bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonparticipation Selection Bias in the MOBI-Kids Study
Authors: Turner Michelle C. , Gracia-Lavedan Esther , Momoli Franco , Langer Chelsea E. , Castaño-Vinyals Gemma , Kundi Michael , Maule Milena , Merletti Franco , Sadetzki Siegal , Vermeulen Roel , Albert Alex , Alguacil Juan , Aragones Nuria , Badia Francesc , Bruchim Revital , Carretero Gema , Kojimahara Noriko , Lacour Brigitte , Morales-Suarez-Varela Maria , Radon Katja , Remen Thomas , Weinmann Tobias , Yamaguchi Naohito , Cardis Elisabeth 
Published: October 2018

Background:
MOBI-Kids is a 14-country case–control study designed to investigate the potential effects of electromagnetic field exposure from mobile telecommunications devices on brain tumor risk in children and young adults conducted from 2010 to 2016. This work describes differences in cellular telephone use and personal characteristics among interviewed participants and refusers responding to a brief nonrespondent questionnaire. It also assesses the potential impact of nonparticipation selection bias on study findings.

Methods:
We compared nonrespondent questionnaires completed by 77 cases and 498 control refusers with responses from 683 interviewed cases and 1501 controls (suspected appendicitis patients) in six countries (France, Germany, Israel, Italy, Japan, and Spain). We derived selection bias factors and estimated inverse probability of selection weights for use in analysis of MOBI-Kids data.

Results:
The prevalence of ever-regular use was somewhat higher among interviewed participants than nonrespondent questionnaire respondents 10–14 years of age (68% vs. 62% controls, 63% vs. 48% cases); in those 20–24 years, the prevalence was ≥97%. Interviewed controls and cases in the 15- to 19- and 20- to 24-year-old age groups were more likely to have a time since start of use of 5+ years. Selection bias factors generally indicated a small underestimation in cellular telephone odds ratios (ORs) ranging from 0.96 to 0.97 for ever-regular use and 0.92 to 0.94 for time since start of use (5+ years), but varied in alternative hypothetical scenarios considered.

Conclusions:
Although limited by small numbers of nonrespondent questionnaire respondents, findings generally indicated a small underestimation in cellular telephone ORs due to selective nonparticipation.
Lifestyle Patterns and Survival Following Breast Cancer in the Carolina Breast Cancer Study
Authors: Parada Humberto , Sun Xuezheng , Tse Chiu-Kit , Olshan Andrew F. , Troester Melissa A. 
Published: October 2018

Background:
Few studies have examined the impact of lifestyle patterns on survival following breast cancer. We aimed to identify distinct lifestyle patterns based on five behavior/dietary exposures among a population-based sample of women diagnosed with breast cancer and to examine their association with subsequent survival.

Methods:
In the Carolina Breast Cancer Study Phases I/II, we interviewed 1,808 women 20–74 years of age following diagnosis of invasive breast cancer. We determined vital status using the National Death Index (717 deaths, 427 from breast cancer; median follow-up 13.56 years). We assessed lifestyle patterns using a latent class analysis based on five behavioral and dietary exposures: current versus never/former smokers; low versus high vegetable and fruit intake; high and low/moderate, versus no alcohol consumption; and no and low/moderate, versus high regular physical activity. We used Cox regression to estimate covariate-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause mortality, and cause-specific and subdistribution HRs for breast cancer–specific mortality within 5 years and 13 years postdiagnosis conditional on 5-year survival.

Results:
We identified three distinct lifestyle patterns: healthy behavior and diet (n = 916); healthy behavior and unhealthy diet (n = 624); and unhealthy behavior and diet (n = 268). The unhealthy (vs. healthy) behavior and diet pattern was associated with a 13-year conditional all-cause mortality HR of 1.4 (95% CI = 1.1, 1.9) and with 13-year conditional breast cancer–specific and subdistribution HRs of 1.2 (95% CI = 0.79, 1.9) and 1.2 (95% CI = 0.77, 1.8), respectively.

Conclusions:
Behavioral and dietary patterns can be used to identify lifestyle patterns that influence survival patterns following breast cancer diagnosis.
Optimizing therapy in carbapenem-resistant Enterobacteriaceae infections
Authors: Tumbarello Mario , Losito Angela Raffaella , Giamarellou Helen 
Published: October 2018

Purpose of review
In the absence of randomized clinical trial data, questions remain regarding the optimal treatment of carbapenem-resistant Enterobacteriaceae (CRE) infections. CRE have historically been susceptible to polymyxins, tigecycline or aminoglycosides (mostly gentamicin), and these antibiotics have long been considered the drugs of choice for CRE infections, although varying rates of resistance to all have been reported. This review looks at data from clinical studies assessing the outcomes of CRE infections treated with different antibiotic regimens.

Recent findings
The recently approved fixed-dose combination agent, ceftazidime-avibactam (CAZ-AVI), is active against KPC and OXA-48-producing Enterobacteriaceae. The limited clinical data available on CAZ-AVI indicate that it is associated with survival benefits relative to other commonly used regimens, although development of resistance is a concern. New drugs active against CRE isolates (including the recently approved meropenem-vaborbactam) are in different stages of development.

Summary
CAZ-AVI and meropenem-vaborbactam seem destined to become the backbone of target therapy for high-risk patients with severe infections caused by susceptible CRE strains. However, empirical therapy should be based on risk factors to be defined in the near future, whereas the necessity of combinations with CAZ-AVI requires further studies. Polymyxins are still important options for low-risk patients with susceptible CRE infections, but also for high-risk patients in regions where metallo-β-lactamase-producing CRE predominate because CAZ-AVI and meropenem-vaborbactam are both ineffective against these strains.
Polyclonal and monoclonal antibodies for the treatment of influenza
Authors: Beigel John H. 
Published: October 2018

Purpose of review
This review summarizes past and ongoing efforts for using polyclonal and monoclonal antibodies for the treatment of influenza, and is focused on products that have entered clinical trials.

Recent findings
At least three polyclonal and eight monoclonal antibody products have been tested in clinical trials for the treatment of influenza. Considered across the two classes of therapeutics, these products appear to be safe and well tolerated. However, the efficacy results have been mixed and inconclusive. To date, no products have consistently shown superiority to currently available antivirals.

Summary
No products within these two classes have been licensed, and several products appear to have stopped further clinical development. There are several ongoing studies that are anticipated to be completed or reported in the next 1–2 years which will be critical for understanding the value of polyclonal and monoclonal antibodies in the treatment of influenza.
Remote Intestinal Injury Early After Experimental Polytrauma and Hemorrhagic Shock
Authors: Wrba Lisa , Ohmann Julia J. , Eisele Philipp , Chakraborty Shinjini , Braumüller Sonja , Braun Christian K. , Klohs Bettina , Schultze Anke , von Baum Heike , Palmer Annette , Huber-Lang Markus , Halbgebauer Rebecca 
Published: October 2018

ABSTRACT
Dysfunction of the gut–blood barrier plays an important role in many diseases, such as inflammatory bowel disease, hemorrhagic shock (HS), or burn injury. However, little is known about gut barrier dysfunction after hemodynamically instable polytrauma (PT). Therefore, we aimed to evaluate the effects of PT and HS on remote intestinal damage and barrier dysfunction, especially regarding the role of zonula occludens protein 1 (ZO-1) as an important tight junction protein.
Male C57BL/6 mice were subjected to either PT (thorax trauma, closed head injury, soft tissue injury, and distal femoral fracture), 60 min of pressure-controlled HS (30 ± 5 mmHg), or PT+HS, or sham procedures.
Animals of all trauma groups showed an increase in abdominal girth and dilation of the intestine during the experimental period, which was largest in the PT+HS group. Increased blood–tissue permeability to albumin (assessed by Evans blue dye) was found in the HS group. Experimental groups showed a slight increase in plasma concentration of intestinal fatty acid binding protein and some intestinal damage was histologically detectable. Of note, PT+HS animals revealed significantly reduced expression of ZO-1 in intestinal epithelial cells. In an in-vitro model, stimulation of human colon epithelial cells with peptidoglycan, but not with lipopolysaccharide, resulted in elevated secretion of pro-inflammatory cytokines, reflecting inflammatory activity of the intestinal epithelium.
Taken together, PT and HS lead to increased permeability of the gut–blood barrier. Bacterial components may lead to production of inflammatory and chemotactic mediators by gut epithelial cells, underlining the role of the gut as an immunologically active organ.
Endpoints in clinical trials in cancer cachexia: where to start?
Authors: Laird Barry J.A. , Balstad Trude R. , Solheim Tora S. 
Published: October 2018

