bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recovering the unsigned photospheric magnetic field from Ca II K observations
Authors: Chatzistergos Theodosios , Ermolli Ilaria , Solanki Sami K. , Krivova Natalie A. , Giorgi Fabrizio , Yeo Kok Leng 
Published: May 2019

Context. A number of studies have aimed at defining the exact form of the relation between magnetic field strength and Ca II H and K core brightness. All previous studies have however been restricted to isolated regions on the solar disc or to a limited set of observations.Aims. We reassess the relationship between the photospheric magnetic field strength and the Ca II K intensity for a variety of surface features as a function of the position on the disc and the solar activity level. This relationship can be used to recover the unsigned photospheric magnetic field from images recorded in the core of Ca II K line.Methods. We have analysed 131 pairs of high-quality, full-disc, near-co-temporal observations from the Helioseismic and Magnetic Imager (SDO/HMI) and Precision Solar Photometric Telescope (Rome/PSPT) spanning half a solar cycle. To analytically describe the observationally determined relation, we considered three different functions: a power law with an offset, a logarithmic function, and a power-law function of the logarithm of the magnetic flux density. We used the obtained relations to reconstruct maps of the line-of-sight component of the unsigned magnetic field (unsigned magnetograms) from Ca II K observations, which were then compared to the original magnetograms.Results. We find that both power-law functions represent the data well, while the logarithmic function is good only for quiet periods. We see no significant variation over the solar cycle or over the disc in the derived fit parameters, independently of the function used. We find that errors in the independent variable, which are usually not accounted for, introduce attenuation bias. To address this, we binned the data with respect to the magnetic field strength and Ca II K contrast separately and derived the relation for the bisector of the two binned curves. The reconstructed unsigned magnetograms show good agreement with the original ones. Root mean square differences are less than 90 G. The results were unaffected by the stray-light correction of the SDO/HMI and Rome/PSPT data.Conclusions. Our results imply that accurately processed and calibrated Ca II K observations can be used to reconstruct unsigned magnetograms by using the relations derived in our study.
Operative Therapie des Harnblasenkarzinoms: Fortschritte der letzten 50 Jahre
Authors: Bolenz Christian , Hautmann Richard E. 
Published: May 2019

ZusammenfassungInnerhalb der letzten 5 Jahrzehnte wurden bei der operativen Therapie des Harnblasenkarzinoms enorme Behandlungsfortschritte erzielt. Diese haben die Morbidität und Mortalität der Erkrankung deutlich reduziert. Neben einem kontinuierlich zunehmenden Verständnis der Tumorbiologie trugen zu einer erfolgreicheren Behandlung viele Neuentwicklungen endoskopischer Instrumente und Methoden sowie neue chirurgische Techniken für die radikale Zystektomie (RZ) bei. Durch eine bessere klinisch-pathologische Risikostratifizierung der Patienten stehen mittlerweile unterschiedliche Behandlungspfade zur Verfügung. Diese reichen von wiederholten endoskopischen Resektionen über eine risikoadaptierte adjuvante Instillationstherapie bis hin zur RZ, die darüber hinaus Bestandteil eines multimodalen kurativen Konzeptes sein kann. Zum 50-jährigen Jubiläum der Aktuellen Urologie geben wir einen Überblick über die wichtigsten Fortschritte seit dem Jahr 1969 und die aktuellen Entwicklungen bei der operativen Therapie des Harnblasenkarzinoms. Moderne endoskopische Bildgebungsverfahren („enhanced cystoscopy“) und das molekulare Subtyping verbessern die Risikoeinschätzung. Außerdem bestehen erste Erfahrungen mit der roboterassistierten RZ, neue Tendenzen zur Standardisierung von Techniken, ein verbessertes perioperatives Management sowie Initiativen zur Qualitätsmessung von funktionellem und onkologischem Outcome. All diese Entwicklungen werden die Lebensqualität und die Heilungsraten von Patienten mit einem Harnblasenkarzinom weiter verbessern.
Rheumatologie und Hepatologie: Diagnostik und Therapie von
autoimmunen Lebererkrankungen
Authors: Zipprich Alexander 
Published: May 2019

