bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcriptional events and their relationship to physiological changes during poplar seed germination and post-germination
Authors: Qu Chunpu , Zhao Hancheng , Chen Jinyuan , Zuo Zhuang , Sun Xue , Huang Jiahuan , Yang Chengjun , Zhang Xiuli , Zhang Peng , Quan Xiankui , Xu Zhiru , Liu Guanjun 
Published: November 2019

Abstract

Background
Seed germination, the foundation of plant propagation, involves a series of changes at the molecular level. Poplar is a model woody plant, but the molecular events occurring during seed germination in this species are unclear.

Results
In this study, we investigated changes in gene transcriptional levels during different germination periods in poplar by high-throughput sequencing technology. Analysis of genes expressed at specific germination stages indicated that these genes are distributed in many metabolic pathways. Enrichment analysis of significantly differentially expressed genes based on hypergeometric testing revealed that multiple pathways, such as pathways related to glycolysis, lipid, amino acid, protein and ATP synthesis metabolism, changed significantly at the transcriptional level during seed germination. A comparison of ΣZ values uncovered a series of transcriptional changes in biological processes related to primary metabolism during poplar seed germination. Among these changes, genes related to CHO metabolism were the first to be activated, with subsequent expression of genes involved in lipid metabolism and then those associated with protein metabolism. The pattern of metabolomic and physiological index changes further verified the sequence of some biological events.

Conclusions
Our study revealed molecular events occurring at the transcriptional level during seed germination and determined their order. These events were further verified by patterns of changes of metabolites and physiological indexes. Our findings lay a foundation for the elucidation of the molecular mechanisms responsible for poplar seed germination.
Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans
Authors: Wallner Adrian , King Eoghan , Ngonkeu Eddy L. M. , Moulin Lionel , Béna Gilles 
Published: November 2019

Abstract

Background
Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential.

Results
We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence.

Conclusion
Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.
Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record
Authors: Hughey Jacob J. , Rhoades Seth D. , Fu Darwin Y. , Bastarache Lisa , Denny Joshua C. , Chen Qingxia 
Published: November 2019

AbstractBackgroundThe growth of DNA biobanks linked to data from electronic health records (EHRs) has enabled the discovery of numerous associations between genomic variants and clinical phenotypes. Nonetheless, although clinical data are generally longitudinal, standard approaches for detecting genotype-phenotype associations in such linked data, notably logistic regression, do not naturally account for variation in the period of follow-up or the time at which an event occurs. Here we explored the advantages of quantifying associations using Cox proportional hazards regression, which can account for the age at which a patient first visited the healthcare system (left truncation) and the age at which a patient either last visited the healthcare system or acquired a particular phenotype (right censoring).ResultsIn comprehensive simulations, we found that, compared to logistic regression, Cox regression had greater power at equivalent Type I error. We then scanned for genotype-phenotype associations using logistic regression and Cox regression on 50 phenotypes derived from the EHRs of 49,792 genotyped individuals. Consistent with the findings from our simulations, Cox regression had approximately 10% greater relative sensitivity for detecting known associations from the NHGRI-EBI GWAS Catalog. In terms of effect sizes, the hazard ratios estimated by Cox regression were strongly correlated with the odds ratios estimated by logistic regression.ConclusionsAs longitudinal health-related data continue to grow, Cox regression may improve our ability to identify the genetic basis for a wide range of human phenotypes.
Transcriptome analysis of two inflorescence branching mutants reveals cytokinin is an important regulator in controlling inflorescence architecture in the woody plant Jatropha curcas
Authors: Chen Mao-Sheng , Zhao Mei-Li , Wang Gui-Juan , He Hui-Ying , Bai Xue , Pan Bang-Zhen , Fu Qian-Tang , Tao Yan-Bin , Tang Ming-Yong , Martínez-Herrera Jorge , Xu Zeng-Fu 
Published: November 2019

