes isolated from hyperaccumulating plants have been reported to be effective in achieving higher phytoextraction efficiency. The plant growth-promoting bacteria (PGPB) SaMR12 from the cadmium (Cd)/zinc hyperaccumulator Sedum alfredii Hance could promote the growth of a non-host plant, oilseed rape, under Cd stress. However, the effect of SaMR12 on Brasscia juncea antioxidative response under Cd exposure was still unclear.

Results
A hydroponic experiment was conducted to study the effects of Sphingomonas SaMR12 on its non-host plant Brassica juncea (L.) Czern. under four different Cd treatments. The results showed that SaMR12 could colonize and aggregate in the roots and then move to the shoots. SaMR12 inoculation promoted plant growth by up to 71% in aboveground biomass and 81% in root biomass over that of the non-inoculated plants. SaMR12-inoculated plants significantly enhanced root Cd accumulation in the 10 and 20 μM Cd treatments, with 1.72- and 0.86-fold increases, respectively, over that of the non-inoculated plants. SaMR12 inoculation not only decreased shoot hydrogen peroxide (H2O2) content by up to 38% and malondialdehyde (MDA) content by up to 60% but also reduced proline content by 7–30% in shoots and 17–32% in roots compared to the levels in non-inoculated plants. Additionally, SaMR12 inoculation promoted the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) and facilitated the relative gene expression levels of dehydroascorbate reductase (DHAR) and glutathione reductase (GR) involved in the glutathione (GSH)-ascorbic acid (AsA) cycle.

Conclusions
The results demonstrated that, under Cd stress, SaMR12 inoculation could activate the antioxidative response of B. juncea by decreasing the concentrations of H2O2, MDA and proline, increasing the activities of antioxidative enzymes, and regulating the GSH-AsA cycle. These results provide a theoretical foundation for the potential application of hyperaccumulator endophytic bacteria as remediating agents to improve heavy metal tolerance within non-host plant species, which could further improve phytoextraction efficiency.

Graphical abstract
A rare combination of MODY5 and duodenal atresia in a patient: a case report
Authors: Du Tao , Zeng Nan , Wen Xiaofang , Zhu Peizhuang , Li Wangen 
Published: February 2020

AbstractBackgroundMaturity-onset diabetes of the young (MODY) is a genetically and clinically heterogeneous group of hereditary diabetes, generally caused by one abnormal gene. MODY5 is caused by mutations of the hepatocyte nuclear factor 1 homeobox β gene (HNF1β), always as a part of Chr17q12 deletion, whereas heterozygous mutation in B lymphocyte kinase (BLK) gene is responsible for MODY11.Case presentationWe report a patient who developed diabetes with a 1.58-Mb Chr17q12 microdeletion and BLK gene c.211G > A mutation using the cytoscan high-density array and whole-exome sequencing analysis. The patient received the surgery at five days after birth for the duodenal atresia and had normal growth postoperatively. Mild elevated liver enzymes were found along with the normal renal function. Quantitative analysis of β-cell function markers, including fasting insulin (< 0.2 mIU/L), fasting C-peptide (0.02 μg/L), postprandial-2 h insulin (< 0.2 mIU/L), and postprandial-2 h C-peptide (0.03 μg/L) suggested a severe loss of insulin secreting capacity. Meanwhile, islet autoantibodies (GADA, IA-2, ICA, and IAA) in the patient’s blood appeared negative. Neither dysplasia in other tissues nor abnormality in development and behavior was found.ConclusionTo date, gastrointestinal malformations were extremely rarely reported in patients with MODY. Our clinical report further expands the clinical presentation and variability of MODY5.
Analysis of association between common variants of uncoupling proteins genes and diabetic retinopathy in a Chinese population
Authors: Jin Peiyao , Li Zhiqiang , Xu Xian , He Jiangnan , Chen Jianhua , Xu Xun , Du Xuan , Bai Xuelin , Zhang Bo , He Xiangui , Lu Lina , Zhu Jianfeng , Shi Yongyong , Zou Haidong 
Published: February 2020

Abstract
Background
The aim of this study was to explore the association between diabetic retinopathy (DR) and the variants of uncoupling proteins (UCPs) genes in a Chinese population of type 2 diabetes, in total and in patients of different glycemic status separately.

Methods
This case-control study included a total of 3107 participants from two datasets, among which 662 were DR patients (21.31%). Eighteen tag single nucleotide polymorphisms (SNPs) of UCP1, UCP2, and UCP3 were selected as genetic markers. TaqMan probes, Sequenom MassARRAY MALDI-TOF mass spectrometry platform and Affymetrix Genome-Wide Human SNP Array were used for genotyping. Online SHEsis software was used for association analysis. Bonferroni correction was used for multiple comparisons correction.

