bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea)
Authors: Wall-Palmer Deborah , Janssen Arie W. , Goetze Erica , Choo Le Qin , Mekkes Lisette , Peijnenburg Katja T. C. A. 
Published: September 2020

AbstractBackgroundThe aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Ma, atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown.ResultsBased on a concatenated maximum likelihood phylogeny of three genes (cytochromecoxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae,Atlanta, ProtatlantaandOxygyrus,form monophyletic groups. The genusAtlantais split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events.ConclusionsNow confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.
Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses
Authors: Liu Dong , Zhang Yuanyuan , Zhang Ming , Yang Jinquan , Tang Wenqiao 
Published: September 2020

Abstract
Background
The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species.

Results
We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments.

Conclusions
This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.
Proteomic and metabolic profile analysis of low-temperature storage responses in Ipomoea batata Lam. tuberous roots
Authors: Cui Peng , Li Yongxin , Cui Chenke , Huo Yanrong , Lu Guoquan , Yang Huqing 
Published: September 2020

AbstractBackgroundSweetpotato (Ipomoea batatasL.) is one of the seven major food crops grown worldwide. Cold stress often can cause protein expression pattern and substance contents variations for tuberous roots of sweetpotato during low-temperature storage. Recently, we developed proteometabolic profiles of the fresh sweetpotatoes (cv. Xinxiang) in an attempt to discern the cold stress-responsive mechanism of tuberous root crops during post-harvest storage.ResultsFor roots stored under 4 °C condition, the CI index, REC and MDA content in roots were significantly higher than them at control temperature (13 °C). The activities of SOD, CAT, APX, O2.-producing rate, proline and especially soluble sugar contents were also significantly increased. Most of the differentially expressed proteins (DEPs) were implicated in pathways related to metabolic pathway, especially phenylpropanoids and followed by starch and sucrose metabolism. L-ascorbate peroxidase 3 and catalase were down-regulated during low temperature storage. α-amylase, sucrose synthase and fructokinase were significantly up-regulated in starch and sucrose metabolism, while β-glucosidase, glucose-1-phosphate adenylyl-transferase and starch synthase were opposite. Furthermore, metabolome profiling revealed that glucosinolate biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis as well as protein digestion and absorption played a leading role in metabolic pathways of roots. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.ConclusionsOur proteomic and metabolic profile analysis of sweetpotatoes stored at low temperature reveal that the antioxidant enzymes activities, proline and especially soluble sugar content were significantly increased. Most of the DEPs were implicated in phenylpropanoids and followed by starch and sucrose metabolism. The discrepancy between proteomic (L-ascorbate peroxidase 3 and catalase) and biochemical (CAT/APX activity) data may be explained by higher H2O2levels and increased ascorbate redox states, which enhanced the CAT/APX activity indirectly. Glucosinolate biosynthesis played a leading role in metabolic pathways. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.
Infantile fever-triggered acute liver failure caused by novel neuroblastoma amplified sequence mutations: a case report
Authors: Li Weiran , Zhu Yu , Guo Qin , Wan Chaomin 
Published: September 2020

AbstractBackgroundInfantile liver failure syndrome-2 (ILFS2) is caused by neuroblastoma amplified sequence (NBAS) mutation. The disease is characterized by recurrent episodes of acute liver failure (ALF) or by liver crisis triggered by recurrent episodes of fever and complete recovery.Case presentationHere, we describe the case of a Chinese girl with typical clinical manifestation of ILFS2 without exhibition of extrahepatic involvement. The patient harbored novel compound heterozygous mutations in the NBAS region (c.3386C > T (p.Ser1129Phe), c.1A > C (p.Met1Leu) and c.875G > A (p.Gly292Glu)), mutations which have not been previously reported. After administration of antipyretics and intravenous glucose and electrolyte administration, the patient recovered fully.ConclusionThrough the present study, we recommend that ILFS2 should be taken into consideration during the differential diagnosis of children with recurrent, fever-triggered ALF. While the definitive diagnosis of ILFS2 remains dependent on genetic sequencing and discovery of NBAS, early antipyretic treatment is recommended to prevent liver crisis.
The metagenomic next-generation sequencing in diagnosing central nervous system angiostrongyliasis: a case report
Authors: Feng Li , Zhang Aiwu , Que Jiali , Zhou Hongyan , Wang Haiyan , Guan Yuanlin , Shen Cunzhou , Sun Xunsha , Lai Rong , Peng Fuhua , Feng Huiyu , Chen Ling 
Published: September 2020

Abstract
Backgrounds
The incidence of angiostrongyliasis is increasing in recent decades due to the expanding endemic areas all over the world. Clinicians face tremendous challenge of diagnosing angiostrongyliasis because of the lack of awareness of the disease and less effective definitive laboratory tests.

