bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yersinia pestis
Targets the Host Endosome Recycling Pathway during the Biogenesis of the
Yersinia
-Containing Vacuole To Avoid Killing by Macrophages
Authors: Connor Michael G. , Pulsifer Amanda R. , Chung Donghoon , Rouchka Eric C. , Ceresa Brian K. , Lawrenz Matthew B. 
Published: February 2018

ABSTRACT

Yersinia pestis
has evolved many strategies to evade the innate immune system. One of these strategies is the ability to survive within macrophages. Upon phagocytosis,
Y. pestis
prevents phagolysosome maturation and establishes a modified compartment termed the
Yersinia
-containing vacuole (YCV).
Y. pestis
actively inhibits the acidification of this compartment, and eventually, the YCV transitions from a tight-fitting vacuole into a spacious replicative vacuole. The mechanisms to generate the YCV have not been defined. However, we hypothesized that YCV biogenesis requires
Y. pestis
interactions with specific host factors to subvert normal vesicular trafficking. In order to identify these factors, we performed a genome-wide RNA interference (RNAi) screen to identify host factors required for
Y. pestis
survival in macrophages. This screen revealed that 71 host proteins are required for intracellular survival of
Y. pestis
. Of particular interest was the enrichment for genes involved in endosome recycling. Moreover, we demonstrated that
Y. pestis
actively recruits Rab4a and Rab11b to the YCV in a type three secretion system-independent manner, indicating remodeling of the YCV by
Y. pestis
to resemble a recycling endosome. While recruitment of Rab4a was necessary to inhibit YCV acidification and lysosomal fusion early during infection, Rab11b appeared to contribute to later stages of YCV biogenesis. We also discovered that
Y. pestis
disrupts global host endocytic recycling in macrophages, possibly through sequestration of Rab11b, and this process is required for bacterial replication. These data provide the first evidence that
Y. pestis
targets the host endocytic recycling pathway to avoid phagolysosomal maturation and generate the YCV.

IMPORTANCE
Yersinia pestis
can infect and survive within macrophages. However, the mechanisms that the bacterium use to subvert killing by these phagocytes have not been defined. To provide a better understanding of these mechanisms, we used an RNAi approach to identify host factors required for intracellular
Y. pestis
survival. This approach revealed that the host endocytic recycling pathway is essential for
Y. pestis
to avoid clearance by the macrophage. We further demonstrate that
Y. pestis
remodels the phagosome to resemble a recycling endosome, allowing the bacterium to avoid the normal phagolysosomal maturation pathway. Moreover, we show that infection with
Y. pestis
disrupts normal recycling in the macrophage and that disruption is required for bacterial replication. These findings provide the first evidence that
Y. pestis
targets the host endocytic recycling pathway in order to evade killing by macrophages.
The Essential Genome of
Escherichia coli
K-12
Authors: Goodall Emily C. A. , Robinson Ashley , Johnston Iain G. , Jabbari Sara , Turner Keith A. , Cunningham Adam F. , Lund Peter A. , Cole Jeffrey A. , Henderson Ian R. 
Published: February 2018

ABSTRACT

Transposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed in
Escherichia coli
K-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false-positive identification of essential genes, statistical data analysis included corrections for both gene length and genome length. Through this analysis, new essential genes and genes previously incorrectly designated essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects, and fine-resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis data sets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry.

IMPORTANCE
Incentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes in
Escherichia coli
, we constructed a transposon mutant library of unprecedented density. Initial automated analysis of the resulting data revealed many discrepancies compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high-density TraDIS sequencing data for each putative essential gene for the
E. coli
model laboratory organism. This paper is important because it provides a better understanding of the essential genes of
E. coli
, reveals the limitations of relying on automated analysis alone, and provides a new standard for the analysis of TraDIS data.
Functional and Expression Analyses of the
Pneumocystis MAT
Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs
Authors: Richard S. , Almeida J. M. G. C. F. , Cissé O. H. , Luraschi A. , Nielsen O. , Pagni M. , Hauser P. M. 
Published: February 2018

