bluuebunny/crossref_metadata_2025 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

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

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

Background

Protein-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.

Description

PlaPPISite (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.

Conclusion

PlaPPISite 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

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

Background

Maturity-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 presentation

We 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.

Conclusion

To 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

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

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

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

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

Background

The 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.

Methods

An 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.

Discussion

If 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 approval

NZ Health and Disability Ethics Committee (Ref: 19/STH/204)

Trial registration

Australian New Zealand Clinical Trial Registry (ANZCTRN 12619001605189) Registered 1 November 2019.
Does health insurance coverage reduce informal payments? Evidence from the “red envelopes” in China
Authors: Liu Ning , Bao Guoxian , He Alex Jingwei
Published: February 2020

Background

Representing a major threat to both equity and efficiency of health systems, the corrupt practice of informal payments is widely found in developing and transition countries. As informal payments are more likely to occur in health systems characterized by a high out-of-pocket payment rate, it is argued that formalized prepaid health insurance programs may help to curb such practice.

Methods

Using panel data from the China Health and Retirement Longitudinal Survey, this study examined the association between changes in health insurance coverage on patient’s behavior proxied with informal payments.

Results

The statistical results reveal that health insurance status in fact increases the probability of patients making informal payments to physicians. However, this association varies among population groups and insurance programs, particularly between social health insurance and private health insurance status.

Conclusions

In a health system characterized by unequal allocation of medical resources, the dual pursuit of cost saving and quality of care may drive patients to make informal payments for personal gains. This study argues that health policy interventions aimed at curbing informal payments must be based on a thorough understanding of their complex socioeconomic causes and attack the perverse incentives in a coherent and bona fide manner.
Understanding sexual and reproductive health needs of young women living in Zika affected regions: a qualitative study in northeastern Brazil
Authors: Diniz Debora , Ali Moazzam , Ambrogi Ilana , Brito Luciana
Published: February 2020

Background

In 2016, the World Health Organization declared a Public Health Emergency of International Concern due to Zika’s association with microcephaly and other neurological disorders. Brazil was the epicenter of this epidemic and the most affected region has the lowest Human Development Index and the highest rates of adolescent pregnancy. Despite the end of the epidemic, Brazil continues to be the epicenter of Zika illness. This study examined the barriers faced by young women who seek sexual and reproductive health (SRH) care services living in affected areas and their attitudes towards SRH needs and the available services.

Methods

Individual semi-structured interviews were conducted with 22 young women, aged 14–24 years in three Zika affected municipalities in the Brazilian Northeast. This qualitative research used thematic analysis for data analysis.

Results

Almost half (n = 10) of the participants had their first pregnancy during adolescence (from 12 to 19), all of which were unintended. Lack of information and barriers to access family planning were found to contribute to the unmet need for contraception. Participants reported knowledge gaps about contraception. Zika was not considered a health concern and participants were unaware of the possibility of Zika’s sexual transmission.

Conclusions

The young women’s knowledge and attitudes towards their SRH needs highlight the barriers to access care. It also implies that comprehensive, biopsychosocial and political, understanding is necessary in order to adequately provide SRH to this population and meet their needs. The government should place women at the center of any public health response to an emergency affecting women of reproductive age and focus on improving access to information and family planning services in a culturally and age appropriate manner.
Prenatal diagnosis of maternal partial trisomy 9p23p24.3 and 14q11.2q21.3 in a fetus: a case report
Authors: Wu J. B. , Sha J. , Zhai J. F. , Liu Y. , Zhang B.
Published: February 2020

Objective

This study aimed to report a fetus with maternal partial trisomy 9p and 14q and the phenotype detected in ultrasound.

Methods

The chromosome rearrangements in the fetus were characterized by G-banding and chromosome microarray analysis based on single nucleotide polymorphism (SNP) array of cultured amniocytes and compared with the parents’ karyotypes.

Results

The fetal abnormal karyotype was 47,XY,+der(14)(9;14)(p23;q22). The SNP array revealed a duplicate 11.8-Mb 9p23-p24.3 fragment and a duplicate 29.6-Mb 14q11.2-q21.3 fragment. The peripheral blood karyotype of the mother was 46,XX,t(9;14)(p23;q22), while the father’s was normal at the level of 300~400 bands. A high-resolution karyotype analysis conformed the same abnormality of the mother at the level of 550~650 bands. These results indicated that the fetal chromosomal abnormality probably derived from the mother. The fetal nuchal translucency thickness was 3.5 mm, and the fetal heart was detected with around 1.0-mm ventricular defect by the ultrasound examination at 12-week gestation. The couple decided to terminate the pregnancy. They opted for in vitro fertilization and embryo transfer for the fourth pregnancy, which was successful.