Results
Three SNPs of UCP1: rs7688743 (A allele, OR = 1.192, p = 0.013), rs3811787 (T allele, OR = 0.863, p = 0.023), and rs10011540 (G allele, OR = 1.368, p = 0.004) showed association with DR after the adjustment of glucose, but only rs10011540 was marginally significantly associated with DR when Bonferroni correction was strictly applied (padj = 0.048). In patients with uncontrolled glucose, rs7688743 (A allele, p = 0.012, OR = 1.309), rs10011540 (G allele, p = 0.033, OR = 1.432), and rs3811787 (T allele, p = 0.022, OR = 0.811) were associated with DR, while in participants with well controlled glucose, the rs2734827 of UCP3 was associated with DR (A allele, p = 0.017, OR = 0.532). Rs3811787 of UCP1 showed a protective effect to sight threatening DR (T allele, p = 0.007, OR = 0.490), and the association existed after the adjustment for environmental factors and the correction. In patients with uncontrolled glucose, the rs3811787 of UCP1 (T allele, p = 0.017, OR = 0.467) and the rs591758 of UCP3 (C allele, p = 0.026, OR = 0.103) were associated with STDR. While in those with well controlled glucose, only the rs7688743 of UCP1 showed a protective effect (A allele, p = 0.024, OR = 0.049). None of the associations remain significant when Bonferroni correction was strictly applied (all p < 0.05).

Conclusions
The rs10011540 and rs3811787 of the UCP1 gene was marginally significantly associated with DR in Chinese type 2 diabetes patients. There might be different mechanisms of DR development in patients with different glycemic status.
Neuronal migration genes and a familial translocation t (3;17): candidate genes implicated in the phenotype
Authors: Hadj Amor Meriam , Dimassi Sarra , Taj Amel , Slimani Wafa , Hannachi Hanene , Mlika Adnene , Ben Helel Khaled , Saad Ali , Mougou-Zerelli Soumaya 
Published: February 2020

Abstract
Background
While Miller-Dieker syndrome critical region deletions are well known delineated anomalies, submicroscopic duplications in this region have recently emerged as a new distinctive syndrome. So far, only few cases have been described overlapping 17p13.3 duplications.

Methods
In this study, we report on clinical and cytogenetic characterization of two new cases involving 17p13.3 and 3p26 chromosomal regions in two sisters with familial history of lissencephaly. Fluorescent In Situ Hybridization and array Comparative Genomic Hybridization were performed.

Results
A deletion including the critical region of the Miller-Dieker syndrome of at least 2,9 Mb and a duplication of at least 3,6 Mb on the short arm of chromosome 3 were highlighted in one case. The opposite rearrangements, 17p13.3 duplication and 3p deletion, were observed in the second case. This double chromosomal aberration is the result of an adjacent 1:1 meiotic segregation of a maternal reciprocal translocation t(3,17)(p26.2;p13.3).

Conclusions
17p13.3 and 3p26 deletions have a clear range of phenotypic features while duplications still have an uncertain clinical significance. However, we could suggest that regardless of the type of the rearrangement, the gene dosage and interactions of CNTN4, CNTN6 and CHL1 in the 3p26 and PAFAH1B1, YWHAE in 17p13.3 could result in different clinical spectrums.
Differential significance of molecular subtypes which were classified into EGFR exon 19 deletion on the first line afatinib monotherapy
Authors: Tokudome Nahomi , Koh Yasuhiro , Akamatsu Hiroaki , Fujimoto Daichi , Okamoto Isamu , Nakagawa Kazuhiko , Hida Toyoaki , Imamura Fumio , Morita Satoshi , Yamamoto Nobuyuki 
Published: February 2020

Abstract
Background
Epidermal growth factor receptor (EGFR)-sensitizing mutation, exon 19 deletion consists of several molecular variants. Influences of these variants on clinical response to EGFR tyrosine kinase inhibitors remain elusive.

Methods
West Japan Oncology Group 8114LTR is a prospective, multi-institutional biomarker study. Treatment naïve, advanced non-small-cell lung cancer patients with EGFR-sensitizing mutation received afatinib monotherapy. We conducted a preplanned subset analysis of patients harboring exon 19 deletion. Tumor tissue exon 19 deletion molecular variants were identified by blocking-oligo-dependent polymerase chain reaction (PCR) and by Luminex Technology. Plasma cfDNA was also obtained before and after the treatment and EGFR mutations were detected with multiplexed, pico-droplet digital PCR assay.

Results
Among 57 registered patients, twenty-nine patients were exon 19 deletion. Tissue DNA and cfDNA were available in 26 patients. Among the detected seven molecular variants, the most frequent was p.E746_A750delELREA (65.4%). According to the various classifications of molecular variants, twenty one (80.8%) were classified into 15-nucleotide deletion, one (3.8%) into 18-nucleotide deletion, and four patients (15.4%) into other insertion/substitution variant subgroups. The patient subgroup with 15-nucleotide deletion showed significantly longer progression-free survival than patients in other mixed insertion/substitution variant subgroup (p = 0.0244).

