bluuebunny/crossref_metadata_2025 huggingface dataset:
National Characteristics of Lymphatic Malformations in Children: Inpatient Estimates and Trends in the United States, 2000 to 2009
Authors: Cheng Jeffrey , Liu Beiyu , Farjat Alfredo E. , Routh Jonathan
Published: December 2017

With ever increasing demands to manage finite resources for health care utilization, we performed an investigation to identify inpatient clinical characteristics and trends in children with lymphatic malformations using the Kids’ Inpatient Database, years 2000 to 2009, to help identify populations best suited for resource deployment. Subjects included children 18 years and below with International Classification of Diseases (ICD), ninth revision code: 228.1-lymphangioma, any site. In the United States, between 2000 and 2009, inpatient pediatric patients with lymphatic malformations most commonly affected children aged 3 years and younger, urban hospital locations, and the South and West regions. There was no significant change in age of children with lymphatic malformations or the distribution of their age from year to year, P=0.948 and 0.4223, respectively. No significant evidence for seasonal variation or effect on inpatient admission was identified, P=0.7071. A great majority of admissions (>96%) were in urban locations across each year. There was also no significant change in breakdown of admissions by geographic location, P=0.7133. Further investigation may help to elucidate how to improve access to multidisciplinary vascular anomalies teams to optimize care for these children with unique and complex lymphatic malformations.
Use of clinical measures to document the effect of passive cycling on knee extensor spasticity and the ability to perform activities of daily living in spinal cord injury: a case report
Authors: Pomerleau Pierre , Perron Marc , Bouyer Laurent J. , Maltais Désirée B.
Published: December 2017

The effects, on spasticity-related clinical measure results [initial knee flexion velocity during the pendulum test (F1-VEL); Spinal Cord Injury Spasticity Evaluation Tool (SCI-SET) scores], of a 5-week passive cycling program were assessed in a 67-year-old man with chronic, complete, thoracic-level SCI. Three weekly evaluations were performed before and after training, at the start, middle, and end of the training (ET), and 24 h following ET. The F1-VEL increased significantly from baseline, from ET to the 2-week follow-up evaluation. A trend was found for an improvement from baseline in SCI-SET scores, from middle of training onwards. These findings, which can inform clinical decisions and clinical trial development, suggest that the F1-VEL pendulum test result may be used to document the effect on knee extensor spasticity of a passive cycling program in chronic, complete, thoracic-level SCI. Whether this is also true for the SCI-SET requires future confirmation.
Stopcocks for Infusion Therapy
Authors: Hadaway Lynn
Published: December 2017

Stopcocks have been used for decades to deliver infusion therapy in patients of all ages and in all health care settings. During the past 20 years, a growing number of studies have validated concern about the risk of the open lumen allowing intraluminal contamination. Additional studies highlight fluid flow dynamics associated with stopcocks. This integrative literature review and clinician practice survey analyzes the published evidence and reports of actual practices with stopcocks, and raises issues about practice changes that could reduce these risks.
Improving Time to Antibiotics for Pediatric Oncology Patients With Suspected Infections
Authors: Yoshida Hiromi , Leger Kasey J. , Xu Min , Migita Russell T. , Rutledge Joe C. , Pollard Jessica A. , Kroon Leah , Mazor Suzan S. , Moon Andres , Rutman Lori E.
Published: December 2017

Objective

Studies in pediatric patients with fever and neutropenia demonstrate that shorter time to antibiotics is associated with a decrease in pediatric intensive care unit admissions and in-hospital mortality. In 2012, a 2-phase quality improvement intervention was implemented in a pediatric emergency department (ED) to improve care for this high-risk patient population.

The objective was to determine if the introduction of (1) a rapid absolute neutrophil count (ANC) test and (2) a standardized prearrival process decreased time to antibiotics for febrile hematology/oncology(heme/onc) patients presenting to the ED.

Methods

The rapid ANC test introduced in February 2012 decreased turn-around-times in the laboratory from 60 to 10 minutes. The standardization of the prearrival communication between the heme/onc team and ED was implemented in August 2012 as part of a clinical standard work pathway for heme/onc patients who presented to the ED with fever and possible neutropenia. Time from arrival to the ED to administration of first antibiotic was measured.

Data from January 2011 to December 2013 were analyzed using statistical process control.

Results

Seven hundred eighteen encounters for 327 patients were included. After the rapid ANC test, the proportion of patients who received antibiotics within 60 minutes of arrival increased from 47% to 60%. There was further improvement to 69% with implementation of the clinical standard work pathway. Mean time to antibiotics decreased from 83 to 65 minutes (21% decrease).

Conclusion

This 2-phase quality improvement intervention increased the proportion of patients who received antibiotics within 60 minutes of arrival to the ED. Similar processes may be implemented in other pediatric EDs to improve timeliness of antibiotic administration.
Low Doses of Etanercept Can Be Effective to Maintain Remission in Psoriatic Arthritis Patients
Authors: de Stefano Renato , Frati Elena , de Quattro Davide , de Stefano Ludovico
Published: December 2017

Objectives

We realized a longitudinal open-label study to determine if increasing intervals between etanercept (ETN) administration could be effective in maintaining remission with a stable dose in a patient population affected by psoriatic arthritis (PsA) who had achieved sustained remission with ETN 25 mg biweekly.