Conclusions

The SNP array combined with cytogenetic analysis was particularly effective in identifying abnormal chromosomal rearrangements. These methods combined with the existing database information and fetal ultrasonography might provide a comprehensive and efficient way for the prenatal assessment of fetal situations. Preimplantation genetic diagnosis might effectively assist those women with an adverse pregnancy history in their next pregnancy.
The perspective on standardisation and harmonisation: the viewpoint of the EASI president
Authors: Damoiseaux Jan
Published: February 2020

Standardisation of immuno-assays for autoantibodies is a major challenge. Although multiple organisations participate in the generation of internationally accepted standards, adequate standardisation of assays has not yet been achieved. Harmonisation may offer an alternative approach to better align requesting, testing, reporting and interpretation of autoimmune diagnostics. The European Autoimmunity Standardisation Initiative (EASI) was founded to facilitate both standardisation as well as harmonisation of autoantibody tests, but over the years the focus has drifted away from standardisation in favour of harmonisation. In the current paper the options for harmonisation are highlighted.
Characterization of tea leaf metabolites dependent on tea (Camellia sinensis) plant age through 1H NMR-based metabolomics
Authors: Rubel Mozumder N. H. M. , Lee Yeong-Ran , Hwang Kyeong Hwan , Lee Min-Seuk , Kim Eun-Hee , Hong Young-Shick
Published: February 2020

The chemical or metabolic compositions of tea (Camellia sinensis) varies according to numerous factors, such as geographical origin, cultivar, climate, plucking position, and horticultural practices. However, how the age of tea plants affects the metabolite compositions of tea leaves has not been reported yet. Therefore, we extended the metabolomic approach to the investigation of the age-related differences of tea leaf metabolites in the fresh leaves collected from tea plants aged 8 and 25 years. Multivariate statistical analysis with comprehensive metabolite profiles analyzed by 1H NMR spectroscopy showed the clear metabolic differentiation between the fresh tea leaves from different ages of the tea plants. Of the various tea leaf metabolites varied according to the age of the tea plants, theanine, glutamine, catechin, and gallocatechin were uniquely dependent on the age of tea plants, demonstrating a difference of theanine metabolism between young and old tea plants. These results suggest that leaves from 25-year-old tea plants would still be worthy as a functional ingredient for the production in the food or cosmetic industry rather than quality-enhanced tea infusions for human consumption.
Effects of far-off and close-up transition cow feeding on uterine health, postpartum anestrous interval, and reproductive outcomes in pasture-based dairy cows
Authors: Meier S. , Kay J. K. , Kuhn-Sherlock B. , Heiser A. , Mitchell M. D. , Crookenden M. A. , Riboni M. Vailati , Loor J. J. , Roche J. R.
Published: February 2020

Background

In seasonal, pasture-based, dairy production systems, cows must recover from calving and become pregnant within two to 3 months. To achieve this, the uterus must involute and ovulation must occur and continue at regular intervals. As these processes are affected by the cows’ nutritional or metabolic status post-calving, the objective of this study was to evaluate the effect of cow feeding strategies on uterine health, the length of postpartum anestrous interval, and reproductive outcomes. The treatments consisted of two feeding strategies during late-lactation and early dry period (far-off period; starting 4-month pre-calving) and three close-up dry period feeding regimes (1-month pre-calving) in a 2 × 3 factorial arrangement. We randomly assigned 150 cows to one of two far-off treatments. During late lactation, the herds (n = 75 cows per herd) were either control-fed (Controlfed) or over-fed (Overfed) to achieve a low or high body condition score (4-month pre-calving; BCS; ~ 4.25 and ~ 4.75; 10-point scale) at cessation of lactation. Within each of these treatments, three feeding levels were applied during the close-up period (1-month pre-calving): ~ 65% (Feed65), ~ 90% (Feed90), or ~ 120% (Feed120) of metabolizable energy (ME) intakes relative to pre-calving requirements.

