bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iodine and Fat Quantification for Differentiation of Adrenal Gland Adenomas From Metastases Using Third-Generation Dual-Source Dual-Energy Computed Tomography
Authors: Martin Simon S. , Weidinger Sebastian , Czwikla Rouben , Kaltenbach Benjamin , Albrecht Moritz H. , Lenga Lukas , Vogl Thomas J. , Wichmann Julian L. 
Published: October 2017

Objectives
The aim of this study was to investigate the value of third-generation dual-source dual-energy computed tomography (DECT) iodine and fat quantification in differentiating adrenal gland adenomas from metastases.

Materials and Methods
Sixty-two patients (38 men and 24 women; mean age, 69.1 years) underwent clinically indicated DECT of the abdomen on a third-generation dual-source scanner. Examinations were retrospectively included due to detected adrenal masses. For each adrenal lesion, unenhanced and contrast-enhanced attenuation values, as well as dual-energy iodine density and fat fraction, were recorded. Additional magnetic resonance imaging data, positron emission tomography/computed tomography scans, interval imaging follow-up, and histopathological analysis were used as the reference standard for all adrenal lesions. Mean values of unenhanced and contrast-enhanced attenuation, as well as material densities, were compared between adenomas, metastases, and normal adrenal glands. Furthermore, the diagnostic accuracy of unenhanced, contrast-enhanced, and material density analysis was assessed between adrenal adenomas and metastases.

Results
Adrenal adenomas showed significant differences regarding iodine density and fat fraction values (1.3 ± 0.4 mg/mL and 34.2% ± 12.6%) in comparison with adrenal metastases (3.2 ± 1.4 mg/mL and 10.7% ± 7.8%) and normal adrenal glands (1.7 ± 0.6 mg/mL and 18.7% ± 12.0%) (all P ≤ 0.004). Analysis of unenhanced attenuation values revealed no significant differences between healthy adrenal parenchyma (19.1 ± 15.6 HU) and adrenal metastases (26.9 ± 16.2 HU) (P = 0.135). Iodine density and fat fraction analysis showed significantly higher diagnostic accuracy for the diagnosis of adenomas (sensitivity, 97% and 89%; specificity, 96% and 89%, respectively) compared with unenhanced and contrast-enhanced evaluation (sensitivity, 65% and 58%; specificity, 73% and 85%, respectively) (P ≤ 0.023). The combined diagnostic value of iodine density and fat fraction analysis revealed a sensitivity of 97% and a specificity of 100%.

Conclusions
Third-generation dual-source DECT iodine and fat quantification allow for differentiation between adrenal adenomas and metastases with high diagnostic accuracy.
Vasopressors Do Not Influence Cerebral Critical Closing Pressure During Systemic Inflammation Evoked by Experimental Endotoxemia and Sepsis in Humans
Authors: van den Brule Judith Maria Dimphena , Stolk Roeland , Vinke Elisabeth Janine , van Loon Lex Maxim , Pickkers Peter , van der Hoeven Johannes Gerardus , Kox Matthijs , Hoedemaekers Cornelia Wilhelmina Elisabeth 
Published: October 2017

ABSTRACT

Aim:
The aim of this study was to investigate the effects of different vasopressors on the cerebral vasculature during experimental human endotoxemia and sepsis. We used the critical closing pressure (CrCP) as a measure of cerebral vascular tone.

Methods:
We performed a prospective pilot study, at the intensive care department (ICU) of a tertiary care university hospital in the Netherlands, in 40 healthy male subjects during experimental human endotoxemia (administration of bacterial lipopolysaccharide [LPS]) and in 10 patients with severe sepsis or septic shock.
Subjects in the endotoxemia study were randomized to receive a 5 h infusion of either 0.05 μg/kg/min noradrenaline (n = 10, “LPS-nor”), 0.5 μg/kg/min phenylephrine (n = 10, “LPS-phenyl”), 0.04 IU/min vasopressin (n = 10, “LPS-AVP”), or saline (n = 10, “LPS-placebo”) starting 1 h before intravenous administration of 2 ng/kg LPS. In patients with sepsis, fluid resuscitation and vasopressor use was at the discretion of the medical team, aiming at normovolemia and a mean arterial pressure (MAP) > 65 mm Hg, using noradrenaline.
The mean flow velocity in the middle cerebral artery (MFVMCA) was measured by transcranial Doppler (TCD) with simultaneously recording of heart rate, arterial blood pressure, respiratory rate, and oxygen saturation. CrCP was estimated using the cerebrovascular impedance model.

Results:
The CrCP decreased in the LPS-placebo group from 52.6 [46.6–55.5] mm Hg at baseline to 44.1 [41.2–51.3] mm Hg at 270 min post-LPS (P = 0.03). Infusion of phenylephrine increased the CrCP in the period before LPS administration from 46.9 [38.8–53.4] to 53.8 [52.9–60.2] mm Hg (P = 0.02), but after LPS administration, a similar decrease was observed compared with the LPS-placebo group. Noradrenaline or vasopressin prior to LPS did not affect the CrCP. The decrease in CrCP after LPS bolus was similar in all treatment groups. The CrCP in the sepsis patients equaled 35.7 [34.4–42.0] mm Hg, and was lower compared with that in the LPS-placebo subjects from baseline until 90 min after LPS (P < 0.01).

Conclusions:
Experimental human endotoxemia results in a decreased CrCP due to a loss of vascular resistance of the arterial bed. Vasopressors did not prevent this decrease in CrCP. Findings in patients with sepsis are comparable to those found in subjects after LPS administration.
Patients with sepsis, despite treatment with vasopressors, have a risk for low cerebral blood flow and ischemia.
Defense Automated Neurobehavioral Assessment Accurately Measures Cognition in Patients Undergoing Electroconvulsive Therapy for Major Depressive Disorder
Authors: Hollinger Kristen R. , Woods Steven R. , Adams-Clark Alexis , Choi So Yung , Franke Caroline L. , Susukida Ryoko , Thompson Carol , Reti Irving M. , Kaplin Adam I. 
Published: October 2017

Objectives
The Defense Automated Neurobehavioral Assessment (DANA) is an electronic cognitive test battery. The present study compares DANA to the standard Mini-Mental State Examination (MMSE) in subjects undergoing electroconvulsive therapy for the treatment of major depressive disorder.

Methods
Seventeen inpatient subjects in the Johns Hopkins Hospital Department of Psychiatry were administered longitudinal paired DANA and MMSE tests (7.6 ± 4.1 per patient) from January 10, 2014 to September 26, 2014. Regression analyses were conducted (with or without MMSE scores of 30) to study the impact of the MMSE upper limit, and within-subject regression analyses were conducted to compare MMSE and DANA scores over time.

Results
Statistically significant relationships were measured between DANA and MMSE scores. Relationships strengthened when MMSE scores of 30 were omitted from analyses, demonstrating a ceiling effect of the MMSE. Within-subject analyses revealed relationships between MMSE and DANA scores over the duration of the inpatient stay.

Conclusions
Defense Automated Neurobehavioral Assessment is an electronic, mobile, repeatable, sensitive, and valid method of measuring cognition over time in depressed patients undergoing electroconvulsive therapy treatment. Automation of the DANA allows for more frequent cognitive testing in a busy clinical setting and enhances cognitive assessment sensitivity with a timed component to each test.
Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Authors: Wyder Stefan , Raissig Michael T. , Grossniklaus Ueli 
Published: October 2017

ABSTRACTGenomic imprinting leads to different expression levels of maternally and paternally derived alleles. Over the last years, major progress has been made in identifying novel imprinted candidate genes in plants, owing to affordable next-generation sequencing technologies. However, reports on sequencing the transcriptome of hybrid F1 seed tissues strongly disagree about how many and which genes are imprinted. This raises questions about the relative impact of biological, environmental, technical, and analytic differences or biases. Here, we adopt a statistical approach, frequently used in RNA-seq data analysis, which properly models count overdispersion and considers replicate information of reciprocal crosses. We show that our statistical pipeline outperforms other methods in identifying imprinted genes in simulated and real data. Accordingly, reanalysis of genome-wide imprinting studies inArabidopsisand maize shows that, at least for theArabidopsisdataset, an increased agreement across datasets can be observed. For maize, however, consistent reanalysis did not yield in a larger overlap between the datasets. This suggests that the discrepancy across publications might be partially due to different analysis pipelines but that technical, biological, and environmental factors underlie much of the discrepancy between datasets. Finally, we show that the set of genes that can be characterized regarding allelic bias by all studies with minimal confidence is small (~8,000/27,416 genes forArabidopsisand ~12,000/39,469 for maize). In conclusion, we propose to use biologically replicated reciprocal crosses, high sequence coverage, and a generalized linear model approach to identify differentially expressed alleles in developing seeds.
Pangenomic analysis reveals pathogen-specific regions and novel effector candidates inFusarium oxysporumf. sp.cepae
Authors: Armitage Andrew D. , Taylor Andrew , Sobczyk Maria K. , Baxter Laura , Greenfield Bethany P.J. , Bates Helen J. , Wilson Fiona , Jackson Alison C. , Ott Sascha , Harrison Richard J. , Clarkson John P. 
Published: October 2017

AbstractA reference-quality assembly ofFusarium oxysporumf. sp.cepae(Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage.Genome alignments with otherF. oxysporumff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core.RNA-seq expression studies identified candidate effectors expressedin planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressedin planta.
Response to Qian et al (2017): Daily and seasonal climate variations are both critical in the evolution of species’ elevational range size
Authors: Chan Wei-Ping , Chen I-Ching , Colwell Robert K. , Liu Wei-Chung , Huang Cho-ying , Shen Sheng-Feng 
Published: October 2017

