bluuebunny/crossref_metadata_2025 huggingface dataset:
Semantic Theories of Questions
Authors: Roelofsen Floris
Published: October 2019

This survey article discusses two basic issues that semantