bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electroconvulsive Therapy and All-Cause Mortality in Texas, 1998–2013
Authors: Dennis Nora M. , Dennis Paul A. , Shafer Alan , Weiner Richard D. , Husain Mustafa M. 
Published: July 2016

Introduction
Electroconvulsive therapy (ECT) remains an effective treatment for major depressive disorder. Since 1995, Texas has maintained an ECT database including patient diagnoses and outcomes, and reporting any deaths within 14 days of receiving an ECT treatment, encompassing a total of 166,711 ECT treatments administered in Texas over the previously unreported period of 1998 to 2013.

Methods
Descriptive analysis summarized information on deaths reported during the 16-year period—cause of death, type of treatment (index or maintenance) and patient demographics. Multiple logistic regression of death incidence by treatment session was performed to determine whether patient age, sex, race, diagnosis, or year of treatment was associated with death after ECT.

Results
Of those deaths occurring within 1 day of an ECT treatment, the death rate was 2.4 per 100,000 treatments. Looking at all deaths within 14 days of an ECT treatment, the death rate increased to 18 per 100,000 treatments but included all deaths regardless of likelihood of causal association with ECT, for example, accidents and suicides, the latter a leading cause of death among individuals with severe major depression or other disorders for which ECT is indicated. Death rate increased significantly with increasing patient age (P = 0.001) and male sex (P = 0.009), and there was a nonsignificant trend toward increased death amongst patients with bipolar disorder or schizophrenia (P = 0.058) versus depression.

Conclusions
Our data indicate that ECT is in general a safe procedure with respect to the likelihood of immediate death. Suicide remains a significant risk in ECT patients, despite evidence that ECT reduces suicidal ideation.
Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria
Authors: Krabberød Anders K. , Orr Russell J. S. , Bråte Jon , Kristensen Tom , Bjørklund Kjell R. , Shalchian-Tabrizi Kamran 
Published: July 2016

AbstractThe innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for diverse eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultivable, free-living unicellular eukaryotes: the radiolarian speciesLithomelissa setosaandSticholonche zanclea. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these to a revised phylogeny of Rhizaria reveals lineage-specific gene duplications and neo-functionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution of uncultivable protist species.
The Influence of Canalization on the Robustness of Boolean Networks
Authors: Kadelka C. , Kuipers J. , Laubenbacher R. 
Published: July 2016

AbstractTime- and state-discrete dynamical systems are frequently used to model molecular networks. This paper provides a collection of mathematical and computational tools for the study of robustness in Boolean network models. The focus is on networks governed byk-canalizing functions, a recently introduced class of Boolean functions that contains the well-studied class of nested canalizing functions. The activities and sensitivity of a function quantify the impact of input changes on the function output. This paper generalizes the latter concept toc-sensitivity and provides formulas for the activities andc-sensitivity of generalk-canalizing functions as well as canalizing functions with more precisely defined structure. A popular measure for the robustness of a network, the Derrida value, can be expressed as a weighted sum of thec-sensitivities of the governing canalizing functions, and can also be calculated for a stochastic extension of Boolean networks. These findings provide a computationally efficient way to obtain Derrida values of Boolean networks, deterministic or stochastic, that does not involve simulation.
Neural signatures of value comparison in human cingulate cortex during decisions requiring an effort-reward trade-off
Authors: Klein-Flügge Miriam C , Kennerley Steven W , Friston Karl , Bestmann Sven 
Published: July 2016