ABSTRACT

Fungi of the genus
Pneumocystis
are obligate parasites that colonize mammals’ lungs and are host species specific.
Pneumocystis jirovecii
and
Pneumocystis carinii
infect, respectively, humans and rats. They can turn into opportunistic pathogens in immunosuppressed hosts, causing severe pneumonia. Their cell cycle is poorly known, mainly because of the absence of an established method of culture
in vitro
. It is thought to include both asexual and sexual phases. Comparative genomic analysis suggested that their mode of sexual reproduction is primary homothallism involving a single mating type (
MAT
) locus encompassing plus and minus genes (
matMc
,
matMi
, and
matPi
; Almeida et al., mBio 6:e02250-14, 2015). Thus, each strain would be capable of sexual reproduction alone (self-fertility). However, this is a working hypothesis derived from computational analyses that is, in addition, based on the genome sequences of single isolates. Here, we tested this hypothesis in the wet laboratory. The function of the
P. jirovecii
and
P. carinii matMc
genes was ascertained by restoration of sporulation in the corresponding mutant of fission yeast. Using PCR, we found the same single
MAT
locus in all
P. jirovecii
isolates and showed that all three
MAT
genes are often concomitantly expressed during pneumonia. Extensive homology searches did not identify other types of
MAT
transcription factors in the genomes or
cis
-acting motifs flanking the
MAT
locus that could have been involved in
MAT
switching or silencing. Our observations suggest that
Pneumocystis
sexuality through primary homothallism is obligate within host lungs to complete the cell cycle, i.e., produce asci necessary for airborne transmission to new hosts.

IMPORTANCE
Fungi of the genus
Pneumocystis
colonize the lungs of mammals. In immunosuppressed human hosts,
Pneumocystis jirovecii
may cause severe pneumonia that can be fatal. This disease is one of the most frequent life-threatening invasive fungal infections in humans. The analysis of the genome sequences of these uncultivable pathogens suggested that their sexual reproduction involves a single partner (self-fertilization). Here, we report laboratory experiments that support this hypothesis. The function of the three genes responsible for sexual differentiation was ascertained by the restoration of sexual reproduction in the corresponding mutant of another fungus. As predicted by self-fertilization, all
P. jirovecii
isolates harbored the same three genes that were often concomitantly expressed within human lungs during infection. Our observations suggest that the sexuality of these pathogens relies on the self-fertility of each isolate and is obligate within host lungs to complete the cell cycle and allow dissemination of the fungus to new hosts.
Novel Segment- and Host-Specific Patterns of Enteroaggregative
Escherichia coli
Adherence to Human Intestinal Enteroids
Authors: Rajan Anubama , Vela Lucy , Zeng Xi-Lei , Yu Xiaomin , Shroyer Noah , Blutt Sarah E. , Poole Nina M. , Carlin Lily G. , Nataro James P. , Estes Mary K. , Okhuysen Pablo C. , Maresso Anthony W. 
Published: February 2018

ABSTRACT

Enteroaggregative
Escherichia coli
(EAEC) is an important diarrheal pathogen and a cause of both acute and chronic diarrhea. It is a common cause of pediatric bacterial diarrhea in developing countries. Despite its discovery in 1987, the intestinal tropism of the pathogen remains unknown. Cell lines used to study EAEC adherence include the HEp-2, T-84, and Caco-2 lines, but they exhibit abnormal metabolism and large variations in gene expression. Animal models either do not faithfully manifest human clinical symptoms or are cumbersome and expensive. Using human intestinal enteroids derived from all four segments of the human intestine, we find that EAEC demonstrates aggregative adherence to duodenal and ileal enteroids, with donor-driven differences driving a sheet-like and layered pattern. This contrasts with the colon, where segment-specific tropisms yielded a mesh-like adherence pattern dominated by interconnecting filaments. Very little to no aggregative adherence to jejunal enteroids was observed, regardless of the strain or donor, in contrast to a strong duodenal association across all donors and strains. These unique patterns of intestinal segment- or donor-specific adherence, but not the overall numbers of associated bacteria, were dependent on the major subunit protein of aggregative adherence fimbriae II (AafA), implying that the morphology of adherent clusters and the overall intestinal cell association of EAEC occur by different mechanisms. Our results suggest that we must give serious consideration to inter- and intrapatient variations in what is arguably the first step in pathogenesis, that of adherence, when considering the clinical manifestation of these infections.

