bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symmetry-adapted decomposition of tensor operators and the visualization of coupled spin systems
Authors: Leiner David , Zeier Robert , Glaser Steffen J 
Published: May 2020

Abstract
We study the representation and visualization of finite-dimensional, coupled quantum systems. To establish a generalized Wigner representation, multi-spin operators are decomposed into a symmetry-adapted tensor basis and are mapped to multiple spherical plots that are each assembled from linear combinations of spherical harmonics. We explicitly determine the corresponding symmetry-adapted tensor basis for up to six coupled spins 1/2 (qubits) using a first step that relies on a Clebsch–Gordan decomposition and a second step which is implemented with two different approaches based on explicit projection operators and coefficients of fractional parentage. The approach based on explicit projection operators is currently only applicable for up to four spins 1/2. The resulting generalized Wigner representation is illustrated with various examples for the cases of four to six coupled spins 1/2. We also treat the case of two coupled spins with arbitrary spin numbers (qudits) not necessarily equal to 1/2 and highlight a quantum system of a spin 1/2 coupled to a spin 1 (qutrit). Our work offers a much more detailed understanding of the symmetries appearing in coupled quantum systems.
Effect of aridity on species assembly in gypsum drylands: a response mediated by the soil affinity of species
Authors: Luzuriaga Arantzazu L , Ferrandis Pablo , Flores Joel , Escudero Adrián 
Published: May 2020

AbstractPrevious studies found that plant communities on infertile soils are relatively resistant to climatic variation due to stress tolerance adaptations. However, the species assemblies in gypsum soil habitats require further investigation. Thus, we considered the following questions. (1) Do harsher arid conditions determine the characteristics of the species that form plant assemblages? (2) Is the selection of the species that assemble in arid conditions mediated by their ability to grow on gypsum soils? (3) Is the selection of species that assemble in harsher conditions related to phylogenetically conserved functional traits? Perennial plant communities were analysed in 89 gypsum-soil sites along a 400 km climate gradient from the central to southeastern Iberian Peninsula. Each local assemblage was analysed in 30 × 30 m plots and described based on taxonomic, functional (soil plant affinity) and phylogenetic parameters. The mean maximum temperatures in the hottest month, mean annual precipitation and their interaction terms were used as surrogates for the aridity conditions in generalized linear models. In the hottest locations, the gypsophily range narrowed and the mean gypsophily increased at the community level, thereby suggesting the filtering of species and the dominance of soil specialists in the actual plant assemblies. Drier sites had higher taxonomic diversity. The species that formed the perennial communities were close in evolutionary terms at the two ends of the aridity gradient. The mean maximum temperatures in the hottest month had the main abiotic filtering effect on perennial plant communities, which was mediated by the ability of species to grow on gypsum soils, and thus gypsum specialists dominated the species assemblies in the hottest locations. In contrast, the perennial communities on gypsum soils were relatively resistant to changes in precipitation. Our findings suggest that the warmer environmental conditions predicted by global change models will favour gypsum specialists over generalists.
Group Belief: Lessons from Lies and Bullshit
Authors: Lackey I—Jennifer 
Published: May 2020

Abstract
Groups and other sorts of collective entities are frequently said to believe things. Sarah Huckabee Sanders, for instance, was asked by reporters at White House press conferences whether the Trump administration ‘believes in climate change’ or ‘believes that slavery is wrong’. Similarly, it is said on the website of the Aclu of Illinois that the organization ‘firmly believes that rights should not be limited based on a person’s sexual orientation or gender identity’. A widespread philosophical view is that belief on the part of a group’s members is neither necessary nor sufficient for group belief. In other words, groups are said to be able to believe that p even when not a single individual member of the group believes that p. In this paper, I challenge this view by focusing on two phenomena that have been entirely ignored in the literature: group lies and group bullshit. I show that when group belief is understood in terms of actions over which group members have voluntarily control, as is standardly thought, paradigmatic instances of a group lying or bullshitting end up counting as a group believing. Thus we need to look elsewhere for an adequate account of group belief.
Comparison of high-throughput single-cell RNA sequencing data processing pipelines
Authors: Gao Mingxuan , Ling Mingyi , Tang Xinwei , Wang Shun , Xiao Xu , Qiao Ying , Yang Wenxian , Yu Rongshan 
Published: May 2020

