bluuebunny/crossref_metadata_2025_split huggingface dataset:
Massive Open Online Courses: enhancing caregiver education and support about dementia care towards and at end of life
Authors: Poole Marie , Davis Nuala , Robinson Louise 
Published: November 2019

Abstract
As the ageing population grows globally, the need for informal care—usually provided by family and friends—will continue to increase. Numbers of people with dementia also continue to rise, and much of their care will be provided by relatives. As such, more people who may themselves be older, will take on such caring roles. Consequently, more carers are likely to have education and support needs. Amidst government recognition of the need to provide good quality, person-centred education and support to carers, there are tensions between the potential for such provision to be resource intensive and whether existing services have the capacity to meet the needs of carers. Massive Open Online Courses (MOOCs) are a resource with scope to meet some of these educational and support needs. MOOCs enable flexible learning, are often free, and can be accessed anywhere in the world. Providing supportive dementia care requires carers to have an understanding of the condition, assistance to cope with the responsibilities of caring, and recognition of the importance of their own health and wellbeing as well as the person they support. In response to the needs of family carers of people with advancing dementia identified through a 5 year programme of research, we developed a MOOC—dementia care: living well as dementia progresses. This is an accessible source of relevant and engaging information; which enables carers to learn about advancing dementia, consider their own needs and create an interactive global forum of peer support.
SPDI: data model for variants and applications at NCBI
Authors: Holmes J Bradley , Moyer Eric , Phan Lon , Maglott Donna , Kattman Brandi 
Published: November 2019

Abstract

Motivation
Normalizing sequence variants on a reference, projecting them across congruent sequences and aggregating their diverse representations are critical to the elucidation of the genetic basis of disease and biological function. Inconsistent representation of variants among variant callers, local databases and tools result in discrepancies that complicate analysis. NCBI’s genetic variation resources, dbSNP and ClinVar, require a robust, scalable set of principles to manage asserted sequence variants.

Results
The SPDI data model defines variants as a sequence of four attributes: sequence, position, deletion and insertion, and can be applied to nucleotide and protein variants. NCBI web services convert representations among HGVS, VCF and SPDI and provide two functions to aggregate variants. One, based on the NCBI Variant Overprecision Correction Algorithm, returns a unique, normalized representation termed the ‘Contextual Allele’. The SPDI data model, with its four operations, defines exactly the reference subsequence affected by the variant, even in repeat regions, such as homopolymer and other sequence repeats. The second function projects variants across congruent sequences and depends on an alignment dataset of non-assembly NCBI RefSeq sequences (prefixed NM, NR and NG), as well as inter- and intra-assembly-associated genomic sequences (NCs, NTs and NWs), supporting robust projection of variants across congruent sequences and assembly versions. The variant is projected to all congruent Contextual Alleles. One of these Contextual Alleles, typically the allele based on the latest assembly version, represents the entire set, is designated the unique ‘Canonical Allele’ and is used directly to aggregate variants across congruent sequences.

Availability and implementation
The SPDI services are available for open access at: https://api.ncbi.nlm.nih.gov/variation/v0.

Supplementary information
Supplementary data are available at Bioinformatics online.
Discovery of disease- and drug-specific pathways through community structures of a literature network
Authors: Pham Minh , Wilson Stephen , Govindarajan Harikumar , Lin Chih-Hsu , Lichtarge Olivier 
Published: November 2019

Abstract

Motivation
In light of the massive growth of the scientific literature, text mining is increasingly used to extract biological pathways. Though multiple tools explore individual connections between genes, diseases and drugs, few extensively synthesize pathways for specific diseases and drugs.

Results
Through community detection of a literature network, we extracted 3444 functional gene groups that represented biological pathways for specific diseases and drugs. The network linked Medical Subject Headings (MeSH) terms of genes, diseases and drugs that co-occurred in publications. The resulting communities detected highly associated genes, diseases and drugs. These significantly matched current knowledge of biological pathways and predicted future ones in time-stamped experiments. Likewise, disease- and drug-specific communities also recapitulated known pathways for those given diseases and drugs. Moreover, diseases sharing communities had high comorbidity with each other and drugs sharing communities had many common side effects, consistent with related mechanisms. Indeed, the communities robustly recovered mutual targets for drugs [area under Receiver Operating Characteristic curve (AUROC)=0.75] and shared pathogenic genes for diseases (AUROC=0.82). These data show that literature communities inform not only just known biological processes but also suggest novel disease- and drug-specific mechanisms that may guide disease gene discovery and drug repurposing.

Availability and implementation
Application tools are available at http://meteor.lichtargelab.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems
Authors: Maggioli F , Mancini T , Tronci E 
Published: November 2019

Abstract

Motivation
SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g. enable in silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models. Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems.

Results
In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2—compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialized SBML simulators.

Availability and implementation
SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica.
Convergent evolution in calyptrate flowers of Syzygieae (Myrtaceae)
Authors: Vasconcelos Thais N C , Lucas Eve J , Conejero Maria , Giaretta Augusto , Prenner Gerhard 
Published: November 2019

AbstractShedding a fused perianth as a calyptra at anthesis is a trait that has evolved independently multiple times in angiosperm evolutionary history. However, calyptras do not correspond to homologous structures in all cases. Here, we describe calyptra development in the evolutionary context of Myrtaceae tribe Syzygieae. We use scanning electron and light microscopy to contrast calyptra development in calyptrate and non-calyptrate species in the group. Results show that calyptras in Syzygieae are not all homologous, but correspond to two ontogenetically distinct structures involving different perianth whorls that resemble each other by convergence: a calycine structure, in which the sepals are fused; and a pseudocalyptra, in which petals fall as a single unit but are not fused. Presence of non-calyptrate flowers is the ancestral state in the tribe, and both calyptra types appeared multiple times in the evolution of the group, with infrequent reversals from the calyptrate to the non-calyptrate state. Results highlight the fact that similar terminology in non-homologous structures can affect even relatively restricted lineages. The recurrent evolution of the calyptra in Syzygieae, with little evidence for reversal, shows that these structures may be advantageous in certain conditions but also correspond to an evolutionary dead-end in the group.
Hydrophilic interaction in solid-phase extraction of antisense oligonucleotides
Authors: Nuckowski Łukasz , Kilanowska Anna , Studzińska Sylwia 
Published: November 2019

Abstract
The presented studies aimed to develop a new and simple extraction method based on hydrophilic interaction for antisense oligonucleotides with different modifications. For this purpose, solid-phase extraction cartridges with unmodified silica were used. All extraction steps were performed by utilizing water, acetonitrile, acetone or their mixtures. The results obtained show that a high content (95%) of organic solvent, used during sample loading, is critical to achieve a successful extraction, while elution with pure water allows effective oligonucleotides desorption. The recovery values were greater than 90% in the case of unmodified DNA, phosphorothioate, 2′-O-(2-methoxyethyl) and 2′-O-methyl oligonucleotides. For the mixture of phosphorothioate oligonucleotide and its two synthetic metabolites, the recovery values for the standard solutions were in the range of 70–75%, while for spiked human plasma, 45–50%. The developed method is simple, may be performed in a short time and requires simple solvents like water or acetonitrile/acetone, thus showing promise as an alternative to chaotropic salt-based or ion pair-based SPE methods.
A Validated Green HPTLC Method for Quantitative Determination of Dapoxetine Hydrochloride and Tadalafil in Bulk and Pharmaceutical Formulations
Authors: Naguib Ibrahim A , Magdy Maimana A , Anwar Basma H , Abdelhamid Nessreen S 
Published: November 2019

AbstractDapoxetine hydrochloride (DAP) and Tadalafil (TAD) were separated and determined quantitatively using a validated green high-performance thin layer chromatographic (HPTLC) method in their binary mixtures either as raw materials or in pharmaceutical formulations. The concentration ranges were 0.1–1.6 and 0.2–2.5 μg/band for dapoxetine and tadalafil, respectively, with accuracies of 98.93% ± 0.62 and 99.26% ± 1.39, respectively. Silica gel HPTLC F254 plates were used to carry out the separation. The mobile phase used was a mixture of ethanol–ethyl acetate (1:9 by volume), which is environmentally green and harmless. Densitometric scanning with UV detector was used to detect the separated peaks at 222 nm. ICH guidelines were followed to validate the suggested method, and the results prove that they can be used for regular analysis in quality control laboratories with compatible results.
Early Experience With Meropenem-Vaborbactam for Treatment of Carbapenem-resistant Enterobacteriaceae Infections
Authors: Shields Ryan K , McCreary Erin K , Marini Rachel V , Kline Ellen G , Jones Chelsea E , Hao Binghua , Chen Liang , Kreiswirth Barry N , Doi Yohei , Clancy Cornelius J , Nguyen M Hong 
Published: November 2019

AbstractTwenty patients with carbapenem-resistant Enterobacteriaceae infections were treated with meropenem-vaborbactam. Thirty-day clinical success and survival rates were 65% (13/20) and 90% (18/20), respectively. Thirty-five percent of patients had microbiologic failures within 90 days. One patient developed a recurrent infection due to meropenem-vaborbactam–nonsusceptible, ompK36 porin mutant Klebsiella pneumoniae.
Aging influences cerebrovascular myogenic reactivity and BK channel function in a sex-specific manner
Authors: Reed Joseph T , Pareek Tanya , Sriramula Srinivas , Pabbidi Mallikarjuna R 
Published: November 2019

Abstract

Aims
The myogenic reactivity of the middle cerebral arteries (MCA) protects the brain by altering the diameter in response to changes in lumen pressure. Large conductance potassium (BK) channels are known to regulate the myogenic reactivity, yet, it is not clear how aging alters the myogenic reactivity via the BK channel in males and females. Thus, we hypothesize that age-associated changes in BK channel subunits modulate the myogenic reactivity in a sex-specific manner.

Methods and results
We used vascular reactivity, patch-clamp, and biochemical methods to measure myogenic reactivity, BK channel function, and expression, respectively in cerebral vessels of adult and aged male and female Sprague Dawley rats. Our results suggest that aging and ovariectomy (OVX) exaggerated the myogenic reactivity of MCA in females but attenuated it in males. Aging induced outward eutrophic remodelling in females but inward hypertrophic remodelling in males. Aging decreased total, Kv, BK channel currents, and spontaneous transient outward currents (STOC) in vascular smooth muscle cells isolated from females, but not in males. Aging increased BKα subunit mRNA and protein both in males and females. However, aging decreased BKβ1 subunit protein and mRNA in females only. In males, BKβ1 mRNA is increased, but protein is decreased. Iberiotoxin-induced MCA constriction is lower in aged females but higher in aged males. Activation of BKα (10 µM NS1619) and BKβ1 (10 µM S-Equol) subunits failed to increase STOCs and were unable to decrease the myogenic reactivity of MCA in aged female but not in aged male rats. OVX decreased, but chronic supplementation of oestradiol restored BK channel expression and function.

Conclusion
Overall our results suggest that aging or OVX-associated downregulation of the BKβ1 expression and function in females results in exaggerated myogenic reactivity of MCA. However, age-associated increase in BK channel function in males attenuated myogenic reactivity of MCA.
Consequences of Overeducation among Career Starters in Germany: A Trap for the Vocationally Trained as well as for University Graduates?
Authors: Schmelzer Paul , Schneider Thorsten 
Published: November 2019

AbstractResearch on the consequences of starting in overeducation often focuses on either secondary or tertiary graduates. We focus on both within one country, Germany. While matching and search models imply the improvement of initial overeducation, human capital theory and stigma associated with overeducation predict entrapment. The strongly skill- and occupation-based labour market for the vocationally trained in Germany mitigates the bridge function of overeducation. As the less standardized tertiary system creates more uncertainties, initial overeducation should be more prevalent and should serve as a bridge to better positions. However, depreciation of human capital and the stigma associated with overeducation oppose the bridge function of overeducation here, too. Using data from the German National Educational Panel Study (NEPS), we compare labour market positions of career starters in overeducation with those not in overeducation in subsequent years using propensity score matching. In the fifth year after labour market entrance, the differences in overeducation between initially overeducated and non-overeducated individuals amounts to 38 percentage points for graduates and 28 for vocationally trained persons. In addition, vocationally trained persons starting in overeducation face higher unemployment risks later on. Our findings challenge the assumption of a bridge function in both educational groups.
Diversity of carotenogenic microalgae in the White Sea polar region
Authors: Chekanov K , Fedorenko T , Kublanovskaya A , Litvinov D , Lobakova E 
Published: November 2019

Abstract
Carotenogenic microalgae are unicellular photosynthetic organisms with the ability to accumulate carotenoids. Carotenoid accumulation is a protective reaction against environmental stress factors, such as bright light, extreme temperatures, etc. It makes the survival of these microorganisms under harsh environmental conditions possible. The diversity of carotenogenic microalgae has been described in detail for Central Europe and North America, as well as for tropical and subtropical latitudes with relatively favorable environmes. However, data about these microorganisms in polar and subpolar latitudes is scarce and restricted to few reports. We isolated several strains of carotenogenic microalgae from the coastal zone of the White Sea, where they were abundant. The obtained microalgae related to four species of Chlorophytes: Haematococcus lacustris, H. rubicundus, Coelastrella aeroterrestrica, and Bracteacoccus aggregatus. The last three species have been reported for polar latitudes for the first time. Most likely, carotenogenic algae in the White Sea coast are abundant due to their high physiological and metabolic plasticity, which is essential for surviving under adverse conditions of the northern regions. Pigment composition of the strains is provided. Their predominant carotenoids were astaxanthin and β-carotene. Further, the obtained strains may be considered as potential producers of natural pigments for biotechnology.
Contrasting environmental factors drive bacterial and eukaryotic community successions in freshly deglaciated soils
Authors: Khan Ajmal , Kong Weidong , Muhammad Said , Wang Fei , Zhang Guoshuai , Kang Shichang 
Published: November 2019