Methods

Fifty-four PsA patients were recruited at the Rheumatology Unit of Azienda Ospedaliera Universitaria Senese. Patients, who were in clinical sustained remission with biweekly ETN 25 mg at weeks 12 and 16, and were switched to a weekly regimen. If clinical remission persists at weeks 24 and 28, patients were switched to an every-other-week regimen, continuing with this administration schedule for the entire duration of the study if at weeks 36 and 40 clinical remission was maintained. If, on the contrary, in one of the check there was an increase in disease activity, the therapeutic scheme returned to the previous one.

Results

The results of our study indicate that a consistent percentage (72%) of subjects with PsA, achieving a sustained remission with ETN 25 mg biweekly, maintains a remission, after a year of starting therapy, despite a progressive dose reduction by an increase in the dosing interval, 21% with a weekly regimen and 51% with an every-other-week regimen.

Conclusions

Our results show that the main reasons that hinder the dosing interval increase in ETN in PsA patients in sustained clinical remission at standard doses are peripheral polyarthritis pattern and exacerbation of cutaneous manifestations.
Ectopic Undescended Parathyroid Adenoma—SPECT/CT Avoids False-Negative Interpretation on 99mTc-MIBI Dual-Phase Scintigraphy
Authors: Mahajan Sonia , Schoder Heiko
Published: December 2017

Undescended parathyroid adenomas are rare, and they are easily missed during neck exploration surgery in patients with hyperparathyroidism. Few reports have described ectopic parathyroid adenomas along the carotid arteries at or near the carotid bifurcation. These may be missed on planar 99mTc-MIBI dual-phase scintigraphy because of overlapping submandibular gland activity. Our case demonstrates the potential advantage of SPECT/CT in parathyroid scintigraphy to overcome this limitation.
18F-FDG PET/CT Imaging of Necrotizing Crescentic Glomerulonephritis With Anti–Glomerular Basement Membrane Disease
Authors: Holt Emily , Gough Andrew , Prasad Padmini , Chowdhury Fahmid U.
Published: December 2017

A 30-year-old woman presented with lethargy, night sweats, and fever with raised inflammatory markers. Anti–neutrophil cytoplasmic antibody was negative. Abdominopelvic CT was unremarkable. Subsequently, she underwent FDG PET/CT showing globally enlarged kidneys with diffuse hypermetabolic activity within the renal parenchyma bilaterally. Renal biopsies showed morphologic features of an active necrotizing crescentic glomerulonephritis, which was confirmed clinically and treated. This case demonstrates the role that FDG PET/CT can play in inflammatory conditions, such as glomerulonephritis, where it may be clinically useful when the presentation is atypical.
201Tl Myocardial Perfusion Imaging in a Case of Double-Inlet Left Ventricle
Authors: Chang Ming-Che , Lee Meng-Luen , Yang Po-Ta
Published: December 2017

Double-inlet left ventricle (DILV) is a congenital heart disease that only a single left ventricle and a rudimentary right ventricle are developed. Because of lack of anatomic landmark, interpretation of 201Tl myocardial perfusion imaging in DILV is essentially challenging for unusual anomaly. We report the case of a 44-year-old woman with DILV who presented exertional dyspnea and tachycardia and underwent 201Tl SPECT. The anatomic characteristics of cardiac 201Tl SPECT are correlated with MRI. To obtain accurate interpretation in DILV, it is absolutely necessary to realize the anatomy relationship between perfusion imaging and anatomic imaging such as CT or MRI.
Bronchiectasis as a Cause of Elevated CA-19-9 Demonstrated on 18F-FDG PET/CT
Authors: Mikhail Paul , Le Ken , Bui Chuong , Mansberg Robert
Published: December 2017

A 64-year-old woman with a history of weight loss and a markedly elevated serum carbohydrate antigen 19-9 level of 560 U/mL was referred for an 18F-FDG PET study to evaluate for occult malignancy. In addition to the weight loss, she had suffered from a chronic cough secondary to bronchiectasis and had been investigated for a suspected gastrointestinal malignancy. Multiple FDG-avid foci were detected throughout both lungs on FDG PET, corresponding to areas of bronchiectasis on CT with no obvious suspicious FDG-avid foci elsewhere. This supported an inflammatory process causing her elevated carbohydrate antigen 19-9 rather than malignancy.
Hydrogen-Rich Saline Regulates Intestinal Barrier Dysfunction, Dysbiosis, and Bacterial Translocation in a Murine Model of Sepsis
Authors: Ikeda Mitsunori , Shimizu Kentaro , Ogura Hiroshi , Kurakawa Takashi , Umemoto Eiji , Motooka Daisuke , Nakamura Shota , Ichimaru Naotsugu , Takeda Kiyoshi , Takahara Shiro , Hirano Shin-ichi , Shimazu Takeshi
Published: December 2017

Bacterial translocation is a major cause of multiple organ dysfunction syndrome in critical illness, and its management is an important therapeutic strategy. In this study, we focused on the key factors responsible for bacterial translocation including the intestinal microbiome and investigated the impact of molecular hydrogen therapy as a countermeasure against bacterial translocation in a murine model of sepsis. The experimental protocols were divided into the sham, saline treatment (control), and hydrogen treatment (H2) groups. In the H2 group, 15 mL/kg of hydrogen-rich saline (7 ppm) was gavaged daily for 7 days following cecal ligation and puncture (CLP). In the control group, normal saline was gavaged in the same way. In the results, the 7-day survival rate was significantly improved in the H2 group versus the control group (69% vs. 31%, P < 0.05). The incidence of bacterial translocation at 24 h after CLP as assessed by cultivation of mesenteric lymph nodes and blood was significantly decreased in the H2 group versus the control group. Administration of hydrogen-rich saline also prevented the expansion of facultative anaerobic Enterobacteriaceae and ameliorated intestinal hyperpermeability at 24 h after CLP. Intestinal tissue levels of inflammatory mediators such as inducible nitric oxide synthases, tumor necrosis factor α, interleukin (IL)-1β, IL-6, and oxidative stress marker malondialdehyde at 6 h after CLP were down-regulated in the H2 group. These results suggest luminal administration of hydrogen-rich saline, which prevents intestinal dysbiosis, hyperpermeability, and bacterial translocation, could potentially be a new therapeutic strategy in critical illness.
Metabolomic Profile of ARDS by Nuclear Magnetic Resonance Spectroscopy in Patients With H1N1 Influenza Virus Pneumonia
Authors: Izquierdo-Garcia Jose L. , Nin Nicolas , Jimenez-Clemente Jorge , Horcajada Juan P. , Arenas-Miras Maria del Mar , Gea Joaquim , Esteban Andres , Ruiz-Cabello Jesus , Lorente Jose A.
Published: December 2017

Purpose:

The integrated analysis of changes in the metabolic profile could be critical for the discovery of biomarkers of lung injury, and also for generating new pathophysiological hypotheses and designing novel therapeutic targets for the acute respiratory distress syndrome (ARDS). This study aimed at developing a nuclear magnetic resonance (NMR)-based approach for the identification of the metabolomic profile of ARDS in patients with H1N1 influenza virus pneumonia.

Methods:

Serum samples from 30 patients (derivation set) diagnosed of H1N1 influenza virus pneumonia were analyzed by unsupervised principal component analysis to identify metabolic differences between patients with and without ARDS by NMR spectroscopy. A predictive model of partial least squares discriminant analysis (PLS-DA) was developed for the identification of ARDS. PLS-DA was trained with the derivation set and tested in another set of samples from 26 patients also diagnosed of H1N1 influenza virus pneumonia (validation set).

Results:

Decreased serum glucose, alanine, glutamine, methylhistidine and fatty acids concentrations, and elevated serum phenylalanine and methylguanidine concentrations, discriminated patients with ARDS versus patients without ARDS. PLS-DA model successfully identified the presence of ARDS in the validation set with a success rate of 92% (sensitivity 100% and specificity 91%). The classification functions showed a good correlation with the Sequential Organ Failure Assessment score (R = 0.74, P < 0.0001) and the PaO2/FiO2 ratio (R = 0.41, P = 0.03).

Conclusions:

The serum metabolomic profile is sensitive and specific to identify ARDS in patients with H1N1 influenza A pneumonia. Future studies are needed to determine the role of NMR spectroscopy as a biomarker of ARDS.
Association of BDNF Val66Met Polymorphism and Brain BDNF levels with Major Depression and Suicide
Authors: Youssef Mariam M. , Underwood Mark D. , Huang Yung-Yu , Hsiung Shu-chi , Liu Yan , Simpson Norman R. , Bakalian Mihran J. , Rosoklija Gorazd B. , Dwork Andrew J. , Arango Victoria , Mann J. John
Published: December 2017

Brain-derived neurotrophic factor (BDNF) is implicated in the pathophysiology of major depressive disorder (MDD) and suicide. Both are partly caused by early life adversity (ELA) and ELA reduces both BDNF protein and gene expression. This study examines the association of BDNF Val66Met polymorphism and brain BDNF levels with depression and suicide. We hypothesized that both MDD and ELA would be associated with the Met allele and lower brain BDNF levels. Such an association would be consistent with low BDNF mediating the effect of ELA on adulthood suicide and MDD. BDNF Val66Met polymorphism was genotyped in postmortem brains of 37 suicide decedents and 53 non-suicides. Additionally, BDNF protein levels were determined by Western blot in dorsolateral prefrontal cortex (Brodmann area 9; BA9), anterior cingulate cortex (ACC; BA24), caudal brainstem and rostral brainstem. The relationships between these measures and major depression, death by suicide and reported childhood adversity were examined. Depressed subjects had an excess of the Met allele and lower BDNF levels in ACC and caudal brainstem compared with non-depressed subjects. No effect of history of suicide death or early life adversity was observed with genotype, but lower BDNF levels in ACC were found in subjects who had been exposed to early life adversity and/or died by suicide compared to nonsuicide decedents and no reported childhood adversity. This study provides further evidence for low BDNF in major depression related to the BDNF met risk allele. Future studies should seek to determine how altered BDNF expression contributes to MDD and suicide.
Is a large eye size a risk factor for myopia? A Mendelian randomization study
Authors:   The UK Biobank Eye and Vision Consortium.
Published: December 2017