Abstract
With the development of single-cell RNA sequencing (scRNA-seq) technology, it has become possible to perform large-scale transcript profiling for tens of thousands of cells in a single experiment. Many analysis pipelines have been developed for data generated from different high-throughput scRNA-seq platforms, bringing a new challenge to users to choose a proper workflow that is efficient, robust and reliable for a specific sequencing platform. Moreover, as the amount of public scRNA-seq data has increased rapidly, integrated analysis of scRNA-seq data from different sources has become increasingly popular. However, it remains unclear whether such integrated analysis would be biassed if the data were processed by different upstream pipelines. In this study, we encapsulated seven existing high-throughput scRNA-seq data processing pipelines with Nextflow, a general integrative workflow management framework, and evaluated their performance in terms of running time, computational resource consumption and data analysis consistency using eight public datasets generated from five different high-throughput scRNA-seq platforms. Our work provides a useful guideline for the selection of scRNA-seq data processing pipelines based on their performance on different real datasets. In addition, these guidelines can serve as a performance evaluation framework for future developments in high-throughput scRNA-seq data processing.
RNCE: network integration with reciprocal neighbors contextual encoding for multi-modal drug community study on cancer targets
Authors: Chen Junyi , Wong Ka-Chun 
Published: May 2020

Abstract
Mining drug targets and mechanisms of action (MoA) for novel anticancer drugs from pharmacogenomic data is a path to enhance the drug discovery efficiency. Recent approaches have successfully attempted to discover targets/MoA by characterizing drug similarities and communities with integrative methods on multi-modal or multi-omics drug information. However, the sparse and imbalanced community size structure of the drug network is seldom considered in recent approaches. Consequently, we developed a novel network integration approach accounting for network structure by a reciprocal nearest neighbor and contextual information encoding (RNCE) approach. In addition, we proposed a tailor-made clustering algorithm to perform drug community detection on drug networks. RNCE and spectral clustering are proved to outperform state-of-the-art approaches in a series of tests, including network similarity tests and community detection tests on two drug databases. The observed improvement of RNCE can contribute to the field of drug discovery and the related multi-modal/multi-omics integrative studies. Availabilityhttps://github.com/WINGHARE/RNCE.
Wildfire-Driven Forest Conversion in Western North American Landscapes
Authors: Coop Jonathan D , Parks Sean A , Stevens-Rumann Camille S , Crausbay Shelley D , Higuera Philip E , Hurteau Matthew D , Tepley Alan , Whitman Ellen , Assal Timothy , Collins Brandon M , Davis Kimberley T , Dobrowski Solomon , Falk Donald A , Fornwalt Paula J , Fulé Peter Z , Harvey Brian J , Kane Van R , Littlefield Caitlin E , Margolis Ellis Q , North Malcolm , Parisien Marc-André , Prichard Susan , Rodman Kyle C 
Published: May 2020

Abstract
Changing disturbance regimes and climate can overcome forest ecosystem resilience. Following high-severity fire, forest recovery may be compromised by lack of tree seed sources, warmer and drier postfire climate, or short-interval reburning. A potential outcome of the loss of resilience is the conversion of the prefire forest to a different forest type or nonforest vegetation. Conversion implies major, extensive, and enduring changes in dominant species, life forms, or functions, with impacts on ecosystem services. In the present article, we synthesize a growing body of evidence of fire-driven conversion and our understanding of its causes across western North America. We assess our capacity to predict conversion and highlight important uncertainties. Increasing forest vulnerability to changing fire activity and climate compels shifts in management approaches, and we propose key themes for applied research coproduced by scientists and managers to support decision-making in an era when the prefire forest may not return.
Differential Generation of Saccade, Fixation, and Image-Onset Event-Related Potentials in the Human Mesial Temporal Lobe
Authors: Katz Chaim N , Patel Kramay , Talakoub Omid , Groppe David , Hoffman Kari , Valiante Taufik A 
Published: May 2020

