bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathologic T-cell response in ischaemic failing hearts elucidated by T-cell receptor sequencing and phenotypic characterization
Authors: Tang Ting-Ting , Zhu Yi-Cheng , Dong Nian-Guo , Zhang Si , Cai Jie , Zhang Ling-Xue , Han Yue , Xia Ni , Nie Shao-Fang , Zhang Min , Lv Bing-Jie , Jiao Jiao , Yang Xiang-Ping , Hu Yu , Liao Yu-Hua , Cheng Xiang 
Published: July 2019

Abstract

Aims
A persistent cardiac T-cell response initiated by myocardial infarction is linked to subsequent adverse ventricular remodelling and progression of heart failure. No data exist on T-cell receptor (TCR) repertoire changes in combination with phenotypic characterization of T cells in ischaemic failing human hearts.

Methods and results
Analysis of TCR repertoire with high-throughput sequencing revealed that compared with T cells in control hearts, those in ischaemic failing hearts showed a clonally expanded TCR repertoire but similar usage patterns of TRBV-J rearrangements and V gene segments; compared with T cells in peripheral blood, those in ischaemic failing hearts exhibited a restricted and clonally expanded TCR repertoire and different usage patterns of TRBV-J rearrangements and V gene segments, suggesting the occurrence of tissue-specific T-cell expansion in ischaemic failing hearts. Consistently, TCR clonotype sharing was prominent in ischaemic failing hearts, especially in hearts of patients who shared human leucocyte antigen (HLA) alleles. Furthermore, ischaemia heart failure (IHF) heart-associated clonotypes were more frequent in peripheral blood of IHF patients than in that of controls. Heart-infiltrating T cells displayed memory- and effector-like characteristics. Th1 cells were the predominant phenotype among CD4 + T cells; CD8 + T cells were equally as abundant as CD4 + T cells and produced high levels of interferon-γ, granzyme B, and perforin.

Conclusion
We provide novel evidence for a tissue-specific T-cell response predominated by Th1 cells and cytotoxic CD8 + T cells in ischaemic failing human hearts that may contribute to the progression of heart failure.
Rhizospheric life of Salmonella requires flagella-driven motility and EPS-mediated attachment to organic matter and enables cross-kingdom invasion
Authors: Karmakar Kapudeep , Nair Abhilash Vijay , Chandrasekharan Giridhar , Garai Preeti , Nath Utpal , Nataraj Karaba N , N.B Prakash , Chakravortty Dipshikha 
Published: July 2019

ABSTRACTSalmonella is an established pathogen of the members of the kingdom Animalia. Reports indicate that the association of Salmonella with fresh, edible plant products occurs at the pre-harvest state, i.e. in the field. In this study, we follow the interaction of Salmonella Typhimurium with the model plant Arabidopsis thaliana to understand the process of migration in soil. Plant factors like root exudates serve as chemo-attractants. Our ex situ experiments allowed us to track Salmonella from its free-living state to the endophytic state. We found that genes encoding two-component systems and proteins producing extracellular polymeric substances are essential for Salmonella to adhere to the soil and roots. To understand the trans-kingdom flow of Salmonella, we fed the contaminated plants to mice and observed that it invades and colonizes liver and spleen. To complete the disease cycle, we re-established the infection in plant by mixing the potting mixture with the fecal matter collected from the diseased animals. Our experiments revealed a cross-kingdom invasion by the pathogen via passage through a murine intermediate, a mechanism for its persistence in the soil and invasion in a non-canonical host. These results form a basis to break the life-cycle of Salmonella before it reaches its animal host and thus reduce Salmonella contamination of food products.
Not all saponins have a greater antiprotozoal activity than their related sapogenins
Authors: Ramos-Morales E , Lyons L , de la Fuente G , Braganca R , Newbold C J 
Published: July 2019