Results

Uterine health improved (i.e. polymorphonucleated (PMN) cells declined) with increased feeding during the close-up period for cows in the Overfed group. The reverse was evident for the Controlfed group with the greatest PMN at the highest intakes during the close-up period. The postpartum anoestrous interval (PPAI) was shorter in cows from the Overfed group when moderately fed (Feed90) during the close-up period; in comparison, the PPAI was shorter in the Controlfed group, when those cows were overfed in the close-up period (Feed120). The cows in the Overfed treatment had greater conception and pregnancy rates if cows had moderate dry matter intakes (Feed90) during the close-up period; these reproductive variables were less under excessive feed intakes (Feed120); yet, close-up dry matter intake had little effect on conception and pregnancy rates for the Controlfed group.

Conclusions

The far-off feeding strategies increased early reproductive outcomes at 3 weeks of mating. Additionally, the interaction between far-off and close-up feeding strategies resulted in high six-week pregnancy rate with a slight restriction during the close-up period but only in the far-off Overfed group. Thus, our hypothesis is supported under these conditions.
Correction to: The effect of transactional analysis on the self-esteem of imprisoned women: a clinical trial
Authors: Torkaman Mahya , Farokhzadian Jamileh , Miri Sakineh , Pouraboli Batool
Published: February 2020

Following publication of the original article [1], the authors advised that the name of the 4th author had been submitted incorrectly; the author has the family name ‘Pouraboli’, however, their article was originally published with the family name (mis) spelled as ‘Pouraboili’.
Explicit measurement of multi-tracer arterial input function for PET imaging using blood sampling spectroscopy
Authors: Velasco Carlos , Mota-Cobián Adriana , Mateo Jesús , España Samuel
Published: February 2020

Background

Conventional PET imaging has usually been limited to a single tracer per scan. We propose a new technique for multi-tracer PET imaging that uses dynamic imaging and multi-tracer compartment modeling including an explicitly derived arterial input function (AIF) for each tracer using blood sampling spectroscopy. For that purpose, at least one of the co-injected tracers must be based on a non-pure positron emitter.

Methods

The proposed technique was validated in vivo by performing cardiac PET/CT studies on three healthy pigs injected with 18FDG (viability) and 68Ga-DOTA (myocardial blood flow and extracellular volume fraction) during the same acquisition. Blood samples were collected during the PET scan, and separated AIF for each tracer was obtained by spectroscopic analysis. A multi-tracer compartment model was applied to the myocardium in order to obtain the distribution of each tracer at the end of the PET scan. Relative activities of both tracers and tracer uptake were obtained and compared with the values obtained by ex vivo analysis of excised myocardial tissue segments.

Results

A high correlation was obtained between multi-tracer PET results, and those obtained from ex vivo analysis (18FDG relative activity: r = 0.95, p < 0.0001; SUV: r = 0.98, p < 0.0001).

Conclusions

The proposed technique allows performing PET scans with two tracers during the same acquisition obtaining separate information for each tracer.
Driving forest succession in karst areas of Chongqing municipality over the past decade
Authors: Xiao Qiang , Xiao Yang , Liu Yuan , Tao Jianping
Published: February 2020

Background

Karst areas in southwestern China exhibit ecological degradation in the form of rocky desertification. Local governments launched large-scale afforestation and other ecological restoration programs to curb this trend. Soil thickness is a key limiting factor for vegetation restoration in Karst areas, but the relationship between ecological restoration and soil thickness remains unclear. Further, afforestation consumes large amounts of water, which impacts water supply in karst areas. In this study, we used GIS and statistical analyses to determine rocky desertification sensitivity and its driving factors in karst areas of Chongqing municipality over the past decade.

Results

Soil thickness is one of the key factors that restrict ecological restoration of rocky desertification. From 2000 to 2010, rocky desertification sensitivity in karst areas was on the rise along with an increase in afforestation. Areas of high sensitivity were mainly distributed in Pengshui County, Wulong District, and Youyang County; Shizhu County had the lowest overall incidence of desertification. Spatial distribution of rocky desertification was significantly affected by rainfall and soil thickness. Regression analysis showed that the main factors controlling changes in rocky desertification in natural forest over time were precipitation which explained 23.73% of total variance, and soil thickness which explained 23.42% of total variance. Soil thickness and soil water content had a higher correlation coefficient (at 0.516) in natural forests than in planted forests.