ZusammenfassungUnter autoimmunen Lebererkrankungen werden im klassischen Sinne 3 verschiedene
Entitäten, die Autoimmune Hepatitis (AIH), die Primär biliäre Cholangitis (PBC)
und die Primär sklerosierende Cholangitis (PSC) verstanden. Der nachfolgende
Übersichtartikel fokusiert auf die Diagnostik und die Therapie dieser 3
autoimmunen Lebererkrankungen und gibt eine Übersicht zu möglichen zusätzlich
assoziierten Autoimmunerkrankungen.
Impact of a Two-Filter Cerebral Embolic Protection Device on the Complexity and Risk of Transcatheter Aortic Valve Replacement
Authors: Voss Stephanie , Deutsch Marcus-André , Schechtl Johanna , Erlebach Magdalena , Sideris Konstantinos , Lange Rüdiger , Bleiziffer Sabine 
Published: May 2019

Abstract
Background There is a growing use of cerebral protection devices in patients undergoing transcatheter aortic valve replacement (TAVR). We aimed to analyze if the use of these devices itself has an impact on the complexity and the risk of TAVR.
Methods Between February 2016 and July 2017, 391 patients underwent transfemoral TAVR with Medtronic CoreValve Evolut R (n = 196) or Edwards Sapien 3 (n = 195). In 39 patients, the Claret Sentinel™ embolic protection device (CS-EPD) was used. Prospectively collected data were retrospectively analyzed, comparing fluoroscopy/operation time, amount of contrast used, vascular events, and postprocedural renal function in TAVR patients with (n = 39) and without (n = 352) CS-EPD.
Results The CS-EPD was placed through the right radial (n = 35) or brachial (n = 4) artery. Procedural success rate defined as correct deployment and retraction of both filters was 94.9%. No device-related vascular complications occurred. TAVR patients with CS-EPD showed a significantly higher total operation time, total fluoroscopy time, and amount of used contrast (85.4 ± 39.3 vs. 64 ± 29.8 minutes, p = 0.002; 20.7 ± 9.3 vs. 13.7 ± 7 minutes, p ≤ 0.001; 133.7 ± 42.6 vs. 109.7 ± 44.5 mL, p = 0.001). Comparing the initial third of patients receiving a CS-EPD with the last third of CS-EPD cases, procedural time had decreased significantly (102.5 ± 34.9 vs. 67 ± 11.9; p = 0.002). There were no differences in postprocedural renal failure (p = 0.80).
Conclusion Our data add evidence that the application of the CS-EPD is not associated with an additional risk for the patient. Although procedural time and amount of contrast are still higher when using the CS-EPD, there were no device-related complications or increased incidence of renal failure.
The association of grip strength with health outcomes does not differ if grip strength is used in absolute or relative terms: a prospective cohort study
Authors: Ho Frederick K W , Celis-Morales Carlos A , Petermann-Rocha Fanny , Sillars Anne , Welsh Paul , Welsh Claire , Anderson Jana , Lyall Donald M , Mackay Daniel F , Sattar Naveed , Gill Jason M R , Pell Jill P , Gray Stuart R 
Published: May 2019

AbstractBackgroundhigher grip strength is associated with better health outcomes. The optimal way to report grip strength (i.e. absolute vs. relative) for prediction, however, remains to be established.Methodsin participants (aged 37–73 at baseline) from the UK Biobank, we examined the associations of grip strength, expressed in absolute terms (kilograms) and relative to anthropometric variables, with mortality and disease incidence, after exclusion of the first 2 years of follow-up, and compared risk predictions scores of handgrip strength when differentially expressed.Resultsof the 356 721 participants included in the analysis 6,234 died (1.7%) and 4,523 developed CVD (1.3%) over a mean follow-up of 5.0 years (ranging from 3.3 to 7.8) for mortality and 4.1 years (ranging from 2.4 to 7.0) for disease incidence data. As expected, baseline higher grip strength was associated with lower risk of all-cause and cause specific mortality and incidence. These associations did not meaningfully differ when grip-strength was expressed in absolute terms, vs. relative to height, weight, fat-free mass, BMI, fat-free mass index and fat-free mass, or as z-scores. Similarly the different ways of expressing grip strength had little effect on the ability of grip strength to improve risk prediction, based on C-index change, of an office-based risk score.Conclusionsthe ability of grip strength to predict mortality is not altered by changing how it is expressed.
How demographic processes shape animal social networks
Authors: Shizuka Daizaburo , Johnson Allison E 
Published: May 2019