IMPORTANCE
EAEC is a leading cause of pediatric bacterial diarrhea and a common cause of diarrhea among travelers and immunocompromised individuals. Heterogeneity in EAEC strains and lack of a good model system are major roadblocks to the understanding of its pathogenesis. Utilizing human intestinal enteroids to study the adherence of EAEC, we demonstrate that unique patterns of adherence are largely driven by unidentified factors present in different intestinal segments and from different donors. These patterns are also dependent on aggregative adherence fimbriae II encoded by EAEC. These results imply that we must also consider the contribution of the host to understand the pathogenesis of EAEC-induced inflammation and diarrhea.
Adalimumab for the treatment of refractory active and inactive non-infectious uveitis
Authors: Lee Jonathan TL , Yates William B , Rogers Sophie , Wakefield Denis , McCluskey Peter , Lim Lyndell L 
Published: February 2018

Background/aimsTo compare the efficacy of adalimumab in eyes with active and inactive non-infectious uveitis in the real-world setting.MethodsMulticentre, retrospective, chart review of patients with refractory non-infectious uveitis treated with adalimumab. Main outcome measures included reduction of prednisolone dose, ability to taper immunosuppressives and a composite endpoint of treatment failure encompassing active inflammatory chorioretinal or retinal vascular lesions, intraocular inflammation grade and visual acuity.ResultsThirty-seven eyes of 22 patients were studied. Mean follow-up was 20.1 months (median: 13). Most had either posterior or panuveitis (n=12, 55%). Mean duration of uveitis at baseline was 83.2 months (median: 61), where the majority (n=15, 68%) had already been treated with two or more conventional immunosuppressive agents in addition to prednisolone. Oral prednisolone was reduced to ≤10 mg/day in 9 of 12 patients (75%) by 6 weeks. At 6 months of therapy, nine (90%) of the active eyes achieved a 2-step improvement in anterior chamber inflammation, with six (60%) demonstrating a similar improvement in vitreous haze grade. Almost all (n=17, 94%) of the initially inactive eyes maintained clinical quiescence at this time point. The incidence rate of treatment failure during follow-up was 88 per 100 eye-years for the active eyes and 24 per 100 eye-years for the initially inactive eyes. There were no serious adverse effects.ConclusionAdalimumab appears to reduce the corticosteroid burden in active and inactive non-infectious uveitis in the real-world setting. Inflammatory activity at the time of adalimumab commencement may determine long-term treatment success.
Role of allostatic load and health behaviours in explaining socioeconomic disparities in mortality: a structural equation modelling approach
Authors: Kim Gyu Ri , Jee Sun Ha , Pikhart Hynek 
Published: February 2018

BackgroundThe relationship between socioeconomic status and mortality has been well established; however, the extent to which biological factors mediate this relationship is less clear, and empirical evidence from non-Western settings is limited. Allostasis, a cumulative measure of physiological dysregulation, has been proposed as the underlying mechanism linking socioeconomic status to adverse health outcomes. The current study aimed to ascertain the contribution of allostatic load (AL) and health behaviours to socioeconomic inequalities in mortality among Korean adults.MethodsThe sample comprised 70 713 middle-aged and older-aged adults, aged 40–79 years from the Korean Metabolic Syndrome Mortality Study. Using structural equation modelling (SEM), mediation analyses were performed to estimate the effects of socioeconomic position (SEP) on mortality over the follow-up and the extent to which AL, physical exercise and non-smoking status mediate the association between SEP and mortality.ResultsA total of 5618 deaths (7.9%) occurred during the mean follow-up of 15.2 years (SD 2.9). SEM confirmed a direct significant effect of SEP on mortality, as well as significant indirect paths through AL, physical exercise and non-smoking status.ConclusionsOur findings provide support for the mediating role of AL and health behaviours in the link between SEP and mortality. Policies designed to reduce social disparities in mortality in the long term should primarily focus on reducing stress and promoting healthy lifestyles among the socially disadvantaged groups. Future studies should further assess the role of other mediators such as psychosocial factors, which may contribute to socioeconomic inequalities in mortality.
CrosstalkNet: A Visualization Tool for Differential Co-expression Networks and Communities
Authors: Manem Venkata , Adam George Alexandru , Gruosso Tina , Gigoux Mathieu , Bertos Nicholas , Park Morag , Haibe-Kains Benjamin 
Published: February 2018