Abstract
Event-related potentials (ERPs) are a commonly used electrophysiological signature for studying mesial temporal lobe (MTL) function during visual memory tasks. The ERPs associated with the onset of visual stimuli (image-onset) and eye movements (saccades and fixations) provide insights into the mechanisms of their generation. We hypothesized that since eye movements and image-onset provide MTL structures with salient visual information, perhaps they both engage similar neural mechanisms. To explore this question, we used intracranial electroencephalographic data from the MTLs of 11 patients with medically refractory epilepsy who participated in a visual search task. We characterized the electrophysiological responses of MTL structures to saccades, fixations, and image-onset. We demonstrated that the image-onset response is an evoked/additive response with a low-frequency power increase. In contrast, ERPs following eye movements appeared to arise from phase resetting of higher frequencies than the image-onset ERP. Intriguingly, this reset was associated with saccade onset and not termination (fixation), suggesting it is likely the MTL response to a corollary discharge, rather than a response to visual stimulation. We discuss the distinct mechanistic underpinnings of these responses which shed light on the underlying neural circuitry involved in visual memory processing.
Investigation of Psychiatric and Neuropsychological Correlates of Default Mode Network and Dorsal Attention Network Anticorrelation in Children
Authors: Owens Max M , Yuan DeKang , Hahn Sage , Albaugh Matthew , Allgaier Nicholas , Chaarani Bader , Potter Alexandra , Garavan Hugh 
Published: May 2020

Abstract
The default mode network (DMN) and dorsal attention network (DAN) demonstrate an intrinsic “anticorrelation” in healthy adults, which is thought to represent the functional segregation between internally and externally directed thought. Reduced segregation of these networks has been proposed as a mechanism for cognitive deficits that occurs in many psychiatric disorders, but this association has rarely been tested in pre-adolescent children. The current analysis used data from the Adolescent Brain Cognitive Development study to examine the relationship between the strength of DMN/DAN anticorrelation and psychiatric symptoms in the largest sample to date of 9- to 10-year-old children (N = 6543). The relationship of DMN/DAN anticorrelation to a battery of neuropsychological tests was also assessed. DMN/DAN anticorrelation was robustly linked to attention problems, as well as age, sex, and socioeconomic factors. Other psychiatric correlates identified in prior reports were not robustly linked to DMN/DAN anticorrelation after controlling for demographic covariates. Among neuropsychological measures, the clearest correlates of DMN/DAN anticorrelation were the Card Sort task of executive function and cognitive flexibility and the NIH Toolbox Total Cognitive Score, although these did not survive correction for socioeconomic factors. These findings indicate a complicated relationship between DMN/DAN anticorrelation and demographics, neuropsychological function, and psychiatric problems.
Comparison between lung perfusion scan and single-photon emission computed tomography/computed tomography for predicting postoperative lung function after pulmonary resection in patients with borderline lung function
Authors: Na Kwon Joong , Park Samina , Lee Hyun Joo , Park In Kyu , Kang Chang Hyun , Kim Young Tae 
Published: May 2020

Abstract

OBJECTIVES

We compared the usefulness of single-photon emission computed tomography/computed tomography (SPECT/CT) and lung perfusion scintigraphy (LPS) for predicting postoperative lung function by comparing patients with borderline lung function.

METHODS
A total of 274 patients who underwent simultaneous LPS and SPECT/CT and had a forced expiratory volume in 1 s (FEV1) or diffusing capacity for carbon monoxide (DLCO) under 80% were included. The % uptake by LPS was calculated by the posterior-oblique method. The concordance and difference of the % uptake, predicted postoperative (ppo) FEV1 and ppoDLCO as determined by 2 methods were evaluated. The association between ppo values and actual postoperative FEV1 and DLCO was examined. Subgroup analysis was conducted in redo-operation cases.