ABSTRACT
The antiprotozoal effect of saponins varies according to both the structure of the sapogenin and the composition and linkage of the sugar moieties to the sapogenin. The effect of saponins on protozoa has been considered to be transient as it was thought that when saponins were deglycosilated to sapogenins in the rumen they became inactive; however, no studies have yet evaluated the antiprotozoal effect of sapogenins compared to their related saponins. The aims of this study were to evaluate the antiprotozoal effect of eighteen commercially available triterpenoid and steroid saponins and sapogenins in vitro, to investigate the effect of variations in the sugar moiety of related saponins and to compare different sapogenins bearing identical sugar moieties. Our results show that antiprotozoal activity is not an inherent feature of all saponins and that small variations in the structure of a compound can have a significant influence on their biological activity. Some sapogenins (20(S)-protopanaxatriol, asiatic acid and madecassic acid) inhibited protozoa activity to a greater extent than their corresponding saponins (Re and Rh1 and asiaticoside and madecassoside), thus the original hypothesis that the transient nature of the antiprotozoal action of saponins is due to the deglycosilation of saponins needs to be revisited.
The role of exploitation in the establishment of mutualistic microbial symbioses
Authors: Sørensen Megan E S , Lowe Chris D , Minter Ewan J A , Wood A Jamie , Cameron Duncan D , Brockhurst Michael A 
Published: July 2019

ABSTRACT
Evolutionary theory suggests that the conditions required for the establishment of mutualistic symbioses through mutualism alone are highly restrictive, often requiring the evolution of complex stabilising mechanisms. Exploitation, whereby initially the host benefits at the expense of its symbiotic partner and mutual benefits evolve subsequently through trade-offs, offers an arguably simpler route to the establishment of mutualistic symbiosis. In this review, we discuss the theoretical and experimental evidence supporting a role for host exploitation in the establishment and evolution of mutualistic microbial symbioses, including data from both extant and experimentally evolved symbioses. We conclude that exploitation rather than mutualism may often explain the origin of mutualistic microbial symbioses.
Many plant pathogenic Pseudomonas savastanoi pv glycinea isolates possess an inactive quorum sensing ahlR gene via a point mutation
Authors: Degrassi Giuliano , Mortato Valentina , Devescovi Giulia , Hoshino Rodrigo , Chatnaparat Tiyakhon , Kojic Milan , Carpentieri-Pipolo Valeria , Zhao Youfu , Venturi Vittorio 
Published: July 2019

ABSTRACT
Many plant bacterial pathogens monitor their group behaviour and their population density via production of N-acyl homoserine lactone signals which regulate the expression of several genes via the LuxI/R homologs. This regulatory network, termed quorum sensing (QS), is present in the soybean bacterial pathogen Pseudomonas savastanoi pv glycinea (Psg). The sequenced genomes of two strains of Psg, race 4 and B076, contain an N-acyl homoserine lactone (AHL) based LuxI/R QS system named AhlI/R. While studying the QS system of Psg strains race 4 and B076 isolated in USA, LMG5066 in New Zealand and IBSBF355 in Brazil, we found that B076, LMG5066 and IBSBF355 possess a point mutation in the ahlR gene that causes a frameshift resulting in a truncated AhlR protein. Psg race 4 does not possess the mutation in ahlR and the QS system is functional. The same mutation in the ahlR gene was found to be also present in 9 of 19 Psg strains isolated from diseased soybean in Illinois. Phenotypic analysis of strains showed that swarming motility is repressed whereas phosphate solubilisation was activated by QS in Psg. Analysing the secretome, we also found that four proteins were under QS regulation.
Far-field tsunami data assimilation for the 2015 Illapel earthquake
Authors: Wang Y , Satake K , Cienfuegos R , Quiroz M , Navarrete P 
Published: July 2019

SUMMARYThe 2015 Illapel earthquake (Mw 8.3) occurred off central Chile on September 16, and generated a tsunami that propagated across the Pacific Ocean. The tsunami was recorded on tide gauges and Deep-ocean Assessment and Reporting of Tsunami (DART) tsunameters in east Pacific. Near-field and far-field tsunami forecasts were issued based on the estimation of seismic source parameters. In this study, we retroactively evaluate the potentiality of forecasting this tsunami in the far field based solely on tsunami data assimilation from DART tsunameters. Since there are limited number of DART buoys, virtual stations are assumed by interpolation to construct a more complete tsunami wavefront for data assimilation. The comparison between forecasted and observed tsunami waveforms suggests that our method accurately forecasts the tsunami amplitudes and arrival time in the east Pacific. This approach could be a complementary method of current tsunami warning systems based on seismic observations.
The Relationship Between Viewing Environment, Narrative Environment, and Involvement With Narratives: The Case of Temperature
Authors: Tal-Or Nurit 
Published: July 2019