Purpose of review
The lack of agreement and knowledge of optimal endpoints in cachexia trials have impeded progress in finding interventions counteracting the devastating effects cancer cachexia has on morbidity and mortality. An endpoint should both be sensitive enough to detect change and specific enough not to be influenced by other conditions or treatments.

Recent findings
There is a wealth of potential and applied endpoints in trials investigating cachexia. As of today, there is no generally acknowledged consensus, but assessments of key factors such as body composition should continue to be applied. However, the impact and effect size necessary to achieve clinical benefit using these endpoints are not clear. Further, the use of other endpoints assessing physical function, symptom evaluation and quality of life remains to be elucidated.

Summary
It is essential that endpoints are clinically relevant and further research is therefore needed to develop endpoints that are meaningful for patients with cachexia.
Experimental and Computational Evidence for Self-Assembly of Mitochondrial UCP2 in Lipid Bilayers
Authors: Ardalan A. , Uwumarenogie S. O. , Fish M. , Sowlati-Hashjin S. , Karttunen M. , Smith M. D. , Jelokhani-Niaraki M. 
Published: October 2018

ABSTRACTUncoupling proteins (UCPs) are members of the mitochondrial carrier family (MCF) that transport protons across the inner mitochondrial membrane, thereby uncoupling electron transport from ATP synthesis. The stoichiometry of UCPs, and the possibility of co-existence of this protein as mono-meric and associated forms in lipid membranes remain an intriguing open question. In the current study, the tertiary structure of UCP2 was analyzed both experimentally and through molecular dynamics (MD) simulations. After recombinant expression of UCP2 in the inner membrane of E. coli, the protein was directly extracted from the bacterial membranes with a non-denaturing detergent and purified both as a pure monomer and as a mixture of monomers, dimers and tetramers. Both protein preparations were re-constituted in egg yolk lipid vesicles. Gel electrophoresis, circular dichroism spectroscopy and fluorescence methods were used to characterize the structure and the proton transport function of protein. UCP2 showed unique stable tetrameric forms in lipid bilayers. MD simulations using membrane lipids and principal component analysis support the experimental results and provided new molecular insights into the nature of noncovalent interactions in oligomeric UCP2. MD simulations indicate that UCP2 tetramers are asymmetric dimers of dimers, in which the interactions between the monomers forming the dimer are stronger than the interactions between the dimers within the tetramer. It is also shown that UCP2 has a specific tendency to form functional tetramers in lipid bilayers, capable of proton transport. The asymmetric nature of the UCP2 tetramer could act as a scaffold for regulating the activity of the monomeric units through cooperative intercommunication between these subunits. Under similar experimental conditions, the structurally comparable ADP/ATP carrier protein did not form tetramers in vesicles, implying that spontaneous tetramerization cannot be generalized to all MCF members.STATEMENT OF SIGNIFICANCESelf-assembly of membrane proteins plays a significant role in their biological function. In this article, both experimental and computational evidence are provided for spontaneous tetramerization of one of the mitochondrial uncoupling proteins (UCP2) in model lipid membranes. It is also shown that the tetrameric form of UCP2 is capable of proton transport, which leads to regulation of ATP synthesis in mitochondrion. Molecular dynamics simulations confirm the presence of asymmetric UCP2 tetramers as a potential scaffold for regulating the activity of the monomeric units through mutual intercommunication. The outcome of this study provides a solid ground for potential co-existence of monomeric and multimeric functional forms of UCPs that contributes to a deeper molecular insight into their structure and function.
West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells
Authors: O’Neal Justin T. , Upadhyay Amit A. , Wolabaugh Amber , Patel Nirav B. , Bosinger Steven E. , Suthar Mehul S. 
Published: October 2018

