bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing data discovery with MetaSeek
Authors: Hoarfrost Adrienne , Brown Nick , Brown C Titus , Arnosti Carol 
Published: June 2019

Abstract

Summary
Sequencing data resources have increased exponentially in recent years, as has interest in large-scale meta-analyses of integrated next-generation sequencing datasets. However, curation of integrated datasets that match a user’s particular research priorities is currently a time-intensive and imprecise task. MetaSeek is a sequencing data discovery tool that enables users to flexibly search and filter on any metadata field to quickly find the sequencing datasets that meet their needs. MetaSeek automatically scrapes metadata from all publicly available datasets in the Sequence Read Archive, cleans and parses messy, user-provided metadata into a structured, standard-compliant database and predicts missing fields where possible. MetaSeek provides a web-based graphical user interface and interactive visualization dashboard, as well as a programmatic API to rapidly search, filter, visualize, save, share and download matching sequencing metadata.

Availability and implementation
The MetaSeek online interface is available at https://www.metaseek.cloud/. The MetaSeek database can also be accessed via API to programmatically search, filter and download all metadata. MetaSeek source code, metadata scrapers and documents are available at https://github.com/MetaSeek-Sequencing-Data-Discovery/metaseek/.
Evolutionary and ecological forces underlying ontogenetic loss of decoy coloration
Authors: Watson Charles M , Degon Zachariah , Krogman William , Cox Christian L 
Published: June 2019

AbstractPredator-based selection has resulted in the repeated evolution of a variety of antipredator traits. Despite the effectiveness of these traits, some species experience shifts or even complete loss of antipredator traits during development. The evolutionary forces that favour such a transition are poorly understood. We sought to comprehend the role of predator-based selection and organismal factors underlying developmental loss of antipredator traits by focusing on decoy coloration in skink lizards. To this end, we studied the ontogenetic loss of decoy tail coloration in three Nearctic skink species. We performed natural history collection surveys and clay-model studies on predation to determine the organismal determinants of decoy coloration (body size and energy content of the tail) and predation based upon size and decoy coloration. We found that decoy coloration was lost during development at a similar size in all three species. Although predation rates on juvenile models were similar for both uniform brown and decoy models, predation rates on adult models with decoy coloration were much higher than those on non-decoy adult models. Overall, our results suggest that predator-based selection is an important factor driving the ontogenetic loss of decoy coloration at similar sizes across these species and might be generalizable to other antipredator traits.
Jumping through the hoops: the challenges of daffodil (Narcissus) classification
Authors: Könyves Kálmán , David John , Culham Alastair 
Published: June 2019

AbstractHoop-petticoat daffodils are a morphologically congruent group comprised of two distinct lineages in molecular phylogenetic trees of Narcissus. It is possible that the morphological similarity is a product of both historic and current low-level gene flow between these lineages. For the first time, we report population sampling from across the entire range of distribution covering the Iberian Peninsula and Morocco. In total, 455 samples were collected from 59 populations. Plastid DNA sequences of matK and ndhF were generated alongside 11 microsatellite loci to permit comparison between plastid and nuclear lineage histories. The plastid DNA phylogenetic tree was highly congruent with previous molecular studies and supported the recognition of these two lineages of hoop-petticoat daffodils as separate sections. Assignment of samples to sections sometimes differed between plastid DNA and (nuclear) microsatellite data. In these cases, the taxa had previously been the focus of dissent in taxonomic placement based on morphology. These discrepancies could be explained by hybridization and introgression among the two lineages during the evolution of hoop-petticoat daffodils, and shows that placement of species in sections is dependent on the source of data used. This study underlines the complex evolutionary history of Narcissus and highlights the discrepancies between floral morphology and phylogeny, which provides a continuing challenge for the systematics of Narcissus.
Patient-reported outcome measures as a new application in the Swedish Renal Registry: health-related quality of life through RAND-36
Authors: Pagels Agneta A , Stendahl Maria , Evans Marie 
Published: June 2019

AbstractBackgroundAlthough patient-reported outcome measures (PROMs) are gaining increased interest in developing health care quality and are a useful tool in person-centered care, their use in routine care is still limited. The aim of this study is to describe the implementation and initial results of PROMs via the Swedish Renal Registry (SRR) on a national level.MethodsAfter testing and piloting the electronic PROM application, nationwide measures were carried out in 2017 for completing the RAND-36 questionnaire online or by paper in a wide range of chronic kidney disease (CKD) patients (Stages 3–5, dialysis and transplantation) through the SRR. Cross-sectional results during the first year were analyzed by descriptive statistics and stratified by treatment modality.ResultsA total of 1378 patients from 26 of 68 renal units (39%) completed the questionnaire. The response rate for all participating hemodialysis units was 38.9%. The CKD patients had an impaired health profile compared with a Swedish general population, especially regarding physical functions and assessed general health (GH). Transplanted patients had the highest scores, whereas patients on dialysis treatment had the lowest scores. The youngest age group assessed their physical function higher and experienced fewer physical limitations and less bodily pain than the other age groups but assessed their GH and vitality (VT) relatively low. The oldest age group demonstrated the lowest health profile but rated their mental health higher than the other age groups. The older the patient, the smaller the difference compared with persons of the same age in the general population.ConclusionsNationwide, routine collection of PROMs is feasible in Sweden. However, greater emphasis is needed on motivating clinical staff to embrace the tool and its possibilities in executing person-centered care. CKD patients demonstrate impaired health-related quality of life, especially regarding limitations related to physical problems, GH and VT/energy/fatigue.
Risk factors for chylothorax and persistent serous effusions after congenital heart surgery
Authors: Raatz Anna , Schöber Martin , Zant Robert , Cesnjevar Robert , Rüffer André , Purbojo Ariawan , Dittrich Sven , Alkassar Muhannad 
Published: June 2019

Abstract

OBJECTIVES
This study evaluated the various risk factors for chylothorax and persistent serous effusions (>7 days) after congenital heart surgery and developed equations to calculate the probability of their occurrence.

METHODS
We performed a retrospective review of different medical databases at the University Hospital of Erlangen between January 2014 and December 2016. Full model regression analysis was used to identify risk factors, and prediction algorithms were set up to calculate probabilities. Discriminative power of the models was checked with the help of C-statistics.

RESULTS
Of 745 operations on 667 patients, 68 chylothoraxes (9.1%) and 125 persistent pleural effusions (16.8%) were diagnosed. Lowest temperature [P = 0.043; odds ratio (OR) 0.899], trisomy 21 (P = 0.001; OR 5.548), a higher vasoactive inotropic score on the day of surgery (P = 0.001; OR 1.070) and use of an assist device (P = 0.001; OR 5.779) were significantly associated with chylothorax. Risk factors for persistent serous effusions were a given or possible involvement of the aortic arch during the operation (P = 0.000; OR 3.982 and 2.905), univentricular hearts (P = 0.019; OR 2.644), a higher number of previous heart operations (P = 0.014; OR 1.436), a higher vasoactive inotropic score 72 h after surgery (P = 0.019; OR 1.091), a higher central venous pressure directly after surgery (P = 0.046; OR 1.076) and an aortic cross-clamp time >86 min (P = 0.023; OR 2.223), as well as use of an assist device (P = 0.002; OR 10.281). The prediction models for both types of effusions proved to have excellent discriminative power.

CONCLUSIONS
Persistent serous effusion is associated with a higher vasoactive inotropic score 72 h after surgery, an aortic cross-clamp time >86 min and elevated central venous pressure directly after surgery, which, in combination, potentially indicate cardiac stress. The developed logistic algorithm helps to estimate future likelihood.
Management and outcomes of patients with Crohn’s disease with first vs multiple surgeries: results from the PRACTICROHN study
Authors: Iborra Marisa , Juliá Berta , Martín Arranz Maria Dolores , Barreiro-de Acosta Manuel , Gutiérrez Ana , García-Sánchez Valle , Taxonera Carlos , Gisbert Javier P , Cea-Calvo Luis , Domènech Eugeni 
Published: June 2019

Abstract

Background
Surgery in Crohn’s disease (CD) may be associated with poor prognosis and clinical and surgical recurrence. The aim of this study was to describe and compare the post-operative management and outcomes of patients with CD who underwent first vs recurrent surgeries.

Methods
Observational study that included adult CD patients from 26 Spanish hospitals who underwent ileocolonic resection with ileocolonic anastomosis between January 2007 and December 2010. Data were retrospectively collected from the medical records.

Results
Data from 314 patients were analysed, of whom 262 (83%) underwent first surgery and 52 (17%) referred to previous CD surgeries. Baseline characteristics were similar between the two groups except for a higher rate of stricturing behavior at diagnosis among re-operated patients (P = 0.03). After surgery, a higher proportion of re-operated patients received prophylactic treatment with immunomodulators compared with patients with first surgery (P = 0.04). In re-operated patients, time to clinical recurrence was not associated with the fact of receiving or not prophylaxis, whereas, in patients with first surgery, recurrence-free survival was greater when prophylaxis was received (P = 0.03).

Conclusions
After surgery, a higher proportion of patients with previous surgeries received prophylactic treatment with immunomodulators compared with patients with first surgery. Although prophylactic treatment was beneficial for preventing clinical recurrence in patients operated on for the first time, it did not significantly reduce the risk of further recurrence in patients with previous surgeries. This suggests that effective prophylactic therapies are still needed in this subset of patients.
Three-dimensional numerical modelling of the drained/undrained transition for frequency-dependent elastic moduli and attenuation
Authors: Sun Chao , Tang Genyang , Zhao Jianguo , Zhao Liming , Long Teng , Li Min , Wang Shangxu 
Published: June 2019

SUMMARY
In fully fluid-saturated rocks, two common phenomena are documented both experimentally and theoretically for frequency-dependent elastic moduli and attenuation, that is, the drained/undrained transition and the relaxed/unrelaxed transition. When investigating these transitions with the forced oscillation method in the laboratory, it is crucial to consider the boundary differences between the laboratory and the underground. A 1-D poroelastic numerical model was previously established to describe these differences and their effects; however, the boundary conditions used in the model are actually different from the real experiment case, thus leading to inaccurate predication of the measurement results in a laboratory. In this paper, we established a 3-D poroelastic numerical model with a new set of boundary conditions that better represent the experiment conditions. Furthermore, the 3-D poroelastic modelling results were compared with laboratory measurements under the same boundary conditions, showing a much better fit than the 1-D model. Therefore, the 3-D model provides a more accurate and reliable approach to understand the regimes and transitions of elastic modulus dispersion and attenuation, and thus has great importance in interpreting the measurements of frequency-dependent properties of rocks in the laboratory.
Second-order consensus of multi-agent systems with mixed delays and uncertain parameters via adaptive pinning aperiodically intermittent control
Authors: Zhou Boling , Yang Yongqing , Xu Xianyun 
Published: June 2019

AbstractThis paper investigates the second-order consensus of multi-agent systems with mixed delays and uncertain parameters. On one hand, an adaptive pinning aperiodically intermittent control protocol is designed to make multi-agent systems reach the second-order consensus. Moreover, the intermittent control protocol can be designed to be aperiodic, which means each agent can only obtain the relative states’ information from its neighbours at a sequence of disconnected aperiodic time intervals. On the other hand, based on the assumption that delay is less than the width of communication time, some consensus criterions in the form of matrix inequalities are derived by using Halanay inequality, Jensen inequality and Schur complement. At last, a simulation example is given to illustrate the correctness of the theoretical analysis.
A resolution calculus for MinSAT
Authors: Li Chu-Min , Xiao Fan , Manyà Felip 
Published: June 2019

Abstract
The logical calculus for SAT are not valid for MaxSAT and MinSAT because they preserve satisfiability but not the number of unsatisfied clauses. To overcome this drawback, a MaxSAT resolution rule preserving the number of unsatisfied clauses was defined in the literature. This rule is complete for MaxSAT when it is applied following a certain strategy. In this paper we first prove that the MaxSAT resolution rule also provides a complete calculus for MinSAT if it is applied following the strategy proposed here. We then describe an exact variable elimination algorithm for MinSAT based on that rule. Finally, we show how the results for Boolean MinSAT can be extended to solve the MinSAT problem of the multiple-valued clausal forms known as signed conjunctive normal form formulas.
Chemical abundances in the metal-intermediate GC NGC 6723
Authors: Crestani Juliana , Alves-Brito Alan , Bono Giuseppe , Puls Arthur A , Alonso-García Javier 
Published: June 2019

ABSTRACT
We have performed a detailed spectral analysis of the inner halo Galactic globular cluster (GC) NGC 6723 using high-resolution (R${\approx }$ 22 000–48 000) spectra for for 11 red giant branch stars collected with MIKE (Magellan) and FEROS (MPG/ESO). This globular is located at the minimum of the bimodal metallicity distribution of GCs, which suggests that it might be an excellent transitional system between metal-intermediate and metal-rich GCs. In spite of its metal-intermediate status, it is characterized by an extended horizontal branch and by a large number of RR Lyrae stars. We investigated abundances of a variety of species, including light, $\alpha$-, Fe-peak, and neutron-capture elements. We found a mean metallicity ${}[\mathrm{Fe/H}]=-0.93 \pm 0.05$ dex and typical $\alpha$-enrichment (${}[\alpha /\mathrm{Fe}] \approx 0.39$) that follows the trend of metal-poor and metal-intermediate GCs. The same outcome applies for light metals (Na, Al), Fe-peak (V, Cr, Mn, Fe, Co, Ni, Cu) and s/r-process elements (Ba, Eu), and for the classical anticorrelation: Na–O and Mg–Al. The current findings further support the evidence that the chemical enrichment of NGC 6723 is more in line with metal-intermediate GCs and their lower metallicity counterparts, and it does not bring forward the prodrome of the metal-rich regime.
The star formation history of the Sculptor dwarf spheroidal galaxy
Authors: Bettinelli M , Hidalgo S L , Cassisi S , Aparicio A , Piotto G , Valdes F , Walker A R 
Published: June 2019

ABSTRACT
We present the star formation history (SFH) of the Sculptor dwarf spheroidal galaxy based on deep g, r photometry taken with Dark Energy Camera at the Blanco telescope, focusing our analysis on the central region of the galaxy extended up to ∼3 core radii. We have investigated how the SFH changes radially, subdividing the sampled area into four regions, and have detected a clear trend of star formation. All the SFHs show a single episode of star formation, with the innermost region presenting a longer period of star formation of ∼1.5 Gyr and for the outermost region the main period of star formation is confined to ∼0.5 Gyr. We observe a gradient in the mean age which is found to increase going towards the outer regions. These results suggest that Sculptor continued forming stars after the reionization epoch in its central part, while in the peripheral region, the majority of stars probably formed during the reionization epoch and soon after its end. From our analysis, Sculptor cannot be considered strictly as a fossil of the reionization epoch.
The generalized and extended uncertainty principles and their implications on the Jeans mass
Authors: Moradpour H , Ziaie A H , Ghaffari S , Feleppa F 
Published: June 2019

ABSTRACT
The generalized and extended uncertainty principles affect the Newtonian gravity and also the geometry of the thermodynamic phase space. Under the influence of the latter, the energy–temperature relation of ideal gas may change. Moreover, it seems that the Newtonian gravity is modified in the framework of the Rényi entropy formalism motivated by both the long-range nature of gravity and the extended uncertainty principle. Here, the consequences of employing the generalized and extended uncertainty principles, instead of the Heisenberg uncertainty principle, on the Jeans mass are studied. The results of working in the Rényi entropy formalism are also addressed. It is shown that unlike the extended uncertainty principle and the Rényi entropy formalism that lead to the same increase in the Jeans mass, the generalized uncertainty principle can decrease it. The latter means that a cloud with mass smaller than the standard Jeans mass, obtained in the framework of the Newtonian gravity, may also undergo the gravitational collapse process.
Reproductive biology and ecology of the boreoatlantic armhook squidGonatus fabricii(Cephalopoda: Gonatidae)
Authors: Golikov Alexey V , Blicher Martin E , Jørgensen Lis L , Walkusz Wojciech , Zakharov Denis V , Zimina Olga L , Sabirov Rushan M 
Published: June 2019

AbstractThe squid Gonatus fabricii (Lichtenstein, 1818) is the most abundant pelagic cephalopod in the Arctic and the only squid to spend all of its life cycle in this region. Despite being highly abundant, its reproductive biology remains poorly known, and data on large maturing and mature specimens are especially rare. This study, based on extensive material (51 large specimens and &gt;35,000 specimens in all), fills major gaps in the knowledge of the reproductive biology and ecology of G. fabricii. The fecundity of females ranged from 8,862 to 16,200 oocytes, with mature and late maturing specimens having between 8,862 to c. 10,000 and 11,402 oocytes, respectively. Oogenesis was synchronous, and oocyte resorption was observed; resorbed oocytes constituted up to 23.5% of fecundity. Between two to five ripe oocytes were observed, and these were 4.0–5.5 mm in diameter (maximum dimension). Males possessed between 77 and 257 spermatophores (length = 5.8–10.8 mm). Spermatophores were characterized by a cement body with well-developed collar and discs at the oral end, an ejaculatory apparatus longer than the cement body and the lack of a tapered, sharp tip to the cement body. Spermatophore size showed a uniform increase in relation to increasing male size. In newer spermatophores, the length, width and volume of the seminal reservoir also increased. Females possessed between 62 and 84 spermatangia (length = 1.8–2.6 mm); the spermatangia were present on the buccal membranes and lacked special attachment structures. Seminal receptacles were not found on the buccal membranes of females. Our findings are consistent with the hypothesis of geographically restricted spawning in G. fabricii. The study found evidence for one new breeding area in south-eastern Greenland. No differences in sizes at maturity were found between the breeding areas. Such geographically localized reproduction is relatively common in non-deep-water squids, but is much less common in deep-water squids. Localized reproduction may be especially important for G. fabricii because increased food availability in the epipelagic layers would likely increase the survival of epipelagic juveniles, with surface currents potentially aiding in their dispersal.
Increase in Invasive Group A Streptococcal Disease and Emergence of Mucoid Strains in a Pediatric Population: February–June 2017
Authors: Walker Lorne W , Montoya Lindsay , Chochua Sopio , Beall Bernard , Green Michael 
Published: June 2019

Abstract

Background
Infection with group A Streptococcus (GAS) can cause severe systemic and locally invasive disease. Invasive group A streptococcal (iGAS) disease incidence varies both seasonally and year-to-year, and it may exhibit clustered outbreaks. We observed an upswing in iGAS cases at a tertiary care Children’s Hospital, prompting further characterization of local iGAS disease.

Methods
Cases of iGAS disease were abstracted from the medical record by manual chart review of all positive screening tests and cultures for GAS over a 4-year span. Incidence rates per 1000 hospital admissions and per 100 positive GAS tests were calculated and compared. Selected isolates were further characterized by whole-genome sequencing.

Results
Significant year-to-year differences in per-admission iGAS incidence rate were observed in February and June, although per-positive test incidence rates were not significantly different. Whole-genome sequencing revealed 2 dominant serotypes—emm3 and emm6—with high rates of mucoid phenotype and systemic bacteremia.

Conclusions
We document a significant but transient increase in iGAS disease incidence in 2 months of 2017. Genome sequencing revealed 2 dominant serotypes associated with mucoid phenotypes and severe disease, highlighting the dynamic nature of iGAS disease pattern.
Probing the Higgs sector in the nonrelativistic domain
Authors: Zhang Zhentao 
Published: June 2019

AbstractAs a process that contains direct information from the Higgs self-coupling, we investigate the muon-induced Higgs pair production $\mu^-\mu^+\rightarrow HH$. We calculate the one-loop corrections to the cross section, and in the threshold region we take into account the nonperturbative contribution from the Higgs self-interactions in the final state. We point out that the Higgs pair production in the nonrelativistic domain might be a useful process for probing the Higgs sector.