Conclusions
The clinical significance of molecular variants of exon 19 deletion on the first line afatinib monotherapy is reported here for the first time. Further investigation is needed for development of better therapeutic strategies.

Trial registration
This trial was registered at UMIN Clinical Trials Registry at 2014/12/4 (UMIN000015847).
The social determinants of health of the Urak Lawoi’ of southern Thailand
Authors: Reap Maura , Pornwattanavate Samittra , Thame Charlie , Van der Putten Marc 
Published: February 2020

Abstract
Background
Traditionally, most Western models of health viewed sickness and disease as a product of individual factors such as personal behaviors and genetic predisposition; consequently, healthcare interventions were largely focused on fixing the individual, with little attention placed on contributing external factors. The WHO’s “Social Determinants of Health” (SDH) framework, however, takes a broader ecological perspective that suggests that interventions must occur at multiple levels in order for good health to be achieved on an equitable basis. This model views health as a function of many circumstantial and environmental factors that are continuously and simultaneously interacting across multiple domains. These factors include structural mechanisms, such as laws and policies; socio-economic conditions, such as education and occupation; and intermediary circumstances, such as living and working conditions. Utilizing the SDH framework as a guide, this qualitative study sought to identify which specific determinants are most significant and present the greatest risk to the health and well-being of the Urak Lawoi’ (UL), a “sea nomad” group indigenous to southern Thailand.

Methods
Interviews, household surveys, and focus group discussions were utilized to gather primary data from 71 subjects in three different UL communities in southern Thailand. In addition, a comprehensive literature review of relevant international mechanisms, national laws, and national policies was conducted. All data collected was analyzed and coded utilizing HyperRESEARCH.

Results
In all three communities, education and livelihoods were found to be the most critical determinants. Additionally, land grabbing and living conditions were identified as dire issues on Ko Lipe. The law and policy review revealed several deviations between international mechanisms and national laws and policies in both enshrinement and enforcement, with the Royal Thai Government (RTG) often overlooking the interests of the UL when formulating laws and policies.

Conclusions
The above-mentioned determinants, along other structural and intermediary determinants, are synergizing, thereby placing the UL at increased risk of poorer health and health outcomes compared to other Thais living in the same vicinities. To rectify this, the RTG must reform national laws and policies that harm the UL, and civil society must hold them accountable. Several recommendations are offered to achieve a better future for the Urak Lawoi’.
Manaaki – a cognitive behavioral therapy mobile health app to support people experiencing gambling problems: a randomized control trial protocol
Authors: Humphrey Gayl , Chu Joanna , Dowling Nicki , Rodda Simone , Merkouris Stephanie , Parag Varsha , Newcombe David , Ho Elsie , Nosa Vili , Ruwhui-Collins Rebecca , Whittaker Robyn , Bullen Chris 
Published: February 2020

AbstractBackgroundThe low utilisation of current treatment services by people with gambling problems highlights the need to explore new modalities of delivering treatment interventions. This protocol presents the design of a pragmatic randomized control trial aimed at assessing the effectiveness and acceptability of cognitive behavioral therapy (CBT) delivered via a mobile app for people with self-reported gambling problems.MethodsAn innovative CBT mobile app, based on Deakin University’s GamblingLessonline program, has been adapted with end-users (Manaaki). Six intervention modules have been created. These are interwoven with visual themes to represent a journey of recovery and include attributes such as avatars, videos, and animations to support end-user engagement. An audio facility is used throughout the app to cater for different learning styles. Personalizing the app has been accomplished by using greetings in the participant’s language and their name (e.g. Kia ora Tāne) and by creating personalized feedback.A pragmatic, randomized control two-arm single-blind trial, will be conducted in New Zealand. We aim to recruit 284 individuals. Eligible participants are ≥18 years old, seeking help for their gambling, have access to a smartphone capable of downloading an app, able to understand the English language and are willing to provide follow-up information at scheduled time points. Allocation is 1:1, stratified by ethnicity, gender, and gambling symptom severity based on the Gambling Symptom Assessment Scale (G-SAS). The intervention group will receive the full mobile cognitive behavioural programme and the waitlist group will receive a simple app that counts down the time left before they have access to the full app and the links to the data collection tools. Data collection for both groups are: baseline, 4-, 8-, and 12-weeks post-randomisation. The primary outcome is a change in G-SAS scores. Secondary measures include changes in gambling urges, frequency, expenditure, and readiness to change. Indices of app engagement, utilisation and acceptability will be collected throughout the delivery of the intervention.DiscussionIf effective, this study will contribute to the improvement of health outcomes for people experiencing gambling problems and have great potential to reach population groups who do not readily engage with current treatment services.Ethics approvalNZ Health and Disability Ethics Committee (Ref: 19/STH/204)Trial registrationAustralian New Zealand Clinical Trial Registry (ANZCTRN 12619001605189) Registered 1 November 2019.