Myopia (nearsightedness) is an increasingly common cause of irreversible visual impairment. The ocular structures with greatest impact on refractive error are corneal curvature and axial length. Emmetropic eyes range in size within and across species, yet possess a balance between corneal curvature and axial length that is under genetic control. This scaling goes awry in myopia: 1 mm axial elongation is associated with ~3 Dioptres (D) myopia. Evidence that eye size prior to onset is a risk factor for myopia is conflicting. We applied Mendelian randomisation to test for a causal effect of eye size on refractive error. Genetic variants associated with corneal curvature identified in emmetropic eyes (22,180 individuals) were used as instrumental variables and tested for association with refractive error (139,697 individuals). A genetic risk score for the variants was tested for association with corneal curvature and axial length in an independent sample (315 emmetropes). The genetic risk score explained 2.3% (P=0.007) and 2.7% (P=0.002) of the variance in corneal curvature and axial length, respectively, in the independent sample, confirming these variants are predictive of eye size in emmetropes. The estimated causal effect of eye size on refractive error was + 1.41 D (95% CI. 0.65 to 2.16) less myopic refractive error per mm flatter cornea (P<0.001), corresponding to +0.48 D (95% CI. 0.22 to 0.73) more hypermetropic refractive error for an eye with a 1mm longer axial length. These results do not support the hypothesis that a larger eye size is a risk factor for myopia. We conclude the genetic determinants of normal eye size are not shared with those influencing susceptibility to myopia.
Bias toward long gene misregulation in synaptic disorders can be an artefact of amplification-based methods
Authors: Raman Ayush T. , Pohodich Amy E. , Wan Ying-Wooi , Yalamanchili Hari Krishna , Lowry Bill , Zoghbi Huda Y. , Liu Zhandong
Published: December 2017

Several recent studies have suggested that genes that are longer than 100 kilobases are more likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism and Rett syndrome. These length-dependent transcriptional changes are modest in Mecp2-mutant samples, but, given the low sensitivity of high-throughput transcriptome profiling technology, the statistical significance of these results needs to be re-evaluated. Here, we show that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-Sequencing datasets, particularly in genes with low fold-changes, disappeared after accounting for baseline variability estimated from randomized control samples. As we found no similar bias with NanoString technology, this long-gene bias seems to be particular to PCR amplification-based platforms. In contrast, authentic long gene effects, such as those caused by topoisomerase inhibition, can be detected even after adjustment for baseline variability. Accurate detection of length-dependent trends requires establishing a baseline from randomized control samples.

HIGHLIGHTS

Length-dependent gene misregulation is not intrinsic to Mecp2 disruption.

Topoisomerase inhibition produces an authentic long gene bias.

PCR amplification-based high-throughput datasets are biased toward long genes.
ImprovedAedes aegyptimosquito reference genome assembly enables biological discovery and vector control
Authors: Matthews Benjamin J. , Dudchenko Olga , Kingan Sarah , Koren Sergey , Antoshechkin Igor , Crawford Jacob E. , Glassford William J. , Herre Margaret , Redmond Seth N. , Rose Noah H. , Weedall Gareth D. , Wu Yang , Batra Sanjit S. , Brito-Sierra Carlos A. , Buckingham Steven D. , Campbell Corey L , Chan Saki , Cox Eric , Evans Benjamin R. , Fansiri Thanyalak , Filipović Igor , Fontaine Albin , Gloria-Soria Andrea , Hall Richard , Joardar Vinita S. , Jones Andrew K. , Kay Raissa G.G. , Kodali Vamsi K. , Lee Joyce , Lycett Gareth J. , Mitchell Sara N. , Muehling Jill , Murphy Michael R. , Omer Arina D. , Partridge Frederick A. , Peluso Paul , Aiden Aviva Presser , Ramasamy Vidya , Rašić Gordana , Roy Sourav , Saavedra-Rodriguez Karla , Sharan Shruti , Sharma Atashi , Smith Melissa Laird , Turner Joe , Weakley Allison M. , Zhao Zhilei , Akbari Omar S. , Black William C. , Cao Han , Darby Alistair C. , Hill Catherine , Johnston J. Spencer , Murphy Terence D. , Raikhel Alexander S. , Sattelle David B. , Sharakhov Igor V. , White Bradley J. , Zhao Li , Aiden Erez Lieberman , Mann Richard S. , Lambrechts Louis , Powell Jeffrey R. , Sharakhova Maria V. , Tu Zhijian , Robertson Hugh M. , McBride Carolyn S. , Hastie Alex R. , Korlach Jonas , Neafsey Daniel E. , Phllippy Adam M. , Vosshall Leslie B.
Published: December 2017