Abstract
Three studies explored the mutual effects of the physical environment of watching a narrative text and involvement with that text, using temperature. In Study 1, the temperatures in the room and the film were manipulated. As expected, a match between the temperatures enhanced the enjoyment of the film through the mediation of the perceived match and either transportation into the narrative, identification with the narrative’s protagonist, or engagement with the narrative. In Studies 2 and 3, the temperature in the film and transportation or identification were manipulated. As hypothesized, the temperature depicted in the movie indirectly affected the viewer’s feelings of warmth or coldness, especially when the viewer was transported into the narrative or identified with its protagonist. Moreover, this effect led to the viewers’ desire to consume certain food products. I discuss these findings using theories of transportation and identification.
A single-port video-assisted thoracoscopic surgery with CO2 insufflation for traumatic diaphragmatic hernia
Authors: Lee Jun Hee , Han Kook Nam , Hong Jeong In , Kim Hyun Koo 
Published: July 2019

Abstract
In this article, we present 2 cases with successful reduction of herniated organs and repair of a ruptured diaphragm through a single-port video-assisted thoracoscopic surgery (VATS) approach using CO2 gas insufflation in haemodynamically stable patients. A CO2 insufflation was useful to push the diaphragm down and aided in reducing the size of the herniated organ. This approach did not cause damage to the herniated organs and no additional instrument or assistant was required. Thus, CO2 insufflation makes the single-port VATS procedure easier even in haemodynamically stable trauma patients.
Association between coffee consumption and overall risk of being diagnosed with or dying from cancer among >300 000 UK Biobank participants in a large-scale Mendelian randomization study
Authors: Ong Jue-Sheng , Law Matthew H , An Jiyuan , Han Xikun , Gharahkhani Puya , Whiteman David C , Neale Rachel E , MacGregor Stuart 
Published: July 2019

Abstract

Background
Previous observational studies have suggested that coffee intake may be associated with a reduction in cancer risk. Mendelian randomization (MR) studies can help clarify whether the observed associations are likely to be causal. Here we evaluated whether coffee intake is associated with: (i) overall risk of being diagnosed with/dying from any cancer; and (ii) risk of individual cancers.

Methods
We identified 46 155 cases (of which 6998 were fatal) and 270 342 controls of White British ancestry from the UK Biobank cohort (UKB), based on ICD10 diagnoses. Individuals with benign tumours were excluded. Coffee intake was self-reported and recorded based on cup/day consumption. We conducted both observational and summary data MR analyses.

Results
There was no observational association between coffee intake and overall cancer risk [odds ratio (OR) per one cup/day increase = 0.99, 95% confidence interval (CI) 0.98, 1.00] or cancer death (OR = 1.01, 0.99, 1.03); the estimated OR from MR is 1.01 (0.94, 1.08) for overall cancer risk and 1.11 (0.95, 1.31) for cancer death. The relationship between coffee intake and individual cancer risks were consistent with a null effect, with most cancers showing little or no associations with coffee. Meta-analysis of our MR findings with publicly available summary data on various cancers do not support a strong causal relationship between coffee and risk of breast, ovarian, lung or prostate cancer, upon correction for multiple testing.

Conclusions
Taken together, coffee intake is not associated with overall risk of being diagnosed with or dying from cancer in UKB. For individual cancers, our findings were not statistically inconsistent with earlier observational studies, although for these we were unable to rule out a small effect on specific types of cancer.
Repurposing antihypertensive drugs for the prevention of Alzheimer’s disease: a Mendelian randomization study
Authors: Walker Venexia M , Kehoe Patrick G , Martin Richard M , Davies Neil M 
Published: July 2019

Abstract

Background
Evidence concerning the potential repurposing of antihypertensives for Alzheimer’s disease prevention is inconclusive. We used Mendelian randomization, which can be more robust to confounding by indication and patient characteristics, to investigate the effects of lowering systolic blood pressure, via the protein targets of different antihypertensive drug classes, on Alzheimer’s disease.

Methods
We used summary statistics from genome-wide association studies of systolic blood pressure and Alzheimer’s disease in a two-sample Mendelian randomization analysis. We identified single-nucleotide polymorphisms (SNPs) that mimic the action of antihypertensive protein targets and estimated the effect of lowering systolic blood pressure on Alzheimer’s disease in three ways: (i) combining the protein targets of antihypertensive drug classes, (ii) combining all protein targets and (iii) without consideration of the protein targets.

