bluuebunny/crossref_metadata_2025 huggingface dataset:
“Running the Numbers”: Modes of Microcelebrity Labor in Queer Women’s Self-Representation on Instagram and Vine
Authors: Duguay Stefanie
Published: December 2019

Microcelebrity, as a set of practices contributing to personalized self-branding, has become an increasingly prominent component of self-representation on social media platforms. While “influencers” who have built lucrative followings through microcelebrity give the appearance of having fun without much exertion, recent studies have uncovered multiple forms of labor involved in their practices of cultural production. In addition, scholars analyzing lesbian, gay, bisexual, transgender, and queer (LGBTQ) influencers highlight a tension between labor in service of self-commodification and the representation of sexual minorities. This article examines the microcelebrity labor of everyday queer women who aim to increase their social and economic capital by interweaving personal self-representations with entrepreneurial endeavors on Instagram and Vine. Through a close analysis of these platforms’ markets, governance, and infrastructures alongside interviews with queer female users of each platform, attention is given to both platform influences and participants’ experiences of promoting their jobs, side-gigs, hobbies, or passions alongside the rest of their lives. Findings identify three modes of labor specific to participants’ efforts to build a following: (1) intimate affective labor expended in sharing and managing personal disclosures; (2) developmental aesthetic labor as the acquisition and practice of technical skills and bodily displays to achieve a desired appearance or performance; (3) aspiring relational labor in attempts to forge relationships with established influencers or celebrities. Sexual identity was pivotal across these modes of labor, as it enhanced intimacy with followers, provided a niche audience for self-branding, conveyed authenticity through self-revelation, and established a common ground for forging relationships.
Democratization as institutional change: Hong Kong 1992–2015
Authors: Wong Mathew YH
Published: December 2019

The limited democratization in Hong Kong has been on-going for more than three decades. Unlike typical democratizations as the abrupt breakdown of authoritarian regimes, the case of Hong Kong is characterized by gradual and incremental changes under a constitutional framework. The process, involving actors such as the Chinese government, colonial government, and local democratic forces, provides a wide variety of forms of institutional changes. By utilizing concepts from the literature on institutional change, namely path dependence, layering, and conversion, important junctures of democratization in Hong Kong are analyzed. It is found that the case can be suitably explained by the framework of institutional change. This research carries implications for the study of central-regional interactions, democratization, and Hong Kong politics.
The Spectral Presence of Business in India’s 2019 Election
Authors: Sinha Aseema , Wyatt Andrew
Published: December 2019

Shifts in the balance of India’s economy towards private production have re-opened a debate over the role of the business in its polity. Business interests have found new ways to influence the state at different levels and through multiple institutions. This article concentrates on the composition of the 17th Lok Sabha and its porosity towards business (around 28.4% of these MPs have self-reported business careers). A growing of number of ‘industrialists’ and entrepreneurs have branched out into a legislative career; they complement a fast-emerging group of entrepreneurial politicians, who already use their legislative and institutional location to develop business interests for themselves and their families. We find that the influence and power of business has become diffuse and central at the same time; it seeped into every aspect of the election campaign and voting process: political recruitment, finance, issues, and policies—in tangible and intangible ways. This spectral presence of business is shaping Indian elections, parties, and democracy and in turn consolidating India’s economic reforms and pro-business polity.
How Community Nurses Manage Ethical Conflicts: A Grounded Theory Study
Authors: Porr Caroline , Gaudine Alice , Woo Kevin , Smith-Young Joanne , Green Candace
Published: December 2019

Research is limited on how nurses in community settings manage ethical conflicts. To address this gap, we conducted a study to uncover the process of behaviors enacted by community nurses when experiencing ethical conflicts. Guided by Glaserian grounded theory, we developed a theoretical model (Moral Compassing) that enables us to explain the process how 24 community nurses managed challenging ethical situations. We discovered that the main concern with which nurses wrestle is moral uncertainty (“Should I be addressing what I think is a moral problem?”). Moral Compassing comprises processes that resolve this main concern by providing community nurses with the means to attain the moral agency necessary to decide to act or to decide not to act. The processes are undergoing a visceral reaction, self-talk, seeking validation, and mobilizing support for action or inaction. We also discovered that community nurses may experience continuing distress that we labeled moral residue.
Kinship, Friendship, and Service Provider Social Ties and How They Influence Well-Being among Newly Resettled Refugees
Authors: Greene R. Neil
Published: December 2019