FemaleAedes aegyptimosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, has been slowed by the lack of a high-quality genome assembly. Here we combine diverse genome technologies to produce AaegL5, a dramatically improved and annotated assembly, and demonstrate how it accelerates mosquito science and control. We anchored the physical and cytogenetic maps, resolved the size and composition of the elusive sex-determining “M locus”, significantly increased the known members of the glutathione-S-transferase genes important for insecticide resistance, and doubled the number of chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites. Using high-resolution QTL and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. We predict that AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly arboviral vector.
Extending Tests of Hardy-Weinberg Equilibrium to Structured Populations
Authors: Hao Wei , Storey John D.
Published: December 2017

Testing for Hardy-Weinberg equilibrium (HWE) is an important component in almost all analyses of population genetic data. Genetic markers that violate HWE are often treated as special cases; for example, they may be flagged as possible genotyping errors or they may be investigated more closely for evolutionary signatures of interest. The presence of population structure is one reason why genetic markers may fail a test of HWE. This is problematic because almost all natural populations studied in the modern setting show some degree of structure. Therefore, it is important to be able to detect deviations from HWE for reasons other than structure. To this end, we extend statistical tests of HWE to allow for population structure, which we call a test of “structural HWE” (sHWE). Additionally, our new test allows one to automatically choose tuning parameters and identify accurate models of structure. We demonstrate our approach on several important studies, provide theoretical justification for the test, and present empirical evidence for its utility. We anticipate the proposed test will be useful in a broad range of analyses of genome-wide population genetic data.
A likelihood-free estimator of population structure bridging admixture models and principal components analysis
Authors: Cabreros Irineo , Storey John D.
Published: December 2017

We introduce a simple and computationally efficient method for fitting the admixture model of genetic population structure, calledALStructure. The strategy ofALStructureis to first estimate the low-dimensional linear subspace of the population admixture components and then search for a model within this subspace that is consistent with the admixture model’s natural probabilistic constraints. Central to this strategy is the observation that all models belonging to this constrained space of solutions are risk-minimizing and have equal likelihood, rendering any additional optimization unnecessary. The low-dimensional linear subspace is estimated through a recently introduced principal components analysis method that is appropriate for genotype data, thereby providing a solution that has both principal components and probabilistic admixture interpretations. Our approach differs fundamentally from other existing methods for estimating admixture, which aim to fit the admixture model directly by searching for parameters that maximize the likelihood function or the posterior probability. We observe thatALStructuretypically outperforms existing methods both in accuracy and computational speed under a wide array of simulated and real human genotype datasets. Throughout this work we emphasize that the admixture model is a special case of a much broader class of models for which algorithms similar toALStructuremay be successfully employed.
PEA: an integrated R toolkit for plant epitranscriptome analysis
Authors: Zhai Jingjing , Song Jie , Cheng Qian , Tang Yunjia , Ma Chuang
Published: December 2017

Motivation

The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by high-throughput sequencing technologies. Understanding of the epitranscriptome is hampered by the absence of computational tools for the systematic analysis of epitranscriptome sequencing data. In addition, no tools have yet been designed for accurate prediction of CMRs in plants, or to extend epitranscriptome analysis from a fraction of the transcriptome to its entirety.

Results

Here, we introduce PEA, an integrated R toolkit to facilitate the analysis of plant epitranscriptome data. The PEA toolkit contains a comprehensive collection of functions required for read mapping, CMR calling, motif scanning and discovery, and gene functional enrichment analysis. PEA also takes advantage of machine learning technologies for transcriptome-scale CMR prediction, with high prediction accuracy, using the Positive Samples Only Learning algorithm, which addresses the two-class classification problem by using only positive samples (CMRs), in the absence of negative samples (non-CMRs). Hence PEA is a versatile epitranscriptome analysis pipeline covering CMR calling, prediction, and annotation, and we describe its application to predict N6-methyladenosine (m6A) modifications in Arabidopsis thaliana. Experimental results demonstrate that the toolkit achieved 71.6% sensitivity and 73.7% specificity, which is superior to existing m6A predictors. PEA is potentially broadly applicable to the in-depth study of epitranscriptomics.