AbstractBackgroundIn higher plants, inflorescence architecture is an important agronomic trait directly determining seed yield. However, little information is available on the regulatory mechanism of inflorescence development in perennial woody plants. Based on two inflorescence branching mutants, we investigated the transcriptome differences in inflorescence buds between two mutants and wild-type (WT) plants by RNA-Seq to identify the genes and regulatory networks controlling inflorescence architecture inJatropha curcasL., a perennial woody plant belonging to Euphorbiaceae.ResultsTwo inflorescence branching mutants were identified in germplasm collection ofJatropha.Theduo xiao hua(dxh) mutant has a seven-order branch inflorescence, and thegynoecy(g) mutant has a three-order branch inflorescence, while WTJatrophahas predominantly four-order branch inflorescence, occasionally the three- or five-order branch inflorescences in fields. Using weighted gene correlation network analysis (WGCNA), we identified several hub genes involved in the cytokinin metabolic pathway from modules highly associated with inflorescence phenotypes. Among them,Jatropha ADENOSINE KINASE 2(JcADK2),ADENINE PHOSPHORIBOSYL TRANSFERASE 1(JcAPT1),CYTOKININ OXIDASE 3(JcCKX3),ISOPENTENYLTRANSFERASE 5(JcIPT5),LONELY GUY 3(JcLOG3) andJcLOG5may participate in cytokinin metabolic pathway inJatropha. Consistently, exogenous application of cytokinin (6-benzyladenine, 6-BA) on inflorescence buds induced high-branch inflorescence phenotype in both low-branch inflorescence mutant (g) and WT plants. These results suggested that cytokinin is an important regulator in controlling inflorescence branching inJatropha. In addition, comparative transcriptome analysis showed thatArabidopsishomologous genesJatropha AGAMOUS-LIKE 6(JcAGL6),JcAGL24,FRUITFUL(JcFUL),LEAFY(JcLFY),SEPALLATAs(JcSEPs),TERMINAL FLOWER 1(JcTFL1), andWUSCHEL-RELATED HOMEOBOX 3(JcWOX3), were differentially expressed in inflorescence buds betweendxhandgmutants and WT plants, indicating that they may participate in inflorescence development inJatropha. The expression ofJcTFL1was downregulated, while the expression ofJcLFYandJcAP1were upregulated in inflorescences in low-branchgmutant.ConclusionsCytokinin is an important regulator in controlling inflorescence branching inJatropha.The regulation of inflorescence architecture by the genes involved in floral development, includingTFL1,LFYandAP1, may be conservative inJatrophaandArabidopsis. Our results provide helpful information for elucidating the regulatory mechanism of inflorescence architecture inJatropha.
Quantitative succinyl-proteome profiling of Chinese hickory (Carya cathayensis) during the grafting process
Authors: Yuan Huwei , Chen Juanjuan , Yang Ying , Shen Chenjia , Xu Dongbin , Wang Junfeng , Yan Daoliang , He Yi , Zheng Bingsong 
Published: November 2019

Abstract

Background
Chinese hickory (Carya cathayensis) is a popular nut plant having high economic value. Grafting is applied to accelerate the transition from vegetative phase to reproductive phase. Lysine succinylation occurs frequently in the proteins associated with metabolic pathways, which may participate in the regulation of the grafting process. However, the exact regulatory mechanism underlying grafting process in Chinese hickory has not been studied at post-translational modification level.

Results
A comprehensive proteome-wide lysine succinylation profiling of Chinese hickory was explored by a newly developed method combining affinity enrichment and high-resolution LC-MS/MS. In total, 259 succinylation sites in 202 proteins were identified, representing the first comprehensive lysine succinylome in Chinese hickory. The succinylation was biased to occur in the cytosolic proteins of Chinese hickory. Moreover, four conserved succinylation motifs were identified in the succinylated peptides. Comparison of two grafting stages of Chinese hickory revealed that the differential expressed succinylated proteins were mainly involved in sugar metabolism, carbon fixation, amino acid metabolism and plant-pathogen interaction. Besides, seven heat shock proteins (HSPs) with 11 succinylation sites were also identified, all of which were observed to be up-regulated during the grafting process.