As refugees move from forced displacement to resettlement, their networks change dramatically alongside their living conditions and surroundings. The relative benefit of different kinds of ties in this context is not well known. Data for this study came from quantitative and qualitative interviews that were part of the Refugee Well-Being Project (N = 290), a longitudinal randomized controlled trial study inclusive of refugees resettling from the Great Lakes region of Africa, Afghanistan, Iraq, and Syria. Quantitative results revealed that greater numbers of kinship ties were related to better psychological quality of life ( p < .01) and greater numbers of reported services providers as social ties were related to higher emotional distress ( p < .001). Greater numbers of friendship ties were not statistically related to psychological quality of life or emotional distress. Qualitative findings suggest that cultural brokers—social ties that can bridge cultures, languages, and backgrounds—were particularly important to well-being, blending the benefits of strong and weak ties.
Computed tomography evaluation of palatal form in the transversal and sagittal fabrication process and the effect of first molar and canine crown angulations
Authors: Yamen Taljabini , Ulas Oz
Published: December 2019

The purpose of this study was to investigate changes in the palatal form in patients treated with and without premolar extractions. A total of 40 patients who had undergone orthodontic treatment (extraction and non-extraction) were divided into two groups coequally. Retrospective records were collected at pretreatment and at bracket removal. Stone casts were scanned by cone-beam tomography; linear and angular measurements on the three-dimensional model were then performed for both the sagittal direction and the transverse direction. Paired t-tests for dependent samples were used to compare results within the same group, and t-tests for independent samples were used to compare results between groups. A p value less than 0.05 was considered statistically significant. The sagittal palatal form increased in the non-extraction group, whereas it decreased in the extraction group. There was a decrement in the transversal palatal form in both groups. There were no differences or changes in molar or canine crown angulation in the non-extraction group. Conversely, distal tipping of the upper right first molar and distal tipping and lingual movement of both left and right upper canines were observed in the extraction group.
PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data
Authors: Wang Shudong , Wang Lihua , Zhang Yuanyuan , Pang Shanchen , Wang Xinzeng
Published: December 2019

Background

Tumor purity plays an important role in understanding the pathogenic mechanism of tumors. The purity of tumor samples is highly sensitive to tumor heterogeneity. Due to Intratumoral heterogeneity of genetic and epigenetic data, it is suitable to study the purity of tumors. Among them, there are many purity estimation methods based on copy number variation, gene expression and other data, while few use DNA methylation data and often based on selected information sites. Consequently, how to choose methylation sites as information sites has an important influence on the purity estimation results. At present, the selection of information sites was often based on the differentially methylated sites that only consider the mean signal, without considering other possible signals and the strong correlation among adjacent sites.

Results

Considering integrating multi-signals and strong correlation among adjacent sites, we propose an approach, PEIS, to estimate the purity of tumor samples by selecting informative differential methylation sites. Application to 12 publicly available tumor datasets, it is shown that PEIS provides accurate results in the estimation of tumor purity which has a high consistency with other existing methods. Also, through comparing the results of different information sites selection methods in the evaluation of tumor purity, it shows the PEIS is superior to other methods.

Conclusions

A new method to estimate the purity of tumor samples is proposed. This approach integrates multi-signals of the CpG sites and the correlation between the sites. Experimental analysis shows that this method is in good agreement with other existing methods for estimating tumor purity.
An efficient gene selection method for microarray data based on LASSO and BPSO
Authors: Xiong Ying , Ling Qing-Hua , Han Fei , Liu Qing-Hua
Published: December 2019

Background

The main goal of successful gene selection for microarray data is to find compact and predictive gene subsets which could improve the accuracy. Though a large pool of available methods exists, selecting the optimal gene subset for accurate classification is still very challenging for the diagnosis and treatment of cancer.

Results

To obtain the most predictive genes subsets without filtering out critical genes, a gene selection method based on least absolute shrinkage and selection operator (LASSO) and an improved binary particle swarm optimization (BPSO) is proposed in this paper. To avoid overfitting of LASSO, the initial gene pool is divided into clusters based on their structure. LASSO is then employed to select high predictive genes and further calculate the contribution value which indicates the genes’ sensitivity to samples’ classes. With the second-level gene pool established by double filter strategy, the BPSO encoding the contribution information obtained from LASSO is improved to perform gene selection. Moreover, from the perspective of the bit change probability, a new mapping function is defined to guide the updating of the particle to select the more predictive genes in the improved BPSO.