AbstractIntegrating costs and benefits is crucial for optimal decision-making. While much is known about decisions that involve outcome-related costs (e.g., delay, risk), many of our choices are attached to actions and require an evaluation of the associated motor costs. Yet how the brain incorporates motor costs into choices remains largely unclear. We used human functional magnetic resonance imaging during choices involving monetary reward and physical effort to identify brain regions that serve as a choice comparator for effort-reward trade-offs. By independently varying both options' effort and reward levels, we were able to identify the neural signature of a comparator mechanism. A network involving supplementary motor area (SMA) and the caudal portion of dorsal anterior cingulate cortex (dACC) encoded the difference in reward (positively) and effort levels (negatively) between chosen and unchosen choice options. We next modelled effort-discounted subjective values using a novel behavioural model. This revealed that the same network of regions involving dACC and SMA encoded the difference between the chosen and unchosen options' subjective values, and that activity was best described using a concave model of effort-discounting. In addition, this signal reflected how precisely value determined participants' choices. By contrast, separate signals in SMA and ventro-medial PFC (vmPFC) correlated with participants' tendency to avoid effort and seek reward, respectively. This suggests that the critical neural signature of decision-making for choices involving motor costs is found in human cingulate cortex and not vmPFC as typically reported for outcome-based choice. Furthermore, distinct frontal circuits ‘drive’ behaviour towards reward-maximization and effort-minimization.Significance StatementThe neural processes that govern the trade-off between expected benefits and motor costs remain largely unknown. This is striking because energetic requirements play an integral role in our day-to-day choices and instrumental behaviour, and a diminished willingness to exert effort is a characteristic feature of a range of neurological disorders. We use a new behavioural characterization of how humans trade-off reward-maximization with effort-minimization to examine the neural signatures that underpin such choices, using BOLD MRI neuroimaging data. We find the critical neural signature of decision-making, a signal that reflects the comparison of value between choice options, in human cingulate cortex, whereas two distinct brain circuits ‘drive’ behaviour towards reward-maximization or effort-minimization.
Influence of rotational nucleosome positioning on transcription start site selection in animals promoters
Authors: Dreos René , Ambrosini Giovanna , Bucher Philipp 
Published: July 2016

AbstractThe recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters’ sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters’ primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanismof TSS selection in animals.Author SummaryGene transcription is a complex process that starts with the recruitment and positioning of Pol-II enzyme at the transcription start site (TSS). Specific promoter sequences, known as core promoter elements (CPEs) facilitate this process. Surprisingly, only a fraction of promoters contain them. It is still unknown how Pol-II choses the start site in their absence. Arecently proposed alternative mechanism implicates positioned nucleosomes in the TSS selection. Here, we provide new evidence of the existence of such mechanism with a comparative analysis of promoter’s features across the animal kingdom. We analysed the promoter’s DNA sequence composition in 5 organisms and found conserved and unique consensus sequencesused to organize chromatin in the region of the first nucleosome downstream the TSS (N+1). Moreover, we found that all organisms show a strong correlation between the spread of Pol-II initiation and the strength of the DNA-encoded signal in the N+1 region. A detailed analysis of Pol-II initiation sites reveals also the presence of a 10 bp periodicity that is correlated with the intensity of the DNA signal in the N+1 region. Importantly, we report that genetic variants that alter the DNA-nucleosome affinity in that region alter Pol-II initiation spread as well.
Accelerating computational Bayesian inference for stochastic biochemical reaction network models using multilevel Monte Carlo sampling
Authors: Warne David J. , Baker Ruth E. , Simpson Matthew J. 
Published: July 2016

AbstractInvestigating the behavior of stochastic models of biochemical reactionnetworks generally relies upon numerical stochastic simulation methods to generate many realizations of the model. For many practical applications, such numerical simulation can be computationally expensive. The statistical inference of reaction rate parameters based on observed data is, however, a significantly greater computational challenge; often relying upon likelihood-free methods such as approximate Bayesian computation, that requirethe generation of millions of individual stochastic realizations. In this study, we investigate a new approach to computational inference, based on multilevel Monte Carlo sampling: we approximate the posterior cumulative distribution function through a combination of model samples taken over a range of acceptance thresholds. We demonstrate this approach using a variety of discrete-state, continuous-time Markov models of biochemical reactionnetworks. Results show that a computational gain over standard rejection schemes of up to an order of magnitude is achievable without significant loss in estimator accuracy.Author SummaryWe develop a new method to infer the reaction rate parameters for stochastic models of biochemical reaction networks. Standard computational approaches, based on numerical simulations, are often used to estimate parameters. These computational approaches, however, are extremely expensive, potentially requiring millions of simulations. To alleviate this issue, we apply a different method of sampling allowing us to find an optimal trade-off between performance and accuracy. Our approach is approximately one order of magnitude faster than standard methods, without significant loss in accuracy.
Commentary: Is the Statistic Value All We Should Care about in Neuroimaging?
Authors: Chen Gang , Taylor Paul A. , Cox Robert W. 
Published: July 2016