AbstractIn their recent critique, Qian et al. (2017) claimed that the results of structural equation modeling analysis (SEM) in Chan et al. (2016) were flawed. Here, we show that the source of the difference in their re-analysis is that Qian et al. did not follow the standard, iterative process of SEM, which allows researchers to evaluate which model offers the best account of the data in both absolute and relative senses. Here, we provide step-by-step instructions to reproduce our published results. All of Qian et al.’s concerns regarding SEM can be put to rest. Moreover, in our original paper we used three distinct statistical methods—hierarchical partitioning, SEM, and stationary bootstrap—to show that different temporal scales of environmental variability can differentially impact the elevational range size (ERS) of species. It is time to move on to probing the pressing issue of how and why climatic variability impacts ERS.
Ocular and uteroplacental pathology in macaque congenital Zika virus infection
Authors: Mohr Emma L. , Block Lindsey N. , Newman Christina M. , Stewart Laurel M. , Koenig Michelle , Semler Matthew , Breitbach Meghan E. , Teixeira Leandro B.C. , Zeng Xiankun , Weiler Andrea M. , Barry Gabrielle L. , Thoong Troy H. , Wiepz Gregory J. , Dudley Dawn M. , Simmons Heather A. , Mejia Andres , Morgan Terry K. , Shahriar Salamat M. , Kohn Sarah , Antony Kathleen M. , Aliota Matthew T. , Mohns Mariel S. , Hayes Jennifer M. , Schultz-Darken Nancy , Schotzko Michele L. , Peterson Eric , Capuano Saverio , Osorio Jorge E. , O’Connor Shelby L. , Friedrich Thomas C. , O’Connor David H. , Golos Thaddeus G. 
Published: October 2017

AbstractCongenital Zika virus (ZIKV) infection impacts fetal development and pregnancy outcomes. We infected a pregnant rhesus macaque with a Puerto Rican ZIKV isolate in the first trimester. The pregnancy was complicated by preterm premature rupture of membranes (PPROM) and fetal demise 49 days post infection (gestational day 95). Significant pathology at the maternal-fetal interface included acute chorioamnionitis, placental infarcts, and leukocytoclastic vasculitis of the myometrial radial arteries. ZIKV RNA was disseminated throughout the fetus tissues and maternal immune system at necropsy, as assessed by quantitative RT-PCR for viral RNA. Replicating ZIKV was identified in fetal tissues, maternal lymph node, and maternal spleen by fluorescent in situ hybridization for viral replication intermediates. Fetal ocular pathology included a choroidal coloboma, suspected anterior segment dysgenesis, and a dysplastic retina. This is the first report of ocular pathology and prolonged viral replication in both maternal and fetal tissues following congenital ZIKV infection in rhesus macaques. PPROM followed by fetal demise and severe pathology of the visual system have not been described in macaque congenital infection previously; further nonhuman primate studies are needed to determine if an increased risk for PPROM is associated with congenital Zika virus infection.Author summaryA ZIKV infection during pregnancy is associated with malformations in fetal development including, but not limited to, ocular and brain anomalies, such as microcephaly, and stillbirth. The development of an accurate pregnancy model to study the effects of ZIKV will provide insight into vertical transmission, ZIKV tissue distribution, and fetal injury and malformations. Non-human primates closely resemble human in terms of the reproductive system, immunity, placentation and pregnancy. Our study demonstrates that the rhesus macaque is a compelling model in which to study ZIKV during pregnancy due to similar outcomes between the human and rhesus macaque. These similarities include prolonged viremia, vertical transmission, adverse pregnancy outcomes and fetal pathology, including defects in the visual system.
Comparing average network signals and neural mass signals in systems with low-synchrony
Authors: Tewarie P. , Daffertshofer A. , van Dijk B.W. 
Published: October 2017

1AbstractNeural mass models are accepted as efficient modelling techniques to model empirical observations such as disturbed oscillations or neuronal synchronization. Neural mass models are based on the mean-field assumption, i.e. they capture the mean-activity of a neuronal population. However, it is unclear if neural mass models still describe the mean activity of a neuronal population when the underlying neural network topology is not homogenous. Here, we test whether the mean activity of a neuronal population can be described by neural mass models when there is neuronal loss and when the connections in the network become sparse. To this end, we derive two neural mass models from a conductance based leaky integrate-and-firing (LIF) model. We then compared the power spectral densities of the mean activity of a network of inhibitory and excitatory LIF neurons with that of neural mass models by computing the Kolmogorov-Smirnov test statistic. Firstly, we found that when the number of neurons in a fully connected LIF-network is larger than 300, the neural mass model is a good description of the mean activity. Secondly, if the connection density in the LIF-network does not exceed a crtical value, this leads to desynchronization of neurons within the LIF-network and to failure of neural mass description. Therefore we conclude that neural mass models can be used for analysing empirical observations if the neuronal network of interest is large enough and when neurons in this system synchronize.
Time-resolved neural reinstatement and separation during memory decisions in human hippocampus
Authors: Lohnas Lynn J. , Duncan Katherine , Doyle Werner K. , Devinsky Orrin , Davachi Lila 
Published: October 2017