Case presentation
A 27-year-old man initially manifested skin itching, emesis, myalgia and quadriparesis. With progressive weakness of four limbs and elevated protein in the cerebrospinal fluid (CSF), he was diagnosed as Guillain-Barré syndrome and treated with intravenous methylprednisolone and immunoglobulin. However, the patient deteriorated with hyperpyrexia, headache and then persistent coma. The routine tests for Angiostrongylus cantonensis (A. cantonensis) with both the CSF and the serum were all negative. In contrast, the metagenomic next-generation sequencing (mNGS) was applied with the serum sample and the CSF sample in the middle phase. The central nervous system (CNS) angiostrongyliasis was diagnosed by mNGS with the mid-phase CSF, but not the mid-phase serum. At the same time, the CSF analysis revealed eosinophils ratio up to 67%. The discovery of A. cantonensis was confirmed by PCR with CSF later. Unfortunately, the patient died of severe angiostrongyliasis. During his hospitalization, mNGS was carried out repeatedly after definitive diagnosis and targeted treatment. The DNA strictly map reads number of A. cantonensis detected by mNGS was positively correlated with the CSF opening pressure and clinical manifestations.

Conclusions
The case of A. cantonensis infection highlights the benefit of mNGS as a target-free identification in disclosing the rare CNS angiostrongyliasis in the unusual season, while solid evidence from routine clinical testing was absent. The appropriate sample of mNGS should be chosen according to the life cycle of A. cantonensis. Besides, given the fact that the DNA reads number of A. cantonensis fluctuated with CSF opening pressure and clinical manifestations, whether mNGS could be applied as a marker of effectiveness of treatment is worth further exploration.
Identification of missense and synonymous variants in Iranian patients suffering from autosomal dominant polycystic kidney disease
Authors: Khadangi Fatemeh , Torkamanzehi Adam , Kerachian Mohammad Amin 
Published: September 2020

Abstract
Background
Autosomal dominant polycystic kidney disease (ADPKD), the predominant type of inherited kidney disorder, occurs due to PKD1 and PKD2 gene mutations. ADPKD diagnosis is made primarily by kidney imaging. However, molecular genetic analysis is required to confirm the diagnosis. It is critical to perform a molecular genetic analysis when the imaging diagnosis is uncertain, particularly in simplex cases (i.e. a single occurrence in a family), in people with remarkably mild symptoms, or in individuals with atypical presentations. The main aim of this study is to determine the frequency of PKD1 gene mutations in Iranian patients with ADPKD diagnosis.

Methods
Genomic DNA was extracted from blood samples from 22 ADPKD patients, who were referred to the Qaem Hospital in Mashhad, Iran. By using appropriate primers, 16 end exons of PKD1 gene that are regional hotspots, were replicated with PCR. Then, PCR products were subjected to DNA directional Sanger sequencing.

Results
The DNA sequencing in the patients has shown that exons 35, 36 and 37 were non- polymorphic, and that most mutations had occurred in exons 44 and 45. In two patients, an exon-intron boundary mutation had occurred in intron 44. Most of the variants were missense and synonymous types.

Conclusion
In the present study, we have shown the occurrence of nine novel missense or synonymous variants in PKD1 gene. These data could contribute to an improved diagnostic and genetic counseling in clinical settings.
Caesarean section rates in women in the Republic of Ireland who chose to attend their obstetrician privately: a retrospective observational study
Authors: Turner Michael J. , Reynolds Ciara M. E. , McMahon Léan E. , O’Malley Eimer G. , O’Connell Michael P. , Sheehan Sharon R. 
Published: September 2020

Abstract
Background
Caesarean section (CS) rates are increasing and there are wide variations in rates internationally and nationally. There is evidence that women who attend their obstetrician privately have a higher incidence of CS than those who attend publicly. The purpose of this observational study was to further investigate why CS rates may be higher in women who chose to attend their obstetrician privately.

Methods
This study analysed data collected as part of the clinical records by midwives at the woman’s first antenatal appointment in a large European maternity hospital. All women who delivered between the years 2009 and 2017 were included. Data were analysed both cross-sectionally and longitudinally.