Conclusion

This study showed that increases in soil thickness in a karst area had a significant positive impact on the fragile ecological environment. This indicates that ecosystem restoration in karst areas will benefit from addressing soil thickness.
A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)
Authors:   , for the Zhongnan Hospital of Wuhan University Novel Coronavirus Management and Research Team, Evidence-Based Medicine Chapter of China International Exchange and Promotive Association for Medical and Health Care (CPAM), Jin Ying-Hui , Cai Lin , Cheng Zhen-Shun , Cheng Hong , Deng Tong , Fan Yi-Pin , Fang Cheng , Huang Di , Huang Lu-Qi , Huang Qiao , Han Yong , Hu Bo , Hu Fen , Li Bing-Hui , Li Yi-Rong , Liang Ke , Lin Li-Kai , Luo Li-Sha , Ma Jing , Ma Lin-Lu , Peng Zhi-Yong , Pan Yun-Bao , Pan Zhen-Yu , Ren Xue-Qun , Sun Hui-Min , Wang Ying , Wang Yun-Yun , Weng Hong , Wei Chao-Jie , Wu Dong-Fang , Xia Jian , Xiong Yong , Xu Hai-Bo , Yao Xiao-Mei , Yuan Yu-Feng , Ye Tai-Sheng , Zhang Xiao-Chun , Zhang Ying-Wen , Zhang Yin-Gao , Zhang Hua-Min , Zhao Yan , Zhao Ming-Juan , Zi Hao , Zeng Xian-Tao , Wang Yong-Yan , Wang Xing-Huan
Published: February 2020

In December 2019, a new type viral pneumonia cases occurred in Wuhan, Hubei Province; and then named “2019 novel coronavirus (2019-nCoV)” by the World Health Organization (WHO) on 12 January 2020. For it is a never been experienced respiratory disease before and with infection ability widely and quickly, it attracted the world’s attention but without treatment and control manual. For the request from frontline clinicians and public health professionals of 2019-nCoV infected pneumonia management, an evidence-based guideline urgently needs to be developed. Therefore, we drafted this guideline according to the rapid advice guidelines methodology and general rules of WHO guideline development; we also added the first-hand management data of Zhongnan Hospital of Wuhan University. This guideline includes the guideline methodology, epidemiological characteristics, disease screening and population prevention, diagnosis, treatment and control (including traditional Chinese Medicine), nosocomial infection prevention and control, and disease nursing of the 2019-nCoV. Moreover, we also provide a whole process of a successful treatment case of the severe 2019-nCoV infected pneumonia and experience and lessons of hospital rescue for 2019-nCoV infections. This rapid advice guideline is suitable for the first frontline doctors and nurses, managers of hospitals and healthcare sections, community residents, public health persons, relevant researchers, and all person who are interested in the 2019-nCoV.
Increased age at first-mating interacting with herd size or herd productivity decreases longevity and lifetime reproductive efficiency of sows in breeding herds
Authors: Koketsu Yuzo , Iida Ryosuke , Piñeiro Carlos
Published: February 2020

Background

Our objectives were to characterize sow life and herd-life performance and examine two-way interactions between age at first-mating (AFM) and either herd size or herd productivity groups for the performance of sows. Data contained 146,140 sows in 143 Spanish herds. Sow life days is defined as the number of days from birth to removal, whereas the herd-life days is from AFM date to removal date. Herds were categorized into two herd size groups and two productivity groups based on the respective 75th percentiles of farm means of herd size and the number of piglets weaned per sows per year: large (> 1017 sows) or small-to-mid herds (< 1017 sows), and high productivity (> 26.5 piglets) or ordinary herds (< 26.5 piglets). A two-level liner mixed-effects model was applied to examine AFM, herd size groups, productivity groups and their interactions for sow life or herd-life performance.

Results

No differences were found between either herd size or herd productivity groups for AFM or the number of parity at removal. However, late AFM was associated with decreased removal parity, herd-life days, herd-life piglets born alive and herd-life annualized piglets weaned, as well as with increased sow life days and herd-life nonproductive days (P < 0.05). Also, significant two-way interactions between AFM and both herd size and productivity groups were found for longevity, prolificacy, fertility and reproductive efficiency of sows. For example, as AFM increased from 190 to 370 days, sows in large herds decreased herd-life days by 156 days, whereas for sows in small-to-mid herds the decrease was only 42 days. Also, for the same AFM increase, sows in large herds had 5 fewer sow life annualized piglets weaned, whereas for sows in small-to-mid herds this sow reproductive efficiency measure was only decreased by 3.5 piglets. Additionally, for ordinary herds, sows in large herds had more herd-life annualized piglets weaned than those in small-to-mid herds (P < 0.05), but no such association was found for high productivity herds (P > 0.10).