Abstract
Demographic processes play a key role in shaping the patterns of social relations among individuals in a population. Social network analysis is a powerful quantitative tool for assessing the social structure formed by associations between individuals. However, demographic processes are rarely accounted for in such analyses. Here, we summarize how the structure of animal social networks is shaped by the joint effects of social behavior and turnover of individuals and suggest how a deeper understanding of these processes can open new, exciting avenues for research. Death or dispersal can have the direct effect of removing an individual and all its social connections, and can also have indirect effects, spurring changes in the distribution of social connections between remaining individuals. Recruitment and integration of juveniles and immigrant into existing social networks are critical to the emergence and persistence of social network structure. Together, these behavioral responses to loss and gain of social partners may impact how societies respond to seasonal or catastrophic turnover events. The fitness consequences of social position (e.g., survival and reproductive rates) may also create feedback between the social network structure and demography. Understanding how social structure changes in response to turnover of individuals requires further integration between long-term field studies and network modeling methods. These efforts will likely yield new insights into the connections between social networks and life history, ecological change, and evolutionary dynamics.
A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data
Authors: Chen Moliang , Ji Guoli , Fu Hongjuan , Lin Qianmin , Ye Congting , Ye Wenbin , Su Yaru , Wu Xiaohui 
Published: May 2019

AbstractAlternative polyadenylation (APA) has been implicated to play an important role in post-transcriptional regulation by regulating mRNA abundance, stability, localization and translation, which contributes considerably to transcriptome diversity and gene expression regulation. RNA-seq has become a routine approach for transcriptome profiling, generating unprecedented data that could be used to identify and quantify APA site usage. A number of computational approaches for identifying APA sites and/or dynamic APA events from RNA-seq data have emerged in the literature, which provide valuable yet preliminary results that should be refined to yield credible guidelines for the scientific community. In this review, we provided a comprehensive overview of the status of currently available computational approaches. We also conducted objective benchmarking analysis using RNA-seq data sets from different species (human, mouse and Arabidopsis) and simulated data sets to present a systematic evaluation of 11 representative methods. Our benchmarking study showed that the overall performance of all tools investigated is moderate, reflecting that there is still lot of scope to improve the prediction of APA site or dynamic APA events from RNA-seq data. Particularly, prediction results from individual tools differ considerably, and only a limited number of predicted APA sites or genes are common among different tools. Accordingly, we attempted to give some advice on how to assess the reliability of the obtained results. We also proposed practical recommendations on the appropriate method applicable to diverse scenarios and discussed implications and future directions relevant to profiling APA from RNA-seq data.
Data imbalance in CRISPR off-target prediction
Authors: Gao Yuli , Chuai Guohui , Yu Weichuan , Qu Shen , Liu Qi 
Published: May 2019

Abstract
For genome-wide CRISPR off-target cleavage sites (OTS) prediction, an important issue is data imbalance—the number of true OTS recognized by whole-genome off-target detection techniques is much smaller than that of all possible nucleotide mismatch loci, making the training of machine learning model very challenging. Therefore, computational models proposed for OTS prediction and scoring should be carefully designed and properly evaluated in order to avoid bias. In our study, two tools are taken as examples to further emphasize the data imbalance issue in CRISPR off-target prediction to achieve better sensitivity and specificity for optimized CRISPR gene editing. We would like to indicate that (1) the benchmark of CRISPR off-target prediction should be properly evaluated and not overestimated by considering data imbalance issue; (2) incorporation of efficient computational techniques (including ensemble learning and data synthesis techniques) can help to address the data imbalance issue and improve the performance of CRISPR off-target prediction. Taking together, we call for more efforts to address the data imbalance issue in CRISPR off-target prediction to facilitate clinical utility of CRISPR-based gene editing techniques.
Modeling local dependence in latent vector autoregressive models
Authors: Tran Trung Dung , Lesaffre Emmanuel , Verbeke Geert , Duyck Joke 
Published: May 2019