Results
Overall, 73,266 women had a singleton pregnancy and 1830 had a multiple pregnancy. Of the packages of maternity care, 75.2% chose public, 10.8% chose semiprivate and 14.0% chose private. During the study, 11,991 women attended the hospital for their first and second pregnancies. Overall, women who attended privately were older and had higher proportions of infertility treatment and history of miscarriage (all p < 0.001) compared to those publicly-funded. Private patients were more likely to have a history of infertility, a history of miscarriage, a multiple pregnancy and to be ≥35 yrs. They had lower rates of obesity, smoking and illicit drug use in pregnancy (all p < 0.001). In women who chose private care, the overall rate of CS was higher compared to women choosing publicly-funded (42.7% vs 25.3%, p < 0.001) The increase was due to an increase in elective rather than emergency CS. The increase in elective CS fell after adjustment for clinical risks. In the longitudinal analysis, 89.7% chose the same package second time around. Women who changed from public to private care for the second pregnancy were more likely to have had a previous emergency CS or admission to the Neonatal Unit.

Conclusions
This study suggests that the increased CS rate in women privately insured may be attributed, in part, to the fact that women who can afford health insurance choose continuity of care from a senior obstetrician because they are risk adverse and wish to have the option of an elective CS.
Lived experience research as a resource for recovery: a mixed methods study
Authors: Honey Anne , Boydell Katherine M. , Coniglio Francesca , Do Trang Thuy , Dunn Leonie , Gill Katherine , Glover Helen , Hines Monique , Scanlan Justin Newton , Tooth Barbara 
Published: September 2020

AbstractBackgroundLived experience research is conducted by people who have experience of mental health issues and is therefore better placed than more traditional research to illuminate participants’ experiences. Findings that focus on identifying enablers of recovery from a lived experience perspective have the potential to assist people in their recovery process. However, this lived experience research is often difficult to find, access and interpret. We co-produced user-friendly and engaging resources to disseminate findings from six lived experience research studies. This paper seeks to answer the research questions: a) Did exposure to lived experience research increase hopefulness for participants?; and b) How else did interacting with lived experience research resources influence participants’ lives?MethodsThirty-eight participants were introduced to four resources of their choosing by peer workers over a four-week period. The helpfulness of resources was evaluated using mixed methods, including a quasi-experimental analysis of change in hope, an anonymous survey and in-depth interviews.ResultsFindings indicated that the resources promoted hope, but that increases in hopefulness may not be seen immediately. Other impacts include that the resources: encouraged helpful activities; provided a positive experience; increased valued knowledge; encouraged people to reflect on their journey and think constructively about mental health issues; helped people to feel less alone; and assisted people to explain their situation to others.ConclusionsThe research suggests the potential usefulness of lived experience research resources, presented in user-friendly formats, in the lives of people who experience mental health issues and implies a need to nurture this type of research.
Bayesian frailty modeling of correlated survival data with application to under-five mortality
Authors: Alotaibi Refah M. , Rezk Hoda Ragab , Guure Chris 
Published: September 2020

AbstractBackgroundThere is high rate of under-five mortality in West Africa with little effort made to study determinants that significantly increase or decrease its risk across the West African sub-region. This is important since it will help in the design of effective intervention programs for each country or the entire region. The overall objective of this research evaluates the determinants of under-five mortality prior to the end of the 2015 Millennium Development Goals, to guide West African countries implement strategies that will aid them achieve the Sustainable Development Goal 3 by 2030.MethodThis study used the Demographic and Health Survey (DHS) data from twelve (12) out of the eighteen West African countries; Ghana, Benin, Cote d’ Ivoire, Guinea, Liberia, Mali, Niger, Nigeria, Sierra Leone, Burkina Faso, Gambia and Togo. Data were extracted from the children and women of reproductive age files as provided in the DHS report. The response or outcome variable of interest is under-five mortality rate. A Bayesian exponential, Weibull and Gompertz regression models via a gamma shared frailty model were used for the analysis. The deviance information criteria and Bayes factors were used to discriminate between models. These analyses were carried out using Stata version 15 software.ResultsThe study recorded 101 (95% CI: 98.6–103.5) deaths per 1000 live births occurring among the twelve countries. Burkina Faso (124.4), Cote D’lvoire (110.1), Guinea (116.4), Nigeria (120.6) and Niger (118.3) recorded the highest child under-5 mortality rate. Gambia (48.1), Ghana (60.1) and Benin (70.4) recorded the least unde-5 mortality rate per 1000 livebirths. Multiple birth children were about two times more likely to die compared to singleton birth, in all except Gambia, Nigeria and Sierra Leone. We observed significantly higher hazard rates for male compared to female children in the combined data analysis (HR: 1.14, 95% CI: [1.10–1.18]). The country specific analysis in Benin, Cote D’lvoire, Guinea, Liberia, Mali and Nigeria showed higher under-5 mortality hazard rates among male children compared to female children whilst Niger was the only country to report significantly lower hazard rate of males compared to females.ConclusionThere is still quite a substantial amount of work to be done in order to meet the Sustainable Development Goal 3 in 2030 in West Africa. There exist variant differences among some of the countries with respect to mortality rates and determinants which require different interventions and policy decisions.
Social networks, health and identity: exploring culturally embedded masculinity with the Pakistani community, West Midlands, UK
Authors: Kokab Farina , Greenfield Sheila , Lindenmeyer Antje , Sidhu Manbinder , Tait Lynda , Gill Paramjit 
Published: September 2020