ABSTRACTWest Nile virus (WNV) is a neurotropic mosquito-borne flavivirus of global importance. Neuroinvasive WNV infection results in encephalitis and can lead to prolonged neurological impairment or death. Type I interferon (IFN-I) is crucial for promoting antiviral defenses through the induction of antiviral effectors, which function to restrict viral replication and spread. However, our understanding of the antiviral response to WNV infection is mostly derived from analysis of bulk cell populations. It is becoming increasingly apparent that substantial heterogeneity in cellular processes exists among individual cells, even within a seemingly homogenous cell population. Here, we present WNV-inclusive single-cell RNA sequencing (scRNA-seq), an approach to examine the transcriptional variation and viral RNA burden across single cells. We observed that only a few cells within the bulk population displayed robust transcription of IFN-β mRNA, and this did not appear to depend on viral RNA abundance within the same cell. Furthermore, we observed considerable transcriptional heterogeneity in the IFN-I response, with genes displaying high unimodal and bimodal expression patterns. Broadly, IFN-stimulated genes negatively correlated with viral RNA abundance, corresponding with a precipitous decline in expression in cells with high viral RNA levels. Altogether, we demonstrated the feasibility and utility of WNV-inclusive scRNA-seq as a high-throughput technique for single-cell transcriptomics and WNV RNA detection. This approach can be implemented in other models to provide insights into the cellular features of protective immunity and identify novel therapeutic targets.IMPORTANCEWest Nile virus (WNV) is a clinically relevant pathogen responsible for recurrent epidemics of neuroinvasive disease. Type I interferon is essential for promoting an antiviral response against WNV infection; however, it is unclear how heterogeneity in the antiviral response at the single-cell level impacts viral control. Specifically, conventional approaches lack the ability to distinguish differences across cells with varying viral abundance. The significance of our research is to demonstrate a new technique for studying WNV infection at the single-cell level. We discovered extensive variation in antiviral gene expression and viral abundance across cells. This protocol can be applied to primary cells orin vivomodels to better understand the underlying cellular heterogeneity following WNV infection for the development of targeted therapeutic strategies.
Prevention of EloR/KhpA heterodimerization by introduction of site-specific amino acid substitutions renders the essential elongasome protein PBP2b redundant in Streptococcus pneumoniae
Authors: Ruud Winther Anja , Kjos Morten , Stamsås Gro Anita , Håvarstein Leiv Sigve , Straume Daniel 
Published: October 2018