SummaryWe propose a Bayesian latent vector autoregressive (LVAR) model to analyze multivariate longitudinal data of binary and ordinal variables (items) as a function of a small number of continuous latent variables. We focus on the evolution of the latent variables while taking into account the correlation structure of the responses. Often local independence is assumed in this context. Local independence implies that, given the latent variables, the responses are assumed mutually independent cross-sectionally and longitudinally. However, in practice conditioning on the latent variables may not remove the dependence of the responses. We address local dependence by further conditioning on item-specific random effects. A simulation study shows that wrongly assuming local independence may give biased estimates for the regression coefficients of the LVAR process as well as the item-specific parameters. Novel features of our proposal include (i) correcting biased estimates of the model parameters, especially the regression coefficients of the LVAR process, obtained when local dependence is ignored and (ii) measuring the magnitude of local dependence. We applied our model on data obtained from a registry on the elderly population in Belgium. The purpose was to examine the values of oral health information on top of general health information.
Gaussian process regression for survival time prediction with genome-wide gene expression
Authors: Molstad Aaron J , Hsu Li , Sun Wei 
Published: May 2019

Summary
Predicting the survival time of a cancer patient based on his/her genome-wide gene expression remains a challenging problem. For certain types of cancer, the effects of gene expression on survival are both weak and abundant, so identifying non-zero effects with reasonable accuracy is difficult. As an alternative to methods that use variable selection, we propose a Gaussian process accelerated failure time model to predict survival time using genome-wide or pathway-wide gene expression data. Using a Monte Carlo expectation–maximization algorithm, we jointly impute censored log-survival time and estimate model parameters. We demonstrate the performance of our method and its advantage over existing methods in both simulations and real data analysis. The real data that we analyze were collected from 513 patients with kidney renal clear cell carcinoma and include survival time, demographic/clinical variables, and expression of more than 20 000 genes. In addition to the right-censored survival time, our method can also accommodate left-censored or interval-censored outcomes; and it provides a natural way to combine multiple types of high-dimensional -omics data. An R package implementing our method is available in the Supplementary material available at Biostatistics online.
Prefrontal Computation as Active Inference
Authors: Parr Thomas , Rikhye Rajeev Vijay , Halassa Michael M , Friston Karl J 
Published: May 2019

Abstract
The prefrontal cortex is vital for a range of cognitive processes, including working memory, attention, and decision-making. Notably, its absence impairs the performance of tasks requiring the maintenance of information through a delay period. In this paper, we formulate a rodent task—which requires maintenance of delay-period activity—as a Markov decision process and treat optimal task performance as an (active) inference problem. We simulate the behavior of a Bayes optimal mouse presented with 1 of 2 cues that instructs the selection of concurrent visual and auditory targets on a trial-by-trial basis. Formulating inference as message passing, we reproduce features of neuronal coupling within and between prefrontal regions engaged by this task. We focus on the micro-circuitry that underwrites delay-period activity and relate it to functional specialization within the prefrontal cortex in primates. Finally, we simulate the electrophysiological correlates of inference and demonstrate the consequences of lesions to each part of our in silico prefrontal cortex. In brief, this formulation suggests that recurrent excitatory connections—which support persistent neuronal activity—encode beliefs about transition probabilities over time. We argue that attentional modulation can be understood as the contextualization of sensory input by these persistent beliefs.
Greater Weight Gain in Treatment-naive Persons Starting Dolutegravir-based Antiretroviral Therapy
Authors: Bourgi Kassem , Rebeiro Peter F , Turner Megan , Castilho Jessica L , Hulgan Todd , Raffanti Stephen P , Koethe John R , Sterling Timothy R 
Published: May 2019

Abstract

Background
Recent studies have reported weight gain in virologically suppressed persons living with human immunodeficiency virus (PLWH) switched from older antiretroviral therapy (ART) to newer integrase strand transfer inhibitor (INSTI)–based regimens. In this study, we investigated whether weight gain differs among treatment-naive PLWH starting INSTI-based regimens compared to other ART regimens.