Abstract
Variations in physiological conditions can rewire molecular interactions between biological compartments, which can yield novel insights into gain or loss of interactions specific to perturbations of interest. Networks are a promising tool to elucidate intercellular interactions, yet exploration of these large-scale networks remains a challenge due to their high dimensionality. To retrieve and mine interactions, we developed CrosstalkNet, a user friendly, web-based network visualization tool that provides a statistical framework to infer condition-specific interactions coupled with a community detection algorithm for bipartite graphs to identify significantly dense subnetworks. As a case study, we used CrosstalkNet to mine a set of 54 and 22 gene-expression profiles from breast tumor and normal samples, respectively, with epithelial and stromal compartments extracted via laser microdissection. We show how CrosstalkNet can be used to explore large-scale co-expression networks and to obtain insights into the biological processes that govern cross-talk between different tumor compartments.
Significance: This web application enables researchers to mine complex networks and to decipher novel biological processes in tumor epithelial-stroma cross-talk as well as in other studies of intercompartmental interactions. Cancer Res; 78(8); 2140–3. ©2018 AACR.
Tamoxifen Metabolism and Efficacy in Breast Cancer: A Prospective Multicenter Trial
Authors: Neven Patrick , Jongen Lynn , Lintermans Anneleen , Van Asten Kathleen , Blomme Chantal , Lambrechts Diether , Poppe An , Wildiers Hans , Dieudonné Anne-Sophie , Brouckaert Olivier , Decloedt Jan , Berteloot Patrick , Verhoeven Didier , Joerger Markus , Vuylsteke Peter , Wynendaele Wim , Casteels Minne , Van Huffel Sabine , Lybaert Willem , Van Ginderachter Johan , Paridaens Robert , Vergote Ignace , Dezentjé Vincent Olaf , Van Calster Ben , Guchelaar Henk-Jan 
Published: February 2018

Abstract
Purpose: Levels of endoxifen, the most active metabolite of tamoxifen, vary by the highly polymorphic cytochrome P450 (CYP) 2D6 enzyme. We prospectively investigated tamoxifen efficacy by serum endoxifen levels and the tamoxifen activity score (TAS).
Experimental Design: A prospective observational multicenter study included postmenopausal women with an estrogen receptor–positive breast cancer receiving first-line tamoxifen, 20 mg daily in the neoadjuvant or metastatic setting, recruited between February 2009 and May 2014. The primary endpoint was the objective response rate (ORR) using RECIST criteria 1.0. Secondary endpoints were clinical benefit (CB), progression-free survival (PFS), and tolerability of tamoxifen. The main analysis used logistic regression to relate ORR to serum endoxifen levels after 3 months. Endpoints were also related to other tamoxifen metabolites and to TAS.
Results: Endoxifen levels were available for 247 of all 297 patients (83%), of which 209 with target lesions (85%). Median follow-up time for PFS was 32.5 months, and 62% progressed. ORR and CB were 45% and 84%, respectively. ORR was not related to endoxifen, and the OR of ORR was 1.008 per μg/L increase in endoxifen (95% confidence interval, 0.971–1.046; P = 0.56). In general, none of the endpoints was associated with endoxifen levels, tamoxifen metabolites, or TAS.
Conclusions: Under the prespecified assumptions, the results from this prospective clinical trial do not suggest therapeutic drug monitoring of endoxifen to be of clinical value in postmenopausal women treated with tamoxifen for breast cancer in the neoadjuvant or metastatic setting. Clin Cancer Res; 24(10); 2312–8. ©2018 AACR.
Metabolic Predictors of Incident Coronary Heart Disease in Women
Authors: Paynter Nina P. , Balasubramanian Raji , Giulianini Franco , Wang Dong D. , Tinker Lesley F. , Gopal Shuba , Deik Amy A. , Bullock Kevin , Pierce Kerry A. , Scott Justin , Martínez-González Miguel A. , Estruch Ramon , Manson JoAnn E. , Cook Nancy R. , Albert Christine M. , Clish Clary B. , Rexrode Kathryn M. 
Published: February 2018

Background:
Although metabolomic profiling offers promise for the prediction of coronary heart disease (CHD), and metabolic risk factors are more strongly associated with CHD in women than men, limited data are available for women.