Conclusions
Succinylation of the proteins involved in amino acid biosynthesis might be required for a successful grafting. Succinylated HSPs might play a role in stress tolerance of the grafted Chinese hickory plants. Our results can be a good resource for functional validation of the succinylated proteins and a starting point for the investigation of molecular mechanisms during lysine succinylation occurring at grafting site.
Associations between health-related quality of life, physical function and pain in older women with osteoporosis and vertebral fracture
Authors: Stanghelle Brita , Bentzen Hege , Giangregorio Lora , Pripp Are Hugo , Bergland Astrid 
Published: November 2019

Abstract

Background
Osteoporosis and vertebral fractures represent a major health burden worldwide, and the prevalence of osteoporosis is expected to increase as the world’s population ages. Suffering from vertebral fracture has a substantial impact on the individual’s health-related quality of life (HRQoL), physical function and pain. Complex health challenges experienced by older people with osteoporosis and vertebral fractures call for identification of factors that may influence HRQoL, as some of these factors may be modifiable. The objective is to examine the independent associations between HRQoL, physical function and pain in older women with osteoporosis and vertebral fracture.

Methods
This study has a cross-sectional design, using data from 149 home-dwelling Norwegian women with osteoporosis and vertebral fracture, aged 65+. Data on HRQoL (Short Form 36 (SF-36), Quality of Life Questionnaire of the European Foundation for Osteoporosis (QUALEFFO-41)), physical function (walking speed, balance and strength), pain, as well as sociodemographic information were collected. Simple linear regression analyses were conducted and multivariable regression models were fitted to investigate the associations.

Results
Lower levels of HRQoL were significantly associated with lower levels of physical function, measured by walking speed, and higher levels of pain. Pain was significantly associated with all of the subscales in SF-36, with the exception of Mental Health and Mental Component Score, and all the subscales of QUALEFFO-41. Walking speed was significantly associated with 5 of 8 subscales of SF-36 (except Bodily Pain, Vitality, Mental Health and Mental Component Score), and with 4 of 6 subscales of QUALEFFO-41 (except Score Pain and Mood).

Conclusion
This study shows that pain and walking speed were, independently of one another, associated with HRQoL in older women with osteoporosis and vertebral fracture. These findings can inform clinicians and health managers about the importance of pain management and exercise interventions in health care for this group. Future research should address interventions targeting both physical function and pain with HRQoL as an outcome.

Registration
ClincialTrials.gov Identifier: NCT02781974. Registered 18.05.16. Retrospectively registered.
Co-occurrence of human papillomavirus (HPV) in newborns and their parents
Authors: Skoczyński Mariusz , Goździcka-Józefiak Anna , Kwaśniewska Anna 
Published: November 2019

Abstract

Background
The potential HPV transmission route includes horizontal transmission “in utero” and vertical transmission from parents. Less is known about the role of child’s father as a potential source of HPV infection and involved in the pathogen’s epidemic chain. A possible consequence of perinatal infection includes HPV-related childhood diseases and carrying the risk of cervical cancer development in female offspring. In view of the evidence, studies of HPV co-occurrence in one or both parents and their offspring seem vital for the implementation of respective preventive measures. Consequently, the aim of this study was to determine the incidence of common HPV 16/18 infections in newborns and their parents, and to assess its role of the periconceptional transmission.

Methods
To determine the incidence of common HPV infections in newborns from single pregnancies and their parents. The study included 146 pregnant women, as well as their partners, and newborns. They were tested for the presence of HPV 16/18 DNA using the PCR method. HPV types 16 and/or 18 were identified using type-specific PCR primers. The quality of the extracted DNA was evaluated by PCR using PC03/PC04 β-globin-specific primers. The relationship between the presence of neonatal and parental HPV infection was analyzed using a multivariable regression model. Calculations were carried out with the Statistica 10.