Methods
Adult, treatment-naive PLWH in the Vanderbilt Comprehensive Care Clinic cohort initiating INSTI-, protease inhibitor (PI)–, and nonnucleoside reverse transcriptase inhibitor (NNRTI)–based ART between January 2007 and June 2016 were included. We used multivariable linear mixed-effects models to generate marginal predictions of weights over time, adjusting for baseline clinical and demographic characteristics. We used restricted cubic splines to relax linearity assumptions and bootstrapping to generate 95% confidence intervals.

Results
Among 1152 ART-naive PLWH, 351 initiated INSTI-based regimens (135 dolutegravir, 153 elvitegravir, and 63 raltegravir), 86% were male, and 49% were white. At ART initiation, median age was 35 years, body mass index was 25.1 kg/m2, and CD4+ T-cell count was 318 cells/μL. Virologic suppression at 18 months was similar between different ART classes. At all examined study time points, weight gain was highest among PLWH starting dolutegravir. At 18 months, PLWH on dolutegravir gained 6.0 kg, compared to 2.6 kg for NNRTIs (P &lt; .05), and 0.5 kg for elvitegravir (P &lt; .05). PLWH starting dolutegravir also gained more weight at 18 months compared to raltegravir (3.4 kg) and PIs (4.1 kg), though these differences were not statistically significant.

Conclusions
Treatment-naive PLWH starting dolutegravir-based regimens gained significantly more weight at 18 months than those starting NNRTI-based and elvitegravir-based regimens.
2019 HRS/EHRA/APHRS/LAHRS focused update to 2015 expert consensus statement on optimal implantable cardioverter-defibrillator programming and testing
Authors: Stiles Martin K , Fauchier Laurent , Morillo Carlos A , Wilkoff Bruce L ,   ESC Scientific Document Group, Boveda Serge , Gold Michael R , Keegan Roberto , Kutyifa Valentina , Lau Chu-Pak , McGuire Mark A , Mulpuru Siva K , Slotwiner David J , Uribe William 
Published: May 2019

Abstract
The 2015 HRS/EHRA/APHRS/SOLAECE Expert Consensus Statement on Optimal Implantable Cardioverter-Deﬁbrillator Programming and Testing provided guidance on bradycardia programming, tachycardia detection, tachycardia therapy, and defibrillation testing for implantable cardioverter-deﬁbrillator (ICD) patient treatment. The 32 recommendations represented the consensus opinion of the writing group, graded by Class of Recommendation and Level of Evidence. In addition, Appendix B provided manufacturer-specific translations of these recommendations into clinical practice consistent with the recommendations within the parent document. In some instances, programming guided by quality evidence gained from studies performed in devices from some manufacturers was translated such that this programming was approximated in another manufacturer’s ICD programming settings. The authors found that the data, although not formally tested, were strong, consistent, and generalizable beyond the specific manufacturer and model of ICD. As expected, because these recommendations represented strategic choices to balance risks, there have been reports in which adverse outcomes were documented with ICDs programmed to Appendix B recommendations. The recommendations have been reviewed and updated to minimize such adverse events. Notably, patients who do not receive unnecessary ICD therapy are not aware of being spared potential harm, whereas patients in whom their ICD failed to treat life-threatening arrhythmias have their event recorded in detail. The revised recommendations employ the principle that the randomized trials and large registry data should guide programming more than anecdotal evidence. These recommendations should not replace the opinion of the treating physician who has considered the patient’s clinical status and desired outcome via a shared clinical decision-making process.