RESULTS
The % uptake of each lobe, except the right middle lobe, showed fair concordance (concordance correlation coefficients for right upper, middle, lower, left upper and lower lobe = 0.61, 0.37, 0.71, 0.66 and 0.69, respectively). ppoFEV1 and ppoDLCO also revealed high concordance between both methods (concordance correlation coefficient = 0.93 for ppoFEV1 and concordance correlation coefficient = 0.92 for ppoDLCO) without a significant difference (P = 0.42 for ppoFEV1; P = 0.31 for ppoDLCO). Both ppoFEV1 and ppoDLCO showed a significantly high correlation with the actual FEV1 (r = 0.77, P &lt; 0.01 for LPS, r = 0.77, P &lt; 0.01 for SPECT/CT) and DLCO (r = 0.62, P &lt; 0.01 for LPS, r = 0.62, P &lt; 0.01 for SPECT/CT). High concordance of % uptake, ppoFEV1 and ppoDLCO was present in redo-operation patients.

CONCLUSIONS
Both LPS and SPECT/CT showed high predictability for actual postoperative lung function, and LPS showed good performance to estimate ppoFEV1 and ppoDLCO with reference to SPECT/CT, even in redo-operation cases.
Pregnancies, ventricular arrhythmias, and substrate progression in women with arrhythmogenic right ventricular cardiomyopathy in the Nordic ARVC Registry
Authors: Platonov Pyotr G , Castrini Anna I , Svensson Anneli , Christiansen Morten K , Gilljam Thomas , Bundgaard Henning , Madsen Trine , Heliö Tiina , Christensen Alex H , Åström Meriam Aneq , Carlson Jonas , Edvardsen Thor , Jensen Henrik K , Haugaa Kristina H , Svendsen Jesper H 
Published: May 2020

Abstract

Aims
Women with arrhythmogenic right ventricular cardiomyopathy (ARVC) are at relatively lower risk of ventricular arrhythmias (VAs) than men, but the physical burden associated with pregnancy on VA risk remains insufficiently studied. We aimed to assess the risk of VA in relation to pregnancies in women with ARVC.

Methods and results
We included 199 females with definite ARVC (n = 121) and mutation-positive family members without ascertained ARVC diagnosis (n = 78), of whom 120 had at least one childbirth. Ventricular arrhythmia-free survival after the latest childbirth was compared between women with one (n = 20), two (n = 67), and three or more (n = 37) childbirths. Cumulative probability of VA for each pregnancy (n = 261) was assessed from conception through 2 years after childbirth and compared between those pregnancies that occurred before (n = 191) or after (n = 19) ARVC diagnosis and in mutation-positive family members (n = 51). The nulliparous women had lower median age at ARVC diagnosis (38 vs. 42 years, P &lt; 0.001) and first VA (22 vs. 41 years, P &lt; 0.001). Ventricular arrhythmia-free survival after the latest childbirth was not related to the number of pregnancies. No pregnancy-related VA was reported among the family members. Women who gave birth after ARVC diagnosis had elevated risk of VA postpartum (hazard ratio 13.74, 95% confidence interval 2.9–63, P = 0.001), though only two events occurred during pregnancies.

Conclusion
In women with ARVC, pregnancy was uneventful for the overwhelming majority and the number of prior completed pregnancies was not associated with VA risk. Pregnancy-related VA was primarily related to the phenotypical severity rather than pregnancy itself.
Long-term outcome of patients with invasive electrophysiology procedure-related cardiac tamponade
Authors: von Olshausen Gesa , Bourke Tara , Schwieler Jonas , Drca Nikola , Bastani Hamid , Tapanainen Jari , Saluveer Ott , Benson Lina , Goedel Alexander , Kennebäck Göran , Insulander Per , Jensen-Urstad Mats , Braunschweig Frieder 
Published: May 2020

Abstract

Aims
Iatrogenic cardiac tamponades are a rare but dreaded complication of invasive electrophysiology procedures (EPs). Their long-term impact on clinical outcomes is unknown. This study analysed the risk of death or serious cardiovascular events in patients suffering from EP-related cardiac tamponade requiring pericardiocentesis during long-term follow-up.