Results
The presence of HPV DNA was detected in 19 (13,01%) newborns, 28 (19,18%) mothers, and 20 (13,7%) fathers. The viral DNA was detected in 14 newborns delivered by HPV-positive mothers (OR = 26,08; CI: 8,07-84,31, p < 0.001), 12 descendants of HPV-positive fathers (OR = 22,13; CI: 6,97-70,27, p < 0.001), and 10 children originating from two infected parents (OR = 24,20; CI: 6,84–85,57 p < 0.001). Those findings points to a increase risk of an acquired infection in newborns with HPV-positive parents.

Conclusion
Our findings suggest the possible role of the periconceptional transmission in the mode of acquired HPV 16/18 infections.
Co-existence of virulence factors and antibiotic resistance in new Klebsiella pneumoniae clones emerging in south of Italy
Authors: Fasciana Teresa , Gentile Bernardina , Aquilina Maria , Ciammaruconi Andrea , Mascarella Chiara , Anselmo Anna , Fortunato Antonella , Fillo Silvia , Petralito Giancarlo , Lista Florigio , Giammanco Anna 
Published: November 2019

Abstract

Background
Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; however, recent studies suggest an ongoing epidemiological change in this geographical area.

Methods
50 K. pneumoniae strains, 25 carbapenem-resistant (CR-Kp) and 25 susceptible (CS-Kp), collected from march 2014 to march 2016 at the Laboratory of Bacteriology of the Paolo Giaccone Polyclinic University hospital of Palermo, Italy, were characterized for antibiotic susceptibility and fully sequenced by next generation sequencing (NGS) for the in silico analysis of resistome, virulome, multi-locus sequence typing (MLST) and core single nucleotide polymorphism (SNP) genotypes

Results
MLST in silico analysis of CR-Kp showed that 52% of isolates belonged to CC258, followed by ST395 (12%), ST307 (12%), ST392 (8%), ST348 (8%), ST405 (4%) and ST101 (4%). In the CS-Kp group, the most represented isolate was ST405 (20%), followed by ST392 and ST15 (12%), ST395, ST307 and ST1727 (8%). The in silico β-lactamase analysis of the CR-Kp group showed that the most detected gene was blaSHV (100%), followed by blaTEM (92%), blaKPC (88%), blaOXA (88%) and blaCTX-M (32%). The virulome analysis detected mrk operon in all studied isolates, and wzi-2 was found in three CR-Kp isolates (12%). Furthermore, the distribution of virulence genes encoding for the yersiniabactin system, its receptor fyuA and the aerobactin system did not show significant distribution differences between CR-Kp and CS-Kp, whereas the Klebsiella ferrous iron uptake system (kfuA, kfuB and kfuC genes), the two-component system kvgAS and the microcin E495 were significantly (p < 0.05) prevalent in the CS-Kp group compared to the CR-Kp group.
Core SNP genotyping, correlating with the MLST data, allowed greater strain tracking and discrimination than MLST analysis.

Conclusions
Our data support the idea that an epidemiological change is ongoing in the Palermo area (Sicily, Italy). In addition, our analysis revealed the co-existence of antibiotic resistance and virulence factors in CR-Kp isolates; this characteristic should be considered for future genomic surveillance studies.
Peripheral T cell lymphoma after chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS): a case report
Authors: Liu Xiao-hang , Jin Fan , Zhang Meng , Liu Mei-xi , Wang Tao , Pan Bo-ju , Zhang Lu 
Published: November 2019

Abstract

Background
Chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS) is an inflammatory disorder in the central nervous system (CNS) with distinct clinical, radiological, and pathological characteristics. The pathophysiology of CLIPPERS still remains unclear. Because a few cases about lymphoma mimicking the manifestations of CLIPPERS were reported and the prognosis of lymphoma is much worse, early identification of lymphoma is very important.

Case presentation
A 31-year-old woman was admitted with 3 months’ history of diplopia, dizziness, gait ataxia, and right facial numbness. The diagnosis of CLIPPERS was established based on the finding of punctate enhancing lesions in the cerebellum, thalamus, pons, medulla, and midbrain region in magnetic resonance imaging (MRI), together with the favorable clinical and radiological responses to corticosteroids. However, she was diagnosed as peripheral T cell lymphoma, not otherwise specified (PTCL-NOS) by the pulmonary nodular and the skin biopsy almost 10 years later, and she got complete remission within 1 year after chemotherapy.