Results
There was limited evidence that lowering systolic blood pressure, via the protein targets of antihypertensive drug classes, affected Alzheimer’s disease risk. For example, the protein targets of calcium channel blockers had an odds ratio (OR) per 10 mmHg lower systolic blood pressure of 1.53 [95% confidence interval (CI): 0.94 to 2.49; p = 0.09; SNPs = 17]. We also found limited evidence for an effect when combining all protein targets (OR per 10 mmHg lower systolic blood pressure: 1.14; 95% CI: 0.83 to 1.56; p = 0.41; SNPs = 59) and without consideration of the protein targets (OR per 10 mmHg lower systolic blood pressure: 1.04; 95% CI: 0.95 to 1.13; p = 0.45; SNPs = 153).

Conclusions
Mendelian randomization suggests that lowering systolic blood pressure via the protein targets of antihypertensive drugs is unlikely to affect the risk of developing Alzheimer’s disease. Consequently, if specific antihypertensive drug classes do affect the risk of Alzheimer’s disease, they may not do so via systolic blood pressure.
Birthweight in offspring and cardiovascular mortality in their parents, aunts and uncles: a family-based cohort study of 1.35 million births
Authors: Shaikh Fareeha , Kjølllesdal Marte Karoline , Carslake David , Stoltenberg Camilla , Davey Smith George , Næss Øyvind 
Published: July 2019

Abstract

Background
A link between suboptimal fetal growth and higher risk of cardiovascular disease (CVD) is well documented. It has been difficult to assess the contribution of environmental versus genetic factors to the association, as these factors are closely connected in nuclear families. We investigated the association between offspring birthweight and CVD mortality in parents, aunts and uncles, and examined whether these associations are explained by CVD risk factors.

Methods
We linked Norwegian data from the Medical Birth Registry, the Cause of Death Registry and cardiovascular surveys. A total of 1 353 956 births (1967–2012) were linked to parents and one maternal and one paternal aunt/uncle. Offspring birthweight and CVD mortality association among all relationships was assessed by hazard ratios (HR) from Cox regressions. The influence of CVD risk factors on the associations was examined in a subgroup.

Results
Offspring birthweight was inversely associated with CVD mortality among parents and aunts/uncles. HR of CVD mortality for one standard deviation (SD) increase in offspring birthweight was 0.72 (0.69–0.75) in mothers and 0.89 (0.86–0.92) in fathers. In aunts/uncles, the HRs were between 0.90 (0.86–0.95) and 0.93 (0.91–0.95). Adjustment for CVD risk factors in a subgroup attenuated all the associations.

Conclusions
Birthweight was associated with increased risk of CVD in parents and in aunts/uncles. These associations were largely explained by CVD risk factors. Our findings suggest that associations between offspring birthweight and CVD in adult relatives involve both behavioural variables (especially smoking) and shared genetics relating to established CVD risk factors.
Assessing longer-term effectiveness of a combined household-level piped water and sanitation intervention on child diarrhoea, acute respiratory infection, soil-transmitted helminth infection and nutritional status: a matched cohort study in rural Odisha, India
Authors: Reese Heather , Routray Parimita , Torondel Belen , Sinharoy Sheela S , Mishra Samir , Freeman Matthew C , Chang Howard H , Clasen Thomas 
Published: July 2019

Abstract

Background
Open defecation is widespread in rural India, and few households have piped water connections. While government and other efforts have increased toilet coverage in India, and evaluations found limited immediate impacts on health, longer-term effects have not been rigorously assessed.

Methods
We conducted a matched cohort study to assess the longer-term effectiveness of a combined household-level piped water and sanitation intervention implemented by Gram Vikas (an Indian NGO) in rural Odisha, India. Forty-five intervention villages were randomly selected from a list of those where implementation was previously completed at least 5 years before, and matched to 45 control villages. We conducted surveys and collected stool samples between June 2015 and October 2016 in households with a child &lt;5 years of age (n = 2398). Health surveillance included diarrhoea (primary outcome), acute respiratory infection (ARI), soil-transmitted helminth infection, and anthropometry.

Results
Intervention villages had higher improved toilet coverage (85% vs 18%), and increased toilet use by adults (74% vs 13%) and child faeces disposal (35% vs 6%) compared with control villages. There was no intervention association with diarrhoea [adjusted OR (aOR): 0.94, 95% confidence interval (CI): 0.74–1.20] or ARI. Compared with controls, children in intervention villages had lower helminth infection (aOR: 0.44, 95% CI: 0.18, 1.00) and improved height-for-age z scores (HAZ) (+0.17, 95% CI: 0.03–0.31).