Availability

PEA is implemented using R and available at https://github.com/cma2015/PEA.
Visualization of class A GPCR oligomerization by image-based fluorescence fluctuation spectroscopy
Authors: Isbilir Ali , Möller Jan , Bock Andreas , Zabel Ulrike , Annibale Paolo , Lohse Martin J.
Published: December 2017

G protein-coupled receptors (GPCRs) represent the largest class of cell surface receptors conveying extracellular information into intracellular signals. Many GPCRs have been shown to be able to oligomerize and it is firmly established that Class C GPCRs (e.g. metabotropic glutamate receptors) function as obligate dimers. However, the oligomerization capability of the larger Class A GPCRs (e.g. comprising the β-adrenergic receptors (β-ARs)) is still, despite decades of research, highly debated.

Here we assess the oligomerization behavior of three prototypical Class A GPCRs, the β1-ARs, β2-ARs, and muscarinic M2Rs in single, intact cells. We combine two image correlation spectroscopy methods based on molecular brightness, i.e. the analysis of fluorescence fluctuations over space and over time, and thereby provide an assay able to robustly and precisely quantify the degree of oligomerization of GPCRs. In addition, we provide a comparison between two labelling strategies, namely C-terminally-attached fluorescent proteins and N-terminally-attached SNAP-tags, in order to rule out effects arising from potential fluorescent protein-driven oligomerization. The degree of GPCR oligomerization is expressed with respect to a set of previously reported as well as newly established monomeric or dimeric control constructs. Our data reveal that all three prototypical GPRCs studied display, under unstimulated conditions, a prevalently monomeric fingerprint. Only the β2-AR shows a slight degree of oligomerization.

From a methodological point of view, our study suggests three key aspects. First, the combination of two image correlation spectroscopy methods allows addressing cells transiently expressing high concentrations of membrane receptors, far from the single molecule regime, at a density where the kinetic equilibrium should favor dimers and higher-order oligomers. Second, our methodological approach, allows to selectively target cell membrane regions devoid of artificial oligomerization hot-spots (such as vesicles). Third, our data suggest that the β1-AR appears to be a superior monomeric control than the widely used membrane protein CD86.

Taken together, we suggest that our combined image correlation spectroscopy method is a powerful approach to assess the oligomerization behavior of GPCRs in intact cells at high expression levels.
Improvements to Bayesian Gene Activity State Estimation from Genome-Wide Transcriptomics Data
Authors: Disselkoen Craig , Hekman Nathan , Gilbert Brian , Benson Sydney , Anderson Matthew , DeJongh Matt , Best Aaron , Tintle Nathan
Published: December 2017

An important question in many biological applications, is to estimate or classify gene activity states (active or inactive) based on genome-wide transcriptomics data. Recently, we proposed a Bayesian method, titled MultiMM, which showed superior results compared to existing methods. In short, MultiMM performed better than existing methods on both simulated and real gene expression data, confirming well-known biological results and yielding better agreement with fluxomics data. Despite these promising results, MultiMM has numerous limitations. First, MultiMM leverages co-regulatory models to improve activity state estimates, but information about co-regulation is incorporated in a manner that assumes that networks are known with certainty. Second, MultiMM assumes that genes that change states in the dataset can be distinguished with certainty from those that remain in one state. Third, the model can be sensitive to extreme measures (outliers) of gene expression. In this manuscript, we propose a modified Bayesian approach, which addresses these three limitations by improving outlier handling and by explicitly modeling network and other uncertainty yielding improved gene activity state estimates when compared to MultiMM.
3.7 Å cryo-EM structure of the core Centromere Binding Factor 3 complex
Authors: Zhang Wenjuan , Lukoynova Natalya , Miah Shomon , Vaughan Cara K
Published: December 2017

The Centromere Binding Factor 3 (CBF3) complex binds the third Centromere DNA Element in organisms with point centromeres, such asS. cerevisiae. It is the only essential centromere binding complex as it facilitates genetic specification of point centromeres. It is therefore the most fundamental complex of the kinetochore in these organisms and its association with centromere DNA allows association of all other kinetochore components. We have determined the atomic structure of the core complex of CBF3, comprising 3 of its 4 components, using cryo-EM. The architecture of the complex is 'U'-shaped, with a deep, strongly basic channel that is narrow at one end and wide at the other. Combining our structure and in vitro assays, we present a model for its association with centromere DNA.
Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance
Authors: Maltas Jeff , Wood Kevin B.
Published: December 2017

Evolved resistance to one antibiotic may be associated with “collateral” sensitivity to other drugs. Here we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict, as independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. While phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in four-drug uniform cycles.
Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation
Authors: Sepulveda Guadalupe , Antkowiak Mark , Brust-Mascher Ingrid , Mahe Karan , Ou Tingyoung , Castro Noemi , Christensen Lana N. , Cheung Lee , Yoon Daniel , Huang Bo , Jao Li-En
Published: December 2017