Conclusions

With the compact gene pool obtained by double filter strategies, the improved BPSO could select the optimal gene subsets with high probability. The experimental results on several public microarray data with extreme learning machine verify the effectiveness of the proposed method compared to the relevant methods.
DynaVenn: web-based computation of the most significant overlap between ordered sets
Authors: Amand Jérémy , Fehlmann Tobias , Backes Christina , Keller Andreas
Published: December 2019

Background

In many research disciplines, ordered lists are compared. One example is to compare a subset of all significant genes or proteins in a primary study to those in a replication study. Often, the top of the lists are compared using Venn diagrams, ore more precisely Euler diagrams (set diagrams showing logical relations between a finite collection of different sets). If different cohort sizes, different techniques or algorithms for evaluation were applied, a direct comparison of significant genes with a fixed threshold can however be misleading and approaches comparing lists would be more appropriate.

Results

We developed DynaVenn, a web-based tool that incrementally creates all possible subsets from two or three ordered lists and computes for each combination a p-value for the overlap. Respectively, dynamic Venn diagrams are generated as graphical representations. Additionally an animation is generated showing how the most significant overlap is reached by backtracking. We demonstrate the improved performance of DynaVenn over an arbitrary cut-off approach on an Alzheimer’s Disease biomarker set.

Conclusion

DynaVenn combines the calculation of the most significant overlap of different cohorts with an intuitive visualization of the results. It is freely available as a web service at http://www.ccb.uni-saarland.de/dynavenn.
The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics
Authors: Mathé Ewy , Zhang Chi , Wang Kai , Ning Xia , Guo Yan , Zhao Zhongming
Published: December 2019

The goal of this editorial is to summarize the 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) conference that took place on June 9–11, 2019 in The Ohio State University, Columbus, OH, and to provide an introductory summary of the seven articles presented in this supplement issue. ICIBM 2019 hosted four keynote speakers, four eminent scholar speakers, five tutorials and workshops, twelve concurrent sessions and a poster session, totaling 23 posters, spanning state-of-the-art developments in bioinformatics, genomics, next-generation sequencing (NGS) analysis, scientific databases, cancer and medical genomics, and computational drug discovery. A total of 105 original manuscripts were submitted to ICIBM 2019, and after careful review, seven were selected for this supplement issue. These articles cover methods and applications for functional annotations of miRNA targeting, clonal evolution of bacterial cells, gene co-expression networks that describe a given phenotype, functional binding site analysis of RNA-binding proteins, normalization of genome architecture mapping data, sample predictions based on multiple NGS data types, and prediction of an individual’s genetic admixture given exonic single nucleotide polymorphisms data.
normGAM: an R package to remove systematic biases in genome architecture mapping data
Authors: Liu Tong , Wang Zheng
Published: December 2019

Background

The genome architecture mapping (GAM) technique can capture genome-wide chromatin interactions. However, besides the known systematic biases in the raw GAM data, we have found a new type of systematic bias. It is necessary to develop and evaluate effective normalization methods to remove all systematic biases in the raw GAM data.

Results

We have detected a new type of systematic bias, the fragment length bias, in the genome architecture mapping (GAM) data, which is significantly different from the bias of window detection frequency previously mentioned in the paper introducing the GAM method but is similar to the bias of distances between restriction sites existing in raw Hi-C data. We have found that the normalization method (a normalized variant of the linkage disequilibrium) used in the GAM paper is not able to effectively eliminate the new fragment length bias at 1 Mb resolution (slightly better at 30 kb resolution). We have developed an R package named normGAM for eliminating the new fragment length bias together with the other three biases existing in raw GAM data, which are the biases related to window detection frequency, mappability, and GC content. Five normalization methods have been implemented and included in the R package including Knight-Ruiz 2-norm (KR2, newly designed by us), normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), and iterative correction and eigenvector decomposition (ICE).

Conclusions

Based on our evaluations, the five normalization methods can eliminate the four biases existing in raw GAM data, with VC and KR2 performing better than the others. We have observed that the KR2-normalized GAM data have a higher correlation with the KR-normalized Hi-C data on the same cell samples indicating that the KR-related methods are better than the others for keeping the consistency between the GAM and Hi-C experiments. Compared with the raw GAM data, the normalized GAM data are more consistent with the normalized distances from the fluorescence in situ hybridization (FISH) experiments. The source code of normGAM can be freely downloaded from http://dna.cs.miami.edu/normGAM/.
Hydrogen cyanamide induces grape bud endodormancy release through carbohydrate metabolism and plant hormone signaling
Authors: Liang Dong , Huang Xiaojing , Shen Yanqiu , Shen Tian , Zhang Huifen , Lin Lijin , Wang Jin , Deng Qunxian , Lyu Xiulan , Xia Hui
Published: December 2019

Background

Grape buds exhibit non-uniform, or delayed, break in early spring in subtropical regions because the accumulation of chilling is insufficient. Hydrogen cyanamide (H2CN2, HC) can partially replace chilling to effectively promote bud sprouting and is used widely in warm winter areas. However, the exact underlying mechanism of grape bud release from endodormancy induced by HC remains elusive.