Methods and results
Out of 19 997 invasive EPs at the Karolinska University Hospital between January 1998 and September 2018, all patients with EP-related periprocedural cardiac tamponade were identified (n = 60) and matched (1:3 ratio) to a control group (n = 180). After a follow-up of 5 years, the composite primary endpoint — death from any cause, acute myocardial infarction, transitory ischaemic attack (TIA)/stroke, and hospitalization for heart failure — occurred in significantly more patients in the tamponade than in the control group [12 patients (20.0%) vs. 19 patients (10.6%); hazard ratio (HR) 2.53 (95% confidence interval, CI 1.15–5.58); P = 0.021]. This was mainly driven by a higher incidence of TIA/stroke in the tamponade than in the control group [HR 3.75 (95% CI 1.01–13.97); P = 0.049]. Death from any cause, acute myocardial infarction, and hospitalization for heart failure did not show a significant difference between the groups. Hospitalization for pericarditis occurred in significantly more patients in the tamponade than in the control group [HR 36.0 (95% CI 4.68–276.86); P = 0.001].

Conclusion
Patients with EP-related cardiac tamponade are at higher risk for cerebrovascular events during the first 2 weeks and hospitalization for pericarditis during the first months after index procedure. Despite the increased risk for early complications tamponade patients have a good long-term prognosis without increased risk for mortality or other serious cardiovascular events.
Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties
Authors: Rejili Mokhtar , BenAbderrahim Mohamed Ali , Mars Mohamed , Sherrier Janine Darla 
Published: May 2020

ABSTRACT
Phylogenetically diverse rhizobial strains endemic to Tunisia were isolated from symbiotic nodules of Lotus creticus, growing in different arid extremophile geographical regions of Tunisia, and speciated using multiloci-phylogenetic analysis as Neorhizobium huautlense (LCK33, LCK35, LCO42 and LCO49), Ensifer numidicus (LCD22, LCD25, LCK22 and LCK25), Ensifer meliloti (LCK8, LCK9 and LCK12) and Mesorhizobium camelthorni (LCD11, LCD13, LCD31 and LCD33). In addition, phylogenetic analyses revealed eight additional strains with previously undescribed chromosomal lineages within the genera Ensifer (LCF5, LCF6 and LCF8),Rhizobium (LCF11, LCF12 and LCF14) and Mesorhizobium (LCF16 and LCF19). Analysis using the nodC gene identified five symbiovar groups, four of which were already known. The remaining group composed of two strains (LCD11 and LCD33) represented a new symbiovar of Mesorhizobium camelthorni, which we propose designating as sv. hedysari. Interestingly, we report that soil properties drive and structure the symbiosis of L. creticus and its rhizobia.
The impact ofCUP1gene copy-number and XVI-VIII/XV-XVI translocations on copper and sulfite tolerance in vineyardSaccharomyces cerevisiaestrain populations
Authors: Crosato Giulia , Nadai Chiara , Carlot Milena , Garavaglia Juliano , Ziegler Denise Righetto , Rossi Rochele Cassanta , De Castilhos Juliana , Campanaro Stefano , Treu Laura , Giacomini Alessio , Corich Viviana 
Published: May 2020

ABSTRACTIn wine production, sulfites are widely used as antimicrobials and antioxidants, whereas copper is associated with fungicides and wine fining treatments. Therefore, wine yeasts are constantly exposed to these agents. Copper tolerance is related to the copy number of the CUP1 gene, encoding for a metallothionein involved in copper detoxification. In wine yeasts, sulfite resistance mainly depends on the presence of the translocation t(XVI;VIII) in the promoter region of the SSU1 gene. This gene encodes for a plasma membrane sulfite pump involved in sulfite metabolism and detoxification. Recently, a new translocation, t(XVI;VIII), was identified. In this work, 253 Saccharomyces cerevisiae strains, representing three vineyard populations from two different continents, were analyzed, along with 20 industrial starters. Copper and sulfites tolerance as well as distribution of CUP1 gene copy-number, t(XVI;VIII)and t(XVI;XV) of SSU1 gene were studied to evaluate the impact of these genomic variations on population phenotypes. The CUP1 gene copy-number was found to be highly variable, ranging from zero to 79 per strain. Moreover it differently impacted the copper tolerance in the populations of the two continents. The diffusion of t(XVI;VIII) and, for the first time, t(XVI;XV) was determined in the three vineyard populations. The correlation between the presence of the translocation and strain sulfite tolerance levels was significant only for the t(XVI;VIII).