Conclusion

We recommend decreasing the number of late AFM sows in the herd and also recommend improving longevity and lifetime efficiency of individual sows.
Findings from an exploration of a social network intervention to promote diet quality and health behaviours in older adults with COPD: a feasibility study
Authors: Bloom Ilse , Welch Lindsay , Vassilev Ivaylo , Rogers Anne , Jameson Karen , Cooper Cyrus , Robinson Sian , Baird Janis
Published: February 2020

Background

Diet quality in older people with chronic obstructive pulmonary disease (COPD) is associated with better health and lung function. Social factors, such as social support, social networks and participation in activities, have been linked with diet quality in older age. A social network tool—GENIE (Generating Engagement in Network Involvement)—was implemented in a COPD community care context. The study aimed to assess the feasibility of the GENIE intervention to promote diet quality and other health behaviours in COPD.

Methods

Twenty-two community-dwelling older adults with COPD were recruited from a local COPD service. Participants were offered usual care or the GENIE intervention. Process evaluation methods were used to assess intervention implementation, context and mechanisms of impact; these included observations of patient interactions with the intervention, documented in observational field notes and in films of a patient group discussion. Diet quality was assessed by food frequency questionnaire; ‘prudent’ diet scores were used to describe diet quality at baseline and at 3-month follow-up. Change in diet quality was expressed per month, from baseline to follow-up.

Results

Feasibility data showed that the GENIE intervention could be implemented in this sample of community-living older people. The intervention was acceptable to clinicians and older people with COPD, especially for those with less severe disease, when facilitated appropriately and considering the levels of literacy of participants. There was no significant change in diet quality in the intervention group over the follow-up period (median change in prudent diet score per month (interquartile range (IQR), 0.03 (− 0.24–0.07)), whereas an overall fall in diet quality was observed in the control group (− 0.15 (− 0.24–0.03)).

Conclusion

The process evaluation findings suggest that this intervention is feasible and acceptable to both patients and clinicians. Although the sample size achieved in this study was small, findings suggest that the intervention may have a protective effect against declines in diet quality, and other health behaviours, in an older COPD population. Findings from this feasibility study indicate that further evaluation of the GENIE intervention is warranted in a larger study, with a longer follow-up.

Trial registration

ClinicalTrials.gov, NCT02935452. NIH U.S. National Library of Medicine. Registered 17 October 2016.
Bedtime Routines Intervention for Children (BRIC) using an automated text messaging system for behaviour change: study protocol for an early phase study
Authors: Kitsaras George , Allan Julia , Pretty Iain A.
Published: February 2020

Background

This work concerns the activities in the last hour before bed for young children born to first-time parents, so called bedtime routines (BTR). These activities include amongst others tooth brushing, reading a book, having a bath and avoiding food and drinks before bed. Having a set bedtime at a suitable hour is also very important. Establishing good bedtime routines has been shown to be really important for a number of health, wellbeing, development and social outcomes. Currently, there is no evidence-based bedtime routine intervention for first-time parents using a novel design (i.e. text messages). Existing research has highlighted the importance of bedtime routines and the lack of appropriate mechanisms in place for parents who sought support.

Methods

The proposed study includes 2 work packages. Work package 1 focuses on the development of the intervention through a combination of qualitative work (1:1 interviews with parents on barriers and facilitators on bedtime routines using the Theoretical Domains Framework) and an expert group of key stakeholders. Work package 2 involves a small-scale (n = 50) feasibility and effectiveness study to examine proof of concept with first-time parents using text messages to communicate the intervention. Quantitative information relating to uptake, engagement, retention and effectiveness of the intervention as well as qualitative information (focus groups with parents who took part in the study) will be collected. Overall, the effectiveness of the intervention will be assessed through the APEASE criteria (acceptability, practicability, effectiveness, affordability, safety, equity).

Discussion

This study can provide initial yet important support for further exploration in the field of bedtime routines in more complicated family structures (parents with more than 1 child, separated families etc.). Also, the implementation of a novel study design (i.e. text messages) could lead to considerable cost savings while maintaining high retention, uptake and engagement from the participants. Should the intervention meet the APEASE criteria, a more comprehensive intervention on bedtime routines for first-time parents will be explored in a more robust (RCT and longitudinal) approach.

Trials registration

Due to the nature of the study, no trial registration is currently in place.