Results

In this study, the transcriptome of grape winter buds under in vitro conditions following HC and water treatment (control) was analyzed using RNA-seq technology. A total of 6772 differentially expressed genes (DEGs) were identified. Furthermore, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that starch and sucrose metabolism and plant hormone signaling transduction were most enriched out of the 50 total pathways. HC treatment induced the upregulated expression of sucrose synthase (SUS), sucrose phosphate synthase (SPS), α-amylase (AM), and β-amylase (BM) and downregulated expression of sucrose invertase (INV), hexokinase (HK), fructokinase (FK), soluble starch synthase (SS), and granule-bound starch synthase (GBSS). Hence, the starch concentration in the HC-treated group was significantly lower than that in control, whereas soluble sugar content in the HC-treated group increased quickly and was higher than that in control between 0 and 8 d. The concentration of indoleacetic acid (IAA) and zeatin (ZT) increased, whereas that of abscisic acid (ABA) and gibberellin (GA) decreased in HC treated group, which coincided with the expression level of genes involved in above hormone signals. The content of hydrogen peroxide (H2O2) and enzyme activity of superoxide dismutase (SOD) and peroxidase (POD) were increased in grape buds with HC treatment, whereas catalase (CAT) activity was decreased. HC treatment increased the expression of POD, SOD, primary amine oxidase (PAO), polyamine oxidase (PAOX), and glutathione peroxidase (GSH-Px).

Conclusion

Based on these results, it is possible to propose a mechanistic model that underlies the regulation of endodormancy release in grapevine buds by exogenous HC application.
De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)
Authors: Li Ying , Zhang Chunxia , Yang Kebin , Shi Jingjing , Ding Yulong , Gao Zhimin
Published: December 2019

Background

Fargesia macclureana(Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence forF. macclureanato investigate the putative mechanisms underlying the flowering time control used byF. macclureanato adapt to its environment.

Results

Illumina deep sequencing of theF. macclureanatranscriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions ofFmFTandFmHd3a, two putativeF. macclureanaorthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding.

Conclusions

F. macclureanamay have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.
Application of LpxC enzyme inhibitor to inhibit some fast-growing bacteria in human gut bacterial culturomics
Authors: Hou Fengyi , Chang Yuxiao , Huang Zongyu , Han Ni , Bin Lei , Deng Huimin , Li Zhengchao , Pan Zhiyuan , Ding Lei , Gao Hong , Yang Ruifu , Zhi Fachao , Bi Yujing
Published: December 2019

Background

Culturomics can ascertain traces of microorganisms to be cultivated using different strategies and identified by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry or 16S rDNA sequencing. However, to cater to all requirements of microorganisms and isolate as many species as possible, multiple culture conditions must be used, imposing a heavy workload. In addition, the fast-growing bacteria (e.g., Escherichia) surpass the slow-growing bacteria in culture by occupying space and using up nutrients. Besides, some bacteria (e.g., Pseudomonas) suppress others by secreting antibacterial metabolites, making it difficult to isolate bacteria with lower competence. Applying inhibitors to restrain fast-growing bacteria is one method to cultivate more bacterial species from human feces.

Results

We applied CHIR-090, an LpxC enzyme inhibitor that has antibacterial activity against most Gram-negative bacteria, to culturomics of human fresh feces. The antibacterial activity of CHIR-090 was first assessed on five Gram-negative species of bacteria (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus vulgaris, and Bacteroides vulgatus), all of which are commonly isolated from the human gut. Then, we assessed suitable concentrations of the inhibitor. Finally, CHIR-090 was applied in blood culture bottles for bacterial cultivation. In total, 102 species from five samples were identified. Of these, we found one new species, two species not reported previously in the human gut, and 11 species not previously isolated from humans.