Conclusions
This combined intervention, where household water connections were contingent on community-wide household toilet construction, was associated with improved HAZ, and reduced soil-transmitted helminth (STH) infection, though not reduced diarrhoea or ARI. Further research should explore the mechanism through which these heterogenous effects on health may occur.
A Randomized, Placebo-Controlled, Pilot Clinical Trial of Dipyridamole to Decrease Human Immunodeficiency Virus–Associated Chronic Inflammation
Authors: Macatangay Bernard J C , Jackson Edwin K , Abebe Kaleab Z , Comer Diane , Cyktor Joshua , Klamar-Blain Cynthia , Borowski Luann , Gillespie Delbert G , Mellors John W , Rinaldo Charles R , Riddler Sharon A 
Published: July 2019

AbstractBackgroundAdenosine is a potent immunoregulatory nucleoside produced during inflammatory states to limit tissue damage. We hypothesized that dipyridamole, which inhibits cellular adenosine uptake, could raise the extracellular adenosine concentration and dampen chronic inflammation associated with human immunodeficiency virus (HIV) type 1.MethodsVirally suppressed participants receiving antiretroviral therapy were randomized 1:1 for 12 weeks of dipyridamole (100 mg 4 times a day) versus placebo capsules. All participants took open-label dipyridamole during weeks 12–24. Study end points included changes in markers of systemic inflammation (soluble CD163 and CD14, and interleukin 6) and levels of T-cell immune activation (HLA-DR+CD38+).ResultsOf 40 participants who were randomized, 17 dipyridamole and 18 placebo recipients had baseline and week 12 data available for analyses. There were no significant changes in soluble markers, apart from a trend toward decreased levels of soluble CD163 levels (P = .09). There was a modest decrease in CD8+ T-cell activation (−17.53% change for dipyridamole vs +13.31% for placebo; P = .03), but the significance was lost in the pooled analyses (P = .058). Dipyridamole also reduced CD4+ T-cell activation (−11.11% change; P = .006) in the pooled analyses. In post hoc analysis, detectable plasma dipyridamole levels were associated with higher levels of inosine, an adenosine surrogate, and of cyclic adenosine monophosphate.ConclusionDipyridamole increased extracellular adenosine levels and decreased T-cell activation significantly among persons with HIV-1 infection receiving virally suppressive therapy.
Emergence of a hybrid plasmid derived from IncN1-F33:A−:B− and mcr-1-bearing plasmids mediated by IS26
Authors: He Dandan , Zhu Yingying , Li Ruichao , Pan Yushan , Liu Jianhua , Yuan Li , Hu Gongzheng 
Published: July 2019

Abstract

Objectives
To characterize the complete sequences of four plasmids in MCR-1-producing clinical Escherichia coli strain D72, and to depict the formation mechanism and characteristics of the cointegrate plasmid derived from the pD72-mcr1 and pD72-F33 plasmids.

Methods
The genetic profiles of plasmids in strain D72 and its transconjugant were determined by conjugation, S1-PFGE, Southern hybridization, WGS analysis and PCR. Plasmid sequences were analysed with bioinformatic tools. The traits of the fusion plasmid were characterized by cointegration, stability and conjugation assays.

Results
Strain D72, belonging to ST1114, contained four plasmids, including mcr-1-carrying pD72-mcr1, blaCTX-M-55-carrying pD72-F33, blaTEM-238-bearing pD72-IncP and pD72-IncX1 carrying aph(3′)-Ia, qnrS2 and floR. A single plasmid, pD72C, in the transconjugant was found to be larger than any plasmid in the original strain D72. Sequence analysis showed that pD72C was the fusion product of pD72-mcr1 and pD72-F33, and the recombinant event involved an intermolecular replicative mechanism. Plasmid fusion occurred at a frequency of 1.75 × 10−4 cointegrates per transconjugant. The fusion plasmid presented a high stability and conjugation frequency of 8.00 × 10−3.

Conclusions
To our knowledge, this is the first report of the IS26-mediated fusion of an IncN1-F33:A−:B− plasmid and an mcr-1-carrying phage-like plasmid, providing evidence for the important role of IS26 in the recombination of plasmids. The biological advantages of the fusion plasmid indicated that the fusion event presumably plays a potential role in the dissemination of mcr-1.