Methods:
We applied a liquid chromatography–tandem mass spectrometry metabolomics platform to measure 371 metabolites in a discovery set of postmenopausal women (472 incident CHD cases, 472 controls) with validation in an independent set of postmenopausal women (312 incident CHD cases, 315 controls).

Results:

Eight metabolites, primarily oxidized lipids, were significantly dysregulated in cases after the adjustment for matching and CHD risk factors in both the discovery and validation data sets. One oxidized phospholipid, C34:2 hydroxy-phosphatidylcholine, remained associated with CHD after further adjustment for other validated metabolites. Subjects with C34:2 hydroxy-phosphatidylcholine levels in the highest quartile had a 4.7-fold increase in CHD odds in comparison with the lowest quartile; C34:2 hydroxy-phosphatidylcholine also significantly improved the area under the curve (
P
<0.01) for CHD. The C34:2 hydroxy-phosphatidylcholine findings were replicated in a third replication data set of 980 men and women (230 cardiovascular events) with a stronger association observed in women.

Conclusions:
These data replicate known metabolite predictors, identify novel markers, and support the relationship between lipid oxidation and subsequent CHD.
Los Angeles Motor Scale to Identify Large Vessel Occlusion
Authors: Noorian Ali Reza , Sanossian Nerses , Shkirkova Kristina , Liebeskind David S. , Eckstein Marc , Stratton Samuel J. , Pratt Franklin D. , Conwit Robin , Chatfield Fiona , Sharma Latisha K. , Restrepo Lucas , Valdes-Sueiras Miguel , Kim-Tenser May , Starkman Sidney , Saver Jeffrey L. 
Published: February 2018

Background and Purpose—
Prehospital scales have been developed to identify patients with acute cerebral ischemia (ACI) because of large vessel occlusion (LVO) for direct routing to Comprehensive Stroke Centers (CSCs), but few have been validated in the prehospital setting, and their impact on routing of patients with intracranial hemorrhage has not been delineated. The purpose of this study was to validate the Los Angeles Motor Scale (LAMS) for LVO and CSC-appropriate (LVO ACI and intracranial hemorrhage patients) recognition and compare the LAMS to other scales.

Methods—
The performance of the LAMS, administered prehospital by paramedics to consecutive ambulance trial patients, was assessed in identifying (1) LVOs among all patients with ACI and (2) CSC-appropriate patients among all suspected strokes. Additionally, the LAMS administered postarrival was compared concurrently with 6 other scales proposed for paramedic use and the full National Institutes of Health Stroke Scale.

Results—
Among 94 patients, age was 70 (±13) and 49% female. Final diagnoses were ACI in 76% (because of LVO in 48% and non-LVO in 28%), intracranial hemorrhage in 19%, and neurovascular mimic in 5%. The LAMS administered by paramedics in the field performed moderately well in identifying LVO among patients with ACI (C statistic, 0.79; accuracy, 0.72) and CSC-appropriate among all suspected stroke transports (C statistic, 0.80; accuracy, 0.72). When concurrently performed in the emergency department postarrival, the LAMS showed comparable or better accuracy versus the 7 comparator scales, for LVO among ACI (accuracies LAMS, 0.70; other scales, 0.62–0.68) and CSC-appropriate (accuracies LAMS, 0.73; other scales, 0.56–0.73).

Conclusions—
The LAMS performed in the field by paramedics identifies LVO and CSC-appropriate patients with good accuracy. The LAMS performs comparably or better than more extended prehospital scales and the full National Institutes of Health Stroke Scale.