AbstractHere we address an important issue that has been embedded within the neuroimaging community for a long time: the absence of effect estimates in results reporting in the literature. The statistic value itself, as a dimensionless measure, does not provide information on the biophysical interpretation of a study, and it certainly does not represent the whole picture of a study. Unfortunately, in contrast to standard practice in most scientific fields, effect (or amplitude) estimates are usually not provided in most results reporting in the current neuroimaging publications and presentations. Possible reasons underlying this general trend include: 1) lack of general awareness, 2) software limitations, 3) inaccurate estimation of the BOLD response, and 4) poor modeling due to our relatively limited understanding of FMRI signal components. However, as we discuss here, such reporting damages the reliability and interpretability of the scientific findings themselves, and there is in fact no overwhelming reason for such a practice to persist. In order to promote meaningful interpretation, cross validation, reproducibility, meta and power analyses in neuroimaging, we strongly suggest that, as part of good scientific practice, effect estimates should be reported together with their corresponding statistic values. We provide several easily adaptable recommendations for facilitating this process.
Comparative metagenomics unveils functions and genome features of microbialite‐associated communities along a depth gradient
Authors: Saghaï Aurélien , Zivanovic Yvan , Moreira David , Benzerara Karim , Bertolino Paola , Ragon Marie , Tavera Rosaluz , López‐Archilla Ana Isabel , López‐García Purificación 
Published: July 2016

SummaryModern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long‐term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single‐copy gene family identification and long‐contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.
EUS‐guided FNA and FNB after on‐site cytological evaluation in gastric subepithelial tumors
Authors: Han Jae Pil , Lee Tae Hee , Hong Su Jin , Kim Hee Kyung , Noh Hyung Min , Lee Yun Nah , Choi Hyun Jong 
Published: July 2016

ObjectiveAcquiring adequate tissue for immunohistochemical (IHC) analysis is important in the differential diagnosis of subepithelial tumors (SETs). In this study, we aimed to compare the diagnostic yield based on IHC analysis between endoscopic ultrasound‐guided fine needle aspiration (EUS‐FNA) and EUS‐guided fine needle biopsy (EUS‐FNB) after on‐site cytological evaluation for cellularity in gastric SETs.MethodsIn 22 patients with gastric SETs, EUS‐guided tissue sampling was performed on the same SET in a randomized sequence, with EUS‐FNA followed by EUS‐FNB, or vice versa. After on‐site cytological evaluation for cellularity, the cytological and histological examinations were performed.ResultsThere was a significant difference in the median number of needle passes to obtain adequate cellularity in the on‐site cytological evaluation (2.0 for EUS‐FNA vs 1.0 for EUS‐FNB, P = 0.008). The proportion of adequate cellularity on the first needle pass was significantly higher in the EUS‐FNB than in the EUS‐FNA group (68.2% vs 31.8%, P = 0.034). However, diagnosis based on IHC examination was established in 15 (68.2%) and 18 (81.8%) cases by EUS‐FNA and EUS‐FNB, respectively (P = 0.488).ConclusionsEUS‐FNB decreases the number of needle passes to obtain adequate cellularity and yields a higher proportion of adequate cellularity during the first needle pass compared with EUS‐FNA in gastric SETs. However, there was no significant difference in diagnostic yield with IHC stain between the two procedures after on‐site cytological evaluation for adequate cellularity.
Arbuscular mycorrhizal fungi induced changes in rhizosphere, essential oil and mineral nutrients uptake in dill/common bean intercropping system
Authors: Weisany W. , Raei Y. , Salmasi S.Z. , Sohrabi Y. , Ghassemi‐Golezani K. 
Published: July 2016

AbstractThe fundamental aim of this research was to evaluate the effects of Funneliformis mosseae on nutrient uptake and distribution in solo cropping and intercropping of common bean Phaseolus vulgaris and dill Anethum graveolens in the field, using a factorial arrangement of treatments. The factors were seven cropping systems including (a) common bean sole cropping (40 plants m−2), (b) dill sole cropping at different densities (25, 50 and 75 plants m−2) and (c) the additive intercropping of dill/common bean (25/40, 50/40 and 75/40 plants m−2), with (+AM) or without (−AM) arbuscular mycorrhiza colonisation. In all cropping systems, AM colonisation improved dry weight and P, K, Fe, Zn and Mn contents of dill plants. Cultivable bacterial community was also increased in the dill/common bean intercropping. Yield of essential oil in dill shoot was improved as a result of AM colonisation and intercropping.
The QT Scale: A Weight Scale Measuring the QTc Interval
Authors: Couderc Jean‐Philippe , Beshaw Connor , Niu Xiaodan , Serrano‐Finetti Ernesto , Casas Oscar , Pallas‐Areny Ramon , Rosero Spencer , Zareba Wojciech 
Published: July 2016