As microtubule-organizing centers of animal cells, centrosomes guide the formation of the bipolar spindle that segregates chromosomes during mitosis. At mitosis onset, centrosomes maximize microtubule-organizing activity by rapidly expanding the pericentriolar material (PCM). This process is in part driven by the large PCM protein pericentrin (PCNT), as its level increases at the PCM and helps recruit additional PCM components. However, the mechanism underlying the timely centrosomal enrichment of PCNT remains unclear. Here we show that PCNT is delivered co-translationally to centrosomes during early mitosis by cytoplasmic dynein, as evidenced by centrosomal enrichment ofPCNTmRNA, its translation near the centrosome, and requirement of intact polysomes forPCNTmRNA localization. Additionally, the microtubule minus-end regulator, ASPM, is also targeted co-translationally to mitotic spindle poles. Together, these findings suggest that co-translational targeting of cytoplasmic proteins to specific subcellular destinations may be a generalized protein targeting mechanism.
Disrupted brain structural connectivity in Pediatric Bipolar Disorder with psychosis
Authors: Fernandes Henrique M. , Cabral Joana , Van Hartevelt Tim J. , Lord Louis-David , Gleesborg Carsten , Moller Arne , Deco Gustavo , Whybrow Peter C. , Petrovic Predrag , James Anthony C. , Kringelbach Morten L.
Published: December 2017

Bipolar disorder (BD) has been linked to disrupted structural and functional connectivity between prefrontal networks and limbic brain regions. Studies of patients with pediatric bipolar disorder (PBD) can help elucidate the developmental origins of altered structural connectivity underlying BD and provide novel insights into the aetiology of BD. Here we compare the network properties of whole-brain structural connectomes of PBD patients with psychosis and euthymic matched healthy controls. Our results show widespread changes in the structural connectivity of PBD patients in both cortical and subcortical networks, notably affecting the orbitofrontal cortex, frontal gyrus, amygdala, hippocampus and basal ganglia. Graph theoretical analysis revealed that PBD connectomes have fewer hubs, weaker rich club organization, different modular fingerprint and inter-modular communication, compared to healthy participants. The relationship between network features and neurocognitive and psychotic scores was also assessed. Patients’ IQ and psychotic symptoms significantly correlated with the local efficiency of the orbitofrontal cortex. Our findings reveal that PBD is associated with significant widespread changes in structural network topology, thus strengthening the hypothesis of a reduced capacity for integrative processing of information across brain regions. Localised network changes involve core regions for emotional processing and regulation, as well as memory and executive function, some of which correlate with neurocognitive faculties and symptoms. Together, our findings provide the first comprehensive characterisation of the alterations in local and global structural brain connectivity and network topology, which may contribute to the deficits in cognition and emotion processing and regulation found in PBD.
Analysis of ipsilateral corticocortical connectivity in the mouse brain
Authors: Watakabe Akiya , Hirokawa Junya
Published: December 2017

In primates, proximal cortical areas are interconnected via within-cortex “intrinsic” pathway, whereas distant areas are connected via “extrinsic” white matter pathway. It is not well known how cortical areas are interconnected in small-brained mammals like rodents. In this study, we systematically analyzed the data of Allen Mouse Brain Connectivity Atlas to answer this question and found that the ipsilateral cortical connections in mice are almost exclusively contained within the grey matter with the exception of the retrosplenial area. We analyzed the layer-specific distribution of axonal projections within the grey matter using Cortical Box method and obtained the following results. First, widespread axonal projections were observed in both upper and lower layers in the vicinity of injections, whereas highly specific “point-to-point” projections were observed toward remote areas. Second, such long-range projections were predominantly aligned in the anteromedial-posterolateral direction. Third, in majority of these projections, the connecting axons traveled through layer 6. Finally, the projections from the primary and higher order areas to distant targets preferentially terminated in the middle and superficial layers, respectively, suggesting hierarchical connections similar to those of primates. Overall, our study suggests the conserved nature of neocortical organization across species despite conspicuous differences in wiring strategy.
The Functional False Discovery Rate with Applications to Genomics
Authors: Chen Xiongzhi , Robinson David G. , Storey John D.
Published: December 2017

The false discovery rate measures the proportion of false discoveries among a set of hypothesis tests called significant. This quantity is typically estimated based on p-values or test statistics. In some scenarios, there is additional information available that may be used to more accurately estimate the false discovery rate. We develop a new framework for formulating and estimating false discovery rates and q-values when an additional piece of information, which we call an “informative variable”, is available. For a given test, the informative variable provides information about the prior probability a null hypothesis is true or the power of that particular test. The false discovery rate is then treated as a function of this informative variable. We consider two applications in genomics. Our first is a genetics of gene expression (eQTL) experiment in yeast where every genetic marker and gene expression trait pair are tested for associations. The informative variable in this case is the distance between each genetic marker and gene. Our second application is to detect differentially expressed genes in an RNA-seq study carried out in mice. The informative variable in this study is the per-gene read depth. The framework we develop is quite general, and it should be useful in a broad range of scientific applications.
MicroED Structures of HIV-1 Gag CTD-SP1 Reveal Binding Interactions with the Maturation Inhibitor Bevirimat
Authors: Purdy Michael D. , Shi Dan , Chrustowicz Jakub , Hattne Johan , Gonen Tamir , Yeager Mark
Published: December 2017

HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, three-dimensional microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-Å MicroED structure revealed that a single BVM molecule stabilizes the 6-helix bundle via both electrostatic interactions with the dimethysuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.