AbstractMnemonic decision-making has long been hypothesized to rely on hippocampal dynamics that bias memory processing toward the formation of new memories or the retrieval of old ones. Successful memory encoding would be best optimized by pattern separation, whereby two highly similar experiences can be represented by underlying neural populations in an orthogonal manner. By contrast, successful memory retrieval is thought to be supported by a recovery of the same neural pattern laid down during encoding. Here we examined how hippocampal pattern completion and separation emerge over time during memory decisions. We measured electrocorticography activity in the human hippocampus and posterior occipitotemporal cortex (OTC) while participants performed continuous recognition of items that were new, repeated (old), or highly similar to a prior item (similar).During retrieval decisions of old items, both regions exhibited significant reinstatement of multivariate high frequency activity (HFA) associated with encoding. Further, the extent of reinstatement of encoding patterns during retrieval was correlated both with the strength (HFA power) of hippocampal encoding and with the strength of hippocampal retrieval. Evidence for encoding pattern reinstatement was also seen in OTC on trials requiring fine-grained discrimination of similar items. By contrast, hippocampal activity showed evidence for pattern separation during these trials. Together, these results underscore the critical role of the hippocampus in supporting both reinstatement of overlapping information and separation of similar events.Significance StatementOne of the biggest computational challenges the memory systems faces is to disambiguate highly similar experiences while at the same time preserving and reinstating prior memories. Remarkably, hippocampal processes have been implicated in both of these functions. However, how this is accomplished is unknown. Leveraging the spatiotemporal resolution of electrocorticography, we found evidence for memory reinstatement in both the hippocampus and occipitotemporal cortex. Reinstatement was differentiated in time across these two regions with earlier reinstatement evident in occipitotemporal cortex. Interestingly, when a current experience was very similar, but not identical to a prior one, occipitotemporal cortical activity still showed reinstatement of the prior memory but hippocampal activity differentiated or disambiguated these two similar experiences.
Phylofactorization - theory and challenges
Authors: Washburne Alex D. 
Published: October 2017

AbstractData from biological communities are composed of species connected by the phylogeny. A greedy algorithm ‘phylofactorization’ - was developed to construct an isometric log-ratio transform whose balances correspond to edges along which traits arose, controlling for previously made inferences.In this paper, the general theory of phylofactorization is presented as a graph-partitioning algorithm. A special case-regression phylofactorization-chooses coordinates based on sequential maximization of objective functions from regression on “contrast” variables such as an isometric log-ratio transform. The connections between regression phylofactorization and other methods is discussed, including matrix factorization, hierarchical regression, factor analysis and latent variable models. Open challenges in the statistical analysis of phylofactorization are presented, including criteria for choosing the number of factors and approximating null-distributions of commonly used test statistics and objective functions. As a graph-partitioning algorithm, cross-validation of phylo factorization across datasets requires graph-topological considerations, such as how to deal with novel nodes and edges and whether or not to control for partition order. Overcoming these challenges can accelerate our analysis of phylogenetically-structured data and allow annotations of edges in an online tree of life.
Linear models enable powerful differential activity analysis in massively parallel reporter assays
Authors: Myint Leslie , Avramopoulos Dimitrios G. , Goff Loyal A. , Hansen Kasper D. 
Published: October 2017

AbstractMassively parallel reporter assays (MPRAs) have emerged as a popular means for understanding noncoding variation in a variety of conditions. While a large number of experiments have been described in the literature, analysis typically uses ad-hoc methods. There has been little attention to comparing performance of methods across datasets.We present the mpralm method which we show is calibrated and powerful, by analyzing its performance on multiple MPRA datasets. We show that it outperforms existing statistical methods for analysis of this data type, in the first comprehensive evaluation of statistical methods on several datasets. We investigate theoretical and real-data properties of barcode summarization methods and show an unappreciated impact of summarization method for some datasets. Finally, we use our model to conduct a power analysis for this assay and show substantial improvements in power by performing up to 6 replicates per condition, whereas sequencing depth has smaller impact; we recommend to always use at least 4 replicates. Together, these results inform recommendations for differential analysis, general group comparisons, and power analysis and will help improve design and analysis of MPRA experiments. An R package is available from the Bioconductor project athttps://bioconductor.org/packages/mpra.