IntroductionDespite the strong evidence of the clinical utility of QTc prolongation as a surrogate marker of cardiac risk, QTc measurement is not part of clinical routine either in hospital or in physician offices. We evaluated a novel device (“the QT scale”) to measure heart rate (HR) and QTc interval.MethodThe QT scale is a weight scale embedding an ECG acquisition system with four limb sensors (feet and hands: lead I, II, and III). We evaluated the reliability of QT scale in healthy subjects (cohort 1) and cardiac patients (cohorts 2 and 3) considering a learning (cohort 2) and two validation cohorts. The QT scale and the standard 12‐lead recorder were compared using intraclass correlation coefficient (ICC) in cohorts 2 and 3. Absolute value of heart rate and QTc intervals between manual and automatic measurements using ECGs from the QT scale and a clinical device were compared in cohort 1.ResultsWe enrolled 16 subjects in cohort 1 (8 w, 8 m; 32 ± 8 vs 34 ± 10 years, P = 0.7), 51 patients in cohort 2 (13 w, 38 m; 61 ± 16 vs 58 ± 18 years, P = 0.6), and 13 AF patients in cohort 3 (4 w, 9 m; 63 ± 10 vs 64 ± 10 years, P = 0.9). Similar automatic heart rate and QTc were delivered by the scale and the clinical device in cohort 1: paired difference in RR and QTc were −7 ± 34 milliseconds (P = 0.37) and 3.4 ± 28.6 milliseconds (P = 0.64), respectively. The measurement of stability was slightly lower in ECG from the QT scale than from the clinical device (ICC: 91% vs 80%) in cohort 3.ConclusionThe “QT scale device” delivers valid heart rate and QTc interval measurements.
Salt‐losing nephropathy in mice with a null mutation of the Clcnk2 gene
Authors: Grill A. , Schießl I. M. , Gess B. , Fremter K. , Hammer A. , Castrop H. 
Published: July 2016

AbstractAimThe basolateral chloride channel ClC‐Kb facilitates Cl reabsorption in the distal nephron of the human kidney. Functional mutations in CLCNKB are associated with Bartter's syndrome type 3, a hereditary salt‐losing nephropathy. To address the function of ClC‐K2 in vivo, we generated ClC‐K2‐deficient mice.MethodsClC‐K2‐deficient mice were generated using TALEN technology.ResultsClC‐K2‐deficient mice were viable and born in a Mendelian ratio. ClC‐K2−/− mice showed no gross anatomical abnormalities, but they were growth retarded. The 24‐h urine volume was increased in ClC‐K2−/− mice (4.4 ± 0.6 compared with 0.9 ± 0.2 mL per 24 h in wild‐type littermates; P = 0.001). Accordingly, ambient urine osmolarity was markedly reduced (590 ± 39 vs. 2216 ± 132 mosmol L−1 in wild types; P < 0.0001). During water restriction (24 h), urinary osmolarity increased to 1633 ± 153 and 3769 ± 129 mosmol L−1 in ClC‐K2−/− and wild‐type mice (n = 12; P < 0.0001), accompanied by a loss of body weight of 12 ± 0.4 and 8 ± 0.2% respectively (P < 0.0001). ClC‐K2−/− mice showed an increased renal sodium excretion and compromised salt conservation during a salt‐restricted diet. The salt‐losing phenotype of ClC‐K2−/− mice was associated with a reduced plasma volume, hypotension, a slightly reduced glomerular filtration rate, an increased renal prostaglandin E2 generation and a massively stimulated renin–angiotensin system. Clckb−/− mice showed a reduced sensitivity to furosemide and were completely resistant to thiazides.ConclusionLoss of ClC‐K2 compromises TAL function and abolishes salt reabsorption in the distal convoluted tubule. Our data suggest that ClC‐K2 is crucial for renal salt reabsorption and concentrating ability. ClC‐K2‐deficient mice in most aspects mimic patients with Bartter's syndrome type 3.