Conclusion
We report the first case of CLIPPERS developing PTCL-NOS. This case proposes that when brain biopsy was difficult to achieve, biopsies in extra-cerebral lesions under the assisting examination of positron emission tomography-computed tomography (PET-CT) can be helpful in further identification.
The items in the Chinese version of the Montreal cognitive assessment basic discriminate among different severities of Alzheimer’s disease
Authors: Zhang Yan-Rong , Ding Yun-Long , Chen Ke-liang , Liu Yan , Wei Can , Zhai Ting-ting , Wang Wen-Juan , Dong Wan-Li 
Published: November 2019

Abstract

Background
To determine whether items of the Chinese version of the Montreal Cognitive Assessment Basic (MoCA-BC) could discriminate among cognitively normal controls (NC), and those with mild cognitive impairment (MCI), mild Alzheimer’s disease (AD), and moderate-severe (AD), as well as their sensitivity and specificity.

Methods
MCI (n = 456), mild AD (n = 502) and moderate-severe AD (n = 102) patients were recruited from the memory clinic, Huashan Hospital, Shanghai, China. NC (n = 329) were recruited from health checkup outpatients. Five MoCA-BC item scores were collected in interviews.

Results
The MoCA-BC orientation test had high sensitivity and specificity for discrimination among MCI, mild AD and moderate-severe AD. The delayed recall memory test had high sensitivity and specificity for MCI screening. The verbal fluency test was efficient for detecting MCI and differentiating AD severity.

Conclusions
Various items of the MoCA-BC can identify MCI patients early and identify the severity of dementia.
A feasibility study of activity tracking devices in pregnancy
Authors: Kominiarek Michelle A. , Balmert Lauren C. , Tolo Hallie , Grobman William , Simon Melissa 
Published: November 2019

Abstract

Background
We aimed to evaluate the feasibility of using an activity-tracking device (ATD) during pregnancy and compare self-reported to ATD-calculated energy expenditure in a 2-phase study.

Methods
(Phase 1) Twenty-five pregnant women were asked about exercise, computer use, smartphone ownership, and ATD attitudes. Descriptive statistics were reported. (Phase 2) Women ≥18 years, smartphone owners, < 16-weeks gestation, and without exercise restrictions were approached to participate in 2016–2017. Women received instructions to wear and sync the ATD daily. We assessed protocol adherence and satisfaction via surveys at 36-weeks and used mixed models to assess the relationship between gestational age and ATD data. Energy expenditure from the Pregnancy Physical Activity Questionnaire (PPAQ) was compared to ATD-calculated energy expenditure.

Results
(Phase 1) Walking was the most common exercise; 8% did not perform any activity during pregnancy. All women had internet access and owned a smartphone. Women stated they would wear the ATD all the time during a pregnancy (88%), with the intent to improve their health (80%). (Phase 2) The characteristics of the 48 women were: pre-pregnancy BMI 28, 62% non-Hispanic black, 62% multiparas. Of the 18 women who completed the 36-week survey, only 56% wore the ATD daily, 33% had a lost or broken ATD, and 17% had technical problems; however, 94% enjoyed wearing it, 94% would recommend it to a pregnant friend, and 78% thought it helped them reach activity goals. According to ATD data, the median number of active days was 41 (IQR 20–73) and the median proportion of active days out of potential days was 22% (IQR 11–40). As gestational age increased, mean log steps decreased, active minutes decreased, and sedentary hours increased in unadjusted and adjusted models (P < 0.05 all comparisons). There were no differences in mean energy expenditure (MET-h/week) estimated by PPAQ or ATD data at 28 weeks gestation [212 (22–992 range) vs. 234 (200–281 range), P = 0.66] and at 36 weeks [233 (86–907 range) vs. 218 (151–273 range), P = 0.68]).

Conclusions
Women reported high motivation to wear an ATD and high satisfaction with actually using an ATD during pregnancy; however adherence to the study protocol was lower than expected and ATD technical problems were frequent.