Conclusions

CHIR-090 can suppress E. coli, P. aeruginosa, K. pneumoniae, Pro. vulgaris, but not B. vulgatus. Compared with the non-inhibitor group, CHIR-090 increased bacteria isolation by 23.50%, including four species not reported in humans and one new species. Application of LpxC enzyme inhibitor in culturomics increased the number of species isolated from the human gut.
Metabolite profiling during graft union formation reveals the reprogramming of primary metabolism and the induction of stilbene synthesis at the graft interface in grapevine
Authors: Prodhomme Duyên , Valls Fonayet Josep , Hévin Cyril , Franc Céline , Hilbert Ghislaine , de Revel Gilles , Richard Tristan , Ollat Nathalie , Cookson Sarah Jane
Published: December 2019

Background

Grafting with rootstocks is essential for the culture of many perennial fruit crops and is increasing being used in the production of annual fruits and vegetables. Our previous work based on microarrays showed that transcripts encoding enzymes of both primary and secondary metabolism were differentially expressed during graft union formation in both homo-grafts (a genotype grafted with itself) and hetero-grafts (two different genotypes grafted together). The aim of this study was to profile primary and secondary metabolites, and quantify the activity of phenylalanine ammonia lyase (PAL) and neutral invertase (NI) in the scion and rootstock tissues and the graft interface of homo and hetero-grafts of grapevine 1 month after grafting. Table-top grafting was done on over-wintering stems (canes) of grapevine and the graft interface tissues (containing some woody stem tissues and callus) were compared to the surrounding rootstock and scion tissues. The objective was to identify compounds involved in graft union formation and hetero-grafting responses.

Results

A total of 54 compounds from primary and secondary metabolism (19 amino acids, five primary and 30 secondary compounds metabolites) and the activity of two enzymes were measured. The graft interface was associated with an increase in the accumulation of the branched-chain amino acids, basic amino acids, certain stilbene compounds and higher PAL and NI activity in comparison to the surrounding woody stem tissues. Some amino acids and stilbenes were identified as being accumulated differently between the graft interfaces of the scion/rootstock combinations in a manner which was unrelated to their concentrations in the surrounding woody stem tissues.

Conclusions

This study revealed the modification of primary metabolism to support callus cell formation and the stimulation of stilbene synthesis at the graft interface, and how these processes are modified by hetero-grafting. Knowledge of the metabolites and/or enzymes required for successful graft union formation offer us the potential to identify markers that could be used by nurseries and researchers for selection and breeding purposes.
Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode
Authors: Lu Nan , Zhang Miaomiao , Xiao Yao , Han Donghua , Liu Ying , Zhang Yu , Yi Fei , Zhu Tianqing , Ma Wenjun , Fan Erqin , Qu Guanzheng , Wang Junhui
Published: December 2019

Background

Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.

Results

Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16–60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9–1, Q18–66 and Q18–73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.

Conclusions

This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.
Nitric oxide- induced AtAO3 differentially regulates plant defense and drought tolerance in Arabidopsis thaliana
Authors: Khan Murtaza , Imran Qari Muhammad , Shahid Muhammad , Mun Bong-Gyu , Lee Sang-Uk , Khan Muhammad Aaqil , Hussain Adil , Lee In-Jung , Yun Byung-Wook
Published: December 2019

Background

Exposure of plants to different environmental insults instigates significant changes in the cellular redox tone driven in part by promoting the production of reactive nitrogen species. The key player, nitric oxide (NO) is a small gaseous diatomic molecule, well-known for its signaling role during stress. In this study, we focused on abscisic acid (ABA) metabolism-related genes that showed differential expression in response to the NO donorS-nitroso-l-cysteine (CySNO) by conducting RNA-seq-based transcriptomic analysis.

Results

CySNO-induced ABA-related genes were identified and further characterized. Gene ontology terms for biological processes showed most of the genes were associated with protein phosphorylation. Promoter analysis suggested that severalcis-regulatory elements were activated under biotic and/or abiotic stress conditions. The ABA biosynthetic geneAtAO3was selected for validation using functional genomics. The loss of function mutantatao3was found to differentially regulate oxidative and nitrosative stress. Further investigations for determining the role ofAtAO3in plant defense suggested a negative regulation of plant basal defense andR-gene-mediated resistance. Theatao3plants showed resistance to virulentPseudomonas syringaepv.tomatostrain DC3000 (PstDC3000) with gradual increase inPR1gene expression. Similarly,atao3plants showed increased hypersensitive response (HR) when challenged withPstDC3000 (avrB). Theatgsnor1–3andatsid2mutants showed a susceptible phenotype with reducedPR1transcript accumulation. Drought tolerance assay indicated thatatao3andatnced3ABA-deficient mutants showed early wilting, followed by plant death. The study of stomatal structure showed thatatao3andatnced3were unable to close stomata even at 7 days after drought stress. Further, they showed reduced ABA content and increased electrolyte leakage than the wild-type (WT) plants. The quantitative polymerase chain reaction analysis suggested that ABA biosynthesis genes were down-regulated, whereas expression of most of the drought-related genes were up-regulated inatao3than in WT.