AbstractBackgroundMigrants from South Asia living in developed countries have an increased risk for developing cardiovascular disease (CVD), with limited research into underlying social causes.MethodsWe used social capital as an interpretive lens to undertake analysis of exploratory qualitative interviews with three generations of at-risk migrant Pakistani men from the West Midlands, UK. Perceptions of social networks, trust, and cultural norms associated with access to healthcare (support and information) were the primary area of exploration.ResultsFindings highlighted the role of social networks within religious or community spaces embedded as part of ethnic enclaves. Local Mosques and gyms remained key social spaces, where culturally specific gender differences played out within the context of a diaspora community, defined ways in which individuals navigated their social spheres and influenced members of their family and community on health and social behaviours.ConclusionsThere are generational and age-based differences in how members use locations to access and develop social support for particular lifestyle choices. The pursuit of a healthier lifestyle varies across the diverse migrant community, determined by social hierarchies and socio-cultural factors. Living close to similar others can limit exposure to novel lifestyle choices and efforts need to be made to promote wider integration between communities and variety of locations catering to health and lifestyle.
Ethnicity classification systems for public health surveys: experiences from HIV behavioural surveillance among men who have sex with men
Authors: Lachowsky Nathan J. , Saxton Peter J.W. , Dickson Nigel P. , Hughes Anthony J. , Jones Rhys G. , Clark Terryann C. , Ho Elsie , Summerlee Alastair J.S. , Dewey Cate E. 
Published: September 2020

Abstract
Background
Race and ethnicity classification systems have considerable implications for public health, including the potential to reveal or mask inequities. Given increasing “super-diversity” and multiple racial/ethnic identities in many global settings, especially among younger generations, different ethnicity classification systems can underrepresent population heterogeneity and can misallocate and render invisible Indigenous people and ethnic minorities. We investigated three ethnicity classification methods and their relationship to sample size, socio-demographics and sexual health indicators.

Methods
We examined data from New Zealand’s HIV behavioural surveillance programme for men who have sex with men (MSM) in 2006, 2008, 2011, and 2014. Participation was voluntary, anonymous and self-completed; recruitment was via community venues and online. Ethnicity allowed for multiple responses; we investigated three methods of dealing with these: Prioritisation, Single/Combination, and Total Response. Major ethnic groups included Asian, European, indigenous Māori, and Pacific. For each classification method, statistically significant associations with ethnicity for demographic and eight sexual health indicators were assessed using multivariable logistic regression.

Results
Overall, 10,525 MSM provided ethnicity data. Classification methods produced different sample sizes, and there were ethnic disparities for every sexual health indicator. In multivariable analysis, when compared with European MSM, ethnic differences were inconsistent across classification systems for two of the eight sexual health outcomes: Māori MSM were less likely to report regular partner condomless anal intercourse using Prioritisation or Total Response but not Single/Combination, and Pacific MSM were more likely to report an STI diagnosis when using Total Response but not Prioritisation or Single/Combination.

Conclusions
Different classification approaches alter sample sizes and identification of health inequities. Future research should strive for equal explanatory power of Indigenous and ethnic minority groups and examine additional measures such as socially-assigned ethnicity and experiences of discrimination and racism. These findings have broad implications for surveillance and research that is used to inform public health responses.