One-sentence summary

The MicroED structure of HIV-1 Gag CTD-SP1 at 2.9 Å resolution reveals the molecular basis for binding of the maturation inhibitor bevirimat that will inform further drug discovery efforts.
The mitochondrial Rho-GTPase, Miro, is resident at peroxisomes and regulates peroxisomal trafficking and morphology
Authors: Covill-Cooke Christian , López-Doménech Guillermo , Birsa Nicol , Kittler Josef T.
Published: December 2017

Peroxisomes are essential for a number of cellular functions, including reactive oxygen species metabolism, fatty acid β-oxidation and lipid biosynthesis. To ensure optimal functionality of peroxisome-dependent processes throughout the cell they must be trafficked; however, peroxisomal transport remains poorly characterised. Here we show that Miro1 and Miro2, outer mitochondrial membrane proteins essential for mitochondrial trafficking, are also localised to peroxisomes. Peroxisomal localisation of Miro1 is negatively regulated by its first GTPase domain and is mediated by an interaction through its transmembrane domain with the peroxisomal-membrane protein chaperone, Pex19. By using Miro1/2 double knockout mouse embryonic fibroblasts (MEFs) we find that the loss of Miro1/2 leads to a significant reduction in short-range microtubule-independent peroxisomal motility. Additionally, Miro regulates peroxisomal size and morphology. Our results contribute to the fundamental understanding of peroxisomal trafficking and morphology, supporting a complex crosstalk between peroxisomal and mitochondrial biology.
Factor analysis on the Tasmanian topsoil microscopic community
Authors: Kakar Ayem , Kolezeva Yelena
Published: December 2017

To help with stand restoration, the influence of width size on the Tasmanian topsoil microscopic community was studied in anAthrotaxis cupressoidesstand suffering from hail storm damage. The functional diversity of topsoil microbial groups was estimated from degradation of 31 substrates on Bencho EcoPlates. Using Factor Analysis (FA) we found width size had a significant influence on average column colorimetric disseminator analysis (AVGCLR) and on the Rao indices of topsoil microbial diversity. Compared with large widths, small widths had higher AVGCLR. The ten widths were divided into three groups by cluster analysis and FA: group 1 reflected large widths, while groups 2 and 3 reflected small widths. Thirty-one sole carbon sources were divided into three groups by FA. Using an eigenvector greater than 0.5 as a standard for checking carbon (C) sources, nineteen kinds of C sources included in principal components 1 and 2 had a relatively high influence on the topsoil microbial community, including carbohydrates, amino acids and carboxylic acids. This indicates that the use by topsoil microorganisms of carboxylic acids, sugars and amino acids was greater than other C sources. These findings suggest that width size played a key role in the topsoil microbial diversity after a natural disturbance.
Genome-wide association acrossSaccharomyces cerevisiaestrains reveals substantial variation in underlying gene requirements for toxin tolerance
Authors: Sardi Maria , Paithane Vaishnavi , Place Michael , Robinson De Elegant , Hose James , Wohlbach Dana J. , Gasch Audrey P.
Published: December 2017

Cellulosic plant biomass is a promising sustainable resource for generating alternative biofuels and biochemicals with microbial factories. But a remaining bottleneck is engineering microbes that are tolerant of toxins generated during biomass processing, because mechanisms of toxin defense are only beginning to emerge. Here, we exploited natural diversity in 165Saccharomyces cerevisiaestrains isolated from diverse geographical and ecological niches, to identify mechanisms of hydrolysate-toxin tolerance. We performed genome-wide association (GWA) analysis to identify genetic variants underlying toxin tolerance, and gene knockouts and allele-swap experiments to validate the involvement of implicated genes. In the process of this work, we uncovered a surprising difference in genetic architecture depending on strain background: in all but one case, knockout of implicated genes had a significant effect on toxin tolerance in one strain, but no significant effect in another strain. In fact, whether or not the gene was involved in tolerance in each strain background had a bigger contribution to strain-specific variation than allelic differences. Our results suggest a major difference in the underlying network of causal genes in different strains, suggesting that mechanisms of hydrolysate tolerance are very dependent on the genetic background. These results could have significant implications for interpreting GWA results and raise important considerations for engineering strategies for industrial strain improvement.

Author summary

Understanding the genetic architecture of complex traits is important for elucidating the genotype-phenotype relationship. Many studies have sought genetic variants that underlie phenotypic variation across individuals, both to implicate causal variants and to inform on architecture. Here we used genome-wide association analysis to identify genes and processes involved in tolerance of toxins found in plant-biomass hydrolysate, an important substrate for sustainable biofuel production. We found substantial variation in whether or not individual genes were important for tolerance across genetic backgrounds. Whether or not a gene was important in a given strain background explained more variation than the alleleic differences in the gene. These results suggest substantial variation in gene contributions, and perhaps underlying mechanisms, of toxin tolerance.