Conclusions

AtAO3negatively regulates pathogen-induced salicylic acid pathway, although it is required for drought tolerance, despite the fact that ABA production is not totally dependent onAtAO3, and that drought-related genes likeDREB2andABI2show response to drought irrespective of ABA content.
Evaluation of alterations in serum immunoglobulin concentrations in components of metabolic syndrome, obesity, diabetes, and dyslipidemia
Authors: Lin Dee , Bridgeman Mary Barna , Brunetti Luigi
Published: December 2019

Purpose

Serum immunoglobulins (Igs) play a critical role in modulating the immune response by neutralizing pathogens, although little is known about the effect of Igs in development of atherosclerotic cardiovascular disease (ASCVD). Elevated serum Immunoglobulin A (IgA) concentrations have been identified in previous studies in populations with obesity and hypertriglyceridemia, whereas variable concentrations of Immunoglobulin M (IgM) have been observed in the setting of dyslipidemia.

Methods

In this cross-sectional study, investigators examined the association of serum Ig concentrations with components of metabolic syndrome, including obesity, diabetes, and dyslipidemia. All consecutive adult patients aged 18 years or older discharged from two academic teaching hospitals with serum Immunoglobulin G (IgG) concentration measured during their admission were evaluated, with a total of 1809 individuals included and stratified into two groups: those with and those without dyslipidemia.

Results

Mean IgG concentration in individuals with and without dyslipidemia was 997 ± 485 mg/dL and 1144 ± 677 mg/dL, respectively (P <  0.0001). After controlling for confounders in the generalized linear model (GLM), the least square mean IgG concentration in individuals with and without dyslipidemia was 1095 and 1239 mg/dL, respectively (P <  0.0001). The mean IgA and IgM concentrations were not significantly different in individuals with and without dyslipidemia both before and after adjusting covariates. After controlling for confounding variables, all three serum Ig concentrations were not significantly different in individuals with and without diabetes.

Conclusion

Dyslipidemia was associated with a lower mean serum IgG concentration. No association with any serum Ig was indentified in individuals with diabetes. Exploration of the association between alterations in serum Igs and metabolic syndrome and the role of alterations of Ig concentrations in disease progression represents an important step in identification of appropriate targeted treatment options for reducing cardiovascular risk.
Why do participants drop-out: findings from a prospective pediatric cohort for fever surveillance established at Vellore, southern India
Authors: Sindhu Kulandaipalayam Natarajan , Srinivasan Manikandan , Subramaniam Sathyapriya , David Anita Shirley , Mohan Venkata Raghava , John Jacob , Kang Gagandeep
Published: December 2019

Background

Cohort studies are pivotal in understanding the natural history, and to thereby determine the incidence of a disease. The conduct of large-scale community-based cohort studies is challenging with reference to money, manpower and time. Further, attrition inherent to cohort studies can affect the power, and thereby the study’s validity. Our objective was to estimate the percentage of participant withdrawal and to subsequently understand reasons for the same in the Vellore Typhoid Surveillance (VTS) cohort.

Methods

VTS study, a prospective community-based pediatric cohort, was established in a semi-urban settlement of Vellore to estimate the incidence rate of typhoid fever. An active weekly surveillance identified children with fever, and blood cultures were performed for fevers of ≥3 days. Reasons for participant drop-out in the cohort were documented. Nine focus group discussions (FGD), each with 5 to 7 parents/primary caregivers of former as well current participants were conducted separately, to understand reasons for consent withdrawal as well as the good aspects of the study that the current participants perceived. A descriptive, as well as an interpretative account of the themes that emerged from the FGDs were done.

Results

Of the 5639 children in the VTS cohort, 404 (7.2%) withdrew consent during the 12-month surveillance. Of these, 50% dropped out due to migration from study area; 18.1% as their parents were unhappy with the blood draws for blood culture; and 14.4% did not clearly put forth the reason for consent withdrawal. Being from an orthodox background, high socio-economic status and joint family were associated with a decision to drop-out. Frequent and voluminous blood draws, male field research assistants (FRA) making weekly home-visits, the perception that inquiring about fever made their child fall sick, and that the study clinic did not initiate antibiotics immediately, were the important themes that emerged from the FGDs conducted among drop-outs.

Conclusion

Our study showed that specific beliefs and behaviours within the community influenced the drop-out rate of the VTS cohort. Background characteristics and perceptions that exist, along with attrition data from previous cohort studies in the specific community are important to be considered while implementing large-scale cohort studies.
Incidence of frailty among community-dwelling older adults: a nationally representative profile in China
Authors: Xu Weihao , Li Ya-Xi , Wu Chenkai
Published: December 2019

Background

Frailty is a clinically recognizable state of reduced resilience to stressors and increased vulnerability to adverse outcomes. The majority of studies have focused on the prevalence and risk factors of frailty, while the incidence of frailty has not been well documented, especially in less developed regions including China—a country that has the largest aging population in the world. We investigated the incidence of frailty among non-frail Chinese older adults by sociodemographic characteristics, disease burden, and geographic region.