AbstractThe RNA binding proteins EloR and KhpA are important components of the regulatory network that controls and coordinates cell elongation and division in S. pneumoniae. Loss of either protein reduce cell length, and makes the essential elongasome proteins PBP2b and RodA dispensable. It has been shown previously in formaldehyde crosslinking experiments that EloR co-precipitates with KhpA, indicating that they form a complex in vivo. In the present study, we used 3D modeling and site directed mutagenesis in combination with protein crosslinking to further study the relationship between EloR and KhpA. Protein-protein interaction studies demonstrated that KhpA forms homodimers and that KhpA in addition binds strongly to the KH-II domain of EloR. Site directed mutagenesis identified isoleucine 61 (I61) as crucial for KhpA homodimerization. When substituting I61 with phenylalanine, KhpA lost the ability to homodimerize, while it still interacted strongly with EloR. In contrast, both homo- and heterodimerization were lost when I61 was substituted with tyrosine. By expressing these KhpA versions in S. pneumoniae, we were able to show that disruption of EloR/KhpA heterodimerization makes the elongasome redundant in S. pneumoniae. Of note, loss of KhpA homodimerization did not give rise to this phenotype, demonstrating that the EloR/KhpA complex is crucial for regulating the activity of the elongasome. In support of this conclusion, we found that localization of KhpA to the pneumococcal mid-cell region depends on its interaction with EloR. Furthermore, we found that the EloR/KhpA complex co-localizes with FtsZ throughout the cell cycle.ImportanceTo ensure correct cell division, bacteria need to monitor the progression of cell division and coordinate the activities of cell division proteins accordingly. Understanding the molecular mechanisms behind these regulatory systems is of high academic interest and might facilitate the development of new therapeutics and strategies to combat pathogens. EloR and KhpA form a heterodimer that is part of a signaling pathway controlling cell elongation in the human pathogen S. pneumoniae. Here we have identified amino acids that are crucial for EloR/KhpA heterodimerization, and demonstrated that disruption of the EloR/KhpA interaction renders the cells independent of a functional elongasome. Furthermore, we found the EloR/KhpA complex to co-localize with the division ring (FtsZ) during cell division.
Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)
Authors: Malcom Jacob W. , Juenger Thomas E. , Leibold Mathew A. 
Published: October 2018

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.
Variation in the plasma membrane monoamine transporter (PMAT, encoded in SLC29A4) and organic cation transporter 1 (OCT1, encoded in SLC22A1) and gastrointestinal intolerance to metformin in type 2 diabetes: an IMI DIRECT study
Authors: Dawed Adem Y , Zhou Kaixin , van Leeuwen Nienke , Mahajan Anubha , Robertson Neil , Koivula Robert , Elders Petra JM , Rauh Simone P , Jones Angus G , Holl Reinhard W , Stingl Julia C , Franks Paul W , McCarthy Mark I , Hart Leen ‘t , Pearson Ewan R ,   for the IMI DIRECT Consortium.
Published: October 2018

AbstractObjectives20-30% of patients with metformin treated type 2 diabetes experience gastrointestinal side effects leading to premature discontinuation in 5-10% of the cases. Gastrointestinal intolerance may reflect localised high concentrations of metformin in the gut. We hypothesized that reduced transport of metformin into the circulation via the plasma membrane monoamine transporter (PMAT) and organic cation transporter 1 (OCT1) could increase the risk of severe GI side effects.Research Design and MethodsThe study included 286 severe metformin intolerant and 1128 tolerant individuals from the IMI DIRECT consortium. We assessed the association of patient characteristics, concomitant medication and the burden of mutations in the SLC29A4 and SLC22A1, genes that encode PMAT and OCT1, respectively, on odds of metformin intolerance using a logistic regression model.ResultsWomen (p < 0.001) and older people (p < 0.001) were more likely to develop metformin intolerance. Concomitant use of metformin transporter inhibiting drugs increased the odds of intolerance by more than 70% (OR = 1.72 [1.26-2.32], p < 0.001). In a logistic regression model adjusted for age, sex, weight and population substructure, the G allele at rs3889348 (SLC29A4) was associated with GI intolerance (OR = 1.34[1.09-1.65], p = 0.005). rs3889348 is the top cis-eQTL for SLC29A4 in gut tissue where carriers of the G allele had reduced expression. Homozygous carriers of the G allele treated with metformin transporter inhibiting drugs had over three times higher odds of intolerance compared to carriers of no G allele and not treated with inhibiting drugs (OR = 3.23 [1.71-6.39], p < 0.001). Using a genetic risk score (GRS) derived from SLC29A4 (rs3889348) and previously reported SLC22A1 variants (M420del, R61C, G401S), the odds of intolerance was more than twice in individuals who carry three or more risk alleles compared with those carrying none (OR = 2.15 [1.20-4.12], p = 0.01).ConclusionsThese results suggest that intestinal metformin transporters and concomitant medications play an important role in gastrointestinal side effects of metformin.