ABSTRACT
Glacier retreats expose deglaciated soils to microbial colonization and succession; however, the differences in drivers of bacterial and eukaryotic succession remain largely elusive. We explored soil bacterial and eukaryotic colonization and yearly community succession along a deglaciation chronosequence (10 years) on the Tibetan Plateau using qPCR, terminal restriction fragment length polymorphism (T-RFLP) and sequencing of clone libraries. The results exhibited that bacteria and eukaryotes rapidly colonized the soils in the first year of deglaciation, thereafter slowly increasing from 107 up to 1010 and 1011 gene copies g−1 soil, respectively. Bacterial and eukaryotic community changes were observed to group into distinct stages, including early (0–2 year old), transition (3–5 year old) and late stages (6–10 year old). Bacterial community succession was dominantly driven by soil factors (47.7%), among which soil moisture played a key role by explaining 26.9% of the variation. In contrast, eukaryotic community succession was dominantly driven by deglaciation age (22.2%). The dominant bacterial lineage was Cyanobacteria, which rapidly decreased from the early to the transition stage. Eukaryotes were dominated by glacier-originated Cercozoa in early stage soils, while green algae Chlorophyta substantially increased in late stage soils. Our findings revealed contrasting environmental factors driving bacterial and eukaryotic community successions.
Fractional Operators Applied to Geophysical Electromagnetics
Authors: Weiss C J , van Bloemen Waanders B G , Antil H 
Published: November 2019

SUMMARY
A growing body of applied mathematics literature in recent years has focused on the application of fractional calculus to problems of anomalous transport. In these analyses, the anomalous transport (of charge, tracers, fluid, etc.) is presumed attributable to long–range correlations of material properties within an inherently complex, and in some cases self-similar, conducting medium. Rather than considering an exquisitely discretized (and computationally intractable) representation of the medium, the complex and spatially correlated heterogeneity is represented through reformulation of the governing equation for the relevant transport physics such that its coefficients are, instead, smooth but paired with fractional–order space derivatives. Here we apply these concepts to the scalar Helmholtz equation and its use in electromagnetic interrogation of Earth’s interior through the magnetotelluric method. We outline a practical algorithm for solving the Helmholtz equation using spectral methods coupled with finite element discretizations. Execution of this algorithm for the magnetotelluric problem reveals several interesting features observable in field data: long–range correlation of the predicted electromagnetic fields; a power–law relationship between the squared impedance amplitude and squared wavenumber whose slope is a function of the fractional exponent within the governing Helmholtz equation; and, a non–constant apparent resistivity spectrum whose variability arises solely from the fractional exponent. In geologic settings characterized by self–similarity (e.g. fracture systems; thick and richly–textured sedimentary sequences, etc.) we posit that these diagnostics are useful for geologic characterization of features far below the typical resolution limit of electromagnetic methods in geophysics.
Life history changes and fisheries assessment performance: a case study for small yellow croaker
Authors: Lee Qi , Lee Alice , Liu Zunlei , Szuwalski Cody S 
Published: November 2019

Abstract
Many intensely exploited fish stocks have experienced changes in trophic structure and environmental conditions, resulting in non-stationary population processes. We evaluate the ability of assessment methods to estimate quantities used in management (like target biomasses and fishing mortalities) when life history processes are non-stationary and comprehensive data are not available. We use the small yellow croaker (Larimichthys polyactis) fishery in the East China and Yellow Seas as a case study. We simulate age-structured populations with time-varying fishery and life history characteristics similar to that of the small yellow croaker in China based on historical studies that demonstrate changes in life history. We then fit surplus production and statistical catch-at-age models to simulated catch and index data from these populations. Given our assumptions, both estimation models yielded biased quantities important to management. The production model estimated reference points associated with target biomass with less bias than the age-structured model, while the latter outperformed the former when estimating reference points associated with target fishing mortality. The age-structured model also better captured relative population trends and provided flexibility to consider impacts of life history changes over time. We suggest that assessments of similar stocks consider the potential of life history variation impact management quantities.