Methods

Participants were 4939 adults aged ≥60 years from the China Health and Retirement Longitudinal Study, a cohort study of a nationally representative sample of middle-aged and older community-dwelling adults from 28 provinces in China. Frailty was assessed by an adapted version of the well-validated Fried’s physical frailty phenotype, in which five criteria were included: weakness, slowness, exhaustion, physical inactivity, and shrinking.

Results

Over an average of 2.1 years of follow-up (10,514.2 person-years), the weighted incidence rate of frailty was 60.6 per 1000 person-years; the incidence rate was 28.8 and 86.6 per 1000 person-years for those who were initially robust and prefrail, respectively. Participants who were older and widowed, had lower education and household income, lived in rural areas, and had higher burden of chronic conditions had higher frailty incidence. Frailty incidence ranged from 44.8 per 1000 person-years in the Southeast to 93.0 per 1000 person-years in the Northwest.

Conclusions

Incidence rate of frailty was 60.6 per 1000 person-years among community-living Chinese adults aged ≥ 60 years. Substantial sociodemographic and geographical disparities exist in frailty incidence.
Cumulative use of therapeutic bladder anticholinergics and the risk of dementia in patients with lower urinary tract symptoms: a nationwide 12-year cohort study
Authors: Wang Yi-Chi , Chen Yung-Liang , Huang Chun-Che , Ho Chung-Han , Huang Yu-Tung , Wu Ming-Ping , Ou Ming-Jung , Yang Chiu-Hsien , Chen Ping-Jen
Published: December 2019

Background

Studies have shown an association between lower urinary tract symptoms (LUTS) and an increased risk of dementia. Whether anticholinergic use contributes to the development of dementia in patients with LUTS remains unknown, especially in Asian populations. This study aims to investigate the association between anticholinergic use and dementia in patients with LUTS.

Methods

This study included patients aged 50 years and over with newly diagnosed LUTS (January 2001 to December 2005), divided into four groups according to their cumulative defined daily doses (cDDDs) of anticholinergics: < 28 cDDDs, 28–84 cDDDs, 85–336 cDDDs, ≥337 cDDDs. Patients were followed up until dementia developed or until the end of 2012.

Results

We recruited a total of 16,412 patients. The incidence of dementia was 10% in the < 28 cDDD group, 8.9% in the 28–84 cDDD group, 11.5% in the 85–336 cDDD group, and 14.4% in the ≥337 cDDD group (p = .005). In a Cox proportional hazards analysis, the adjusted hazard ratio of dementia was 1.15 (95% CI = 0.97–1.37) in the 85–336 cDDD group, and 1.40 (95% CI = 1.12–1.75) in the ≥337 cDDD group after adjusting for covariates.

Conclusions

Our study indicates that higher cumulative anticholinergic exposure is associated with an increase in the risk of incident dementia in patients with LUTS aged 50 years of age and over. Either using one anticholinergic agent or switching anticholinergic agents cumulatively increases this risk. Therapeutic risks and benefits of using anticholinergics in LUTS treatment should be clinically reviewed and weighed.
Determinants of AIDS and non-AIDS related mortality among people living with HIV in Shiraz, southern Iran: a 20-year retrospective follow-up study
Authors: Gheibi Zahra , Shayan Zahra , Joulaei Hassan , Fararouei Mohammad , Beheshti Shohreh , Shokoohi Mostafa
Published: December 2019

Background

Human Immunodeficiency Virus (HIV) infection has become a global concern. Determining the factors leading to death among HIV patients helps controlling Acquired Immune Deficiency Syndrome (AIDS) epidemic. Up to now, little is known about mortality and its determinants among people living with HIV in the Middle East and North Africa (MENA) region, including Iran. The purpose of this study was to assess the risk factors of AIDS-Related Mortality (ARM) and Non-AIDS-Related Mortality (NARM) among people with HIV in Iran.

Methods

This 20-year retrospective study was conducted on 1160 people with HIV whose data were collected from 1997 to 2017. The association of the study outcomes (ARM and NARM) with various study variables, including demographic status at the time of diagnosis and clinical indexes during the follow-up were examined to define the predictors of mortality among the patients. Regarding, Cox proportional hazard and competing risk models were fitted and Adjusted Hazard Ratios (AHR), Sub-distribution Hazard Ratio (SHR) and the 95% Confidence Intervals (CI) were reported.

Results

during the follow-up period, 391 individuals (33.7%) died with 86,375 person-years of follow-up. Of the total deaths, 251 (64.2%) and 140 (35.8%) were ARM and NARM, respectively. Rates of the mortality caused by AIDS and non-AIDS were 3.2 and 4.5 per 1000 person-months, respectively. Responding to combined Antiretroviral Treatment (cART) 6 months after initiation, receiving Pneumocystis Pneumonia (PCP) prophylaxis, and higher CD4 count at diagnosis, reduced the hazard of ARM and NARM. However, older age, late HIV diagnosis, and last HIV clinical stages increased the hazard of AIDS related to mortality. Additionally, male gender, older age, incarceration history, and last HIV clinical stages increased the non-AIDS mortality.

Conclusions

Mortality caused by AIDS and non-AIDS remains high among people with HIV in Iran, particularly among males and those with late diagnosis. It seems that applying effective strategies to identify infected individuals at earlier stage of the infection, and targeting individuals with higher risk of mortality can decrease the mortality rate among HIV infected people.
Urban-rural disparities in treatment outcomes among recurrent TB cases in Southern Province, Zambia
Authors: Mutembo Simon , Mutanga Jane N. , Musokotwane Kebby , Kanene Cuthbert , Dobbin Kevin , Yao Xiaobai , Li Changwei , Marconi Vincent C. , Whalen Christopher C.
Published: December 2019

Background

At least 13–20% of all Tuberculosis (TB) cases are recurrent TB. Recurrent TB has critical public health importance because recurrent TB patients have high risk of Multi-Drug Resistant TB (MDR-TB). It is critical to understand variations in the prevalence and treatment outcomes of recurrent TB between different geographical settings.

The objective of our study was to estimate the prevalence of recurrent TB among TB cases and compare risk of unfavorable treatment outcomes between rural and urban settings.

Methods

In a retrospective cohort study conducted in southern province of Zambia, we used mixed effects logistic regression to asses associations between explanatory and outcome variables. Primary outcome was all-cause mortality and exposure was setting (rural/urban). Data was abstracted from the facility TB registers.

Results

Overall 3566 recurrent TB cases were diagnosed among 25,533 TB patients. The prevalence of recurrent TB was 15.3% (95% CI: 14.8 15.9) in urban and 11.3% (95% CI: 10.7 12.0) in rural areas. Death occurred in 197 (5.5%), 103 (2.9%) were lost to follow-up, and 113 (3.2%) failed treatment. Rural settings had 70% higher risk of death (adjusted OR: 1.7; 95% CI: 1.2 2.7). Risk of lost to follow-up was twice higher in rural than urban (adjusted OR: 2.0 95% CI: 1.3 3.0). Compared to HIV-uninfected, HIV-infected individuals on Antiretroviral Treatment (ART) were 70% more likely to die (adjusted OR: 1.7; 95% CI: 1.2 3.1).

Conclusion

Recurrent TB prevalence was generally high in both urban and rural settings. The risk of mortality and lost to follow-up was higher among rural patients. We recommend a well-organized Directly Observed Therapy strategy adapted to setting where heightened TB control activities are focused on areas with poor treatment outcomes.
Genital Kaposi sarcoma in a HIV and syphilis co-infected patient: case presentation
Authors: Barroso dos Reis Helena Lucia , de Carvalho Ferreira Dennis , Tosato Boldrini Neide Aparecida , Galvão Carolina , Jacomele Caldas João Victor , Santos Neves Marize Freitas , Godefroy Philippe
Published: December 2019

Background

Kaposi sarcoma, as an epidemiological factor, is associated with acquired immunodeficiency syndrome (AIDS) and it is related to human herpes virus (HHV-8), as well as a higher prevalence in males and non-genital involvement. Vulvar localization is quite infrequent; therefore it may be considered in the differential diagnosis of genital lesions, especially in HIV patients.

Case presentation

We describe the atypical presentation of a female HIV patient with multiple comorbidities, with the clinical manifestation of Kaposi sarcoma (KS) in a vulvar region that was initially diagnosed as a syphilitic gumma. The patient underwent a biopsy of the lesion, and histopathology revealed a Kaposi sarcoma.

Discussion

This case reinforces that the pathogenesis of Kaposi sarcoma is still unclear and that probably multiple factors, regarding both the virus and the patient characteristics may lead to carcinogenesis. Conclusion: It is imperative to seek more excellent knowledge about this disease, to facilitate the diagnosis, to warrant the appropriate treatment and to improve the prognosis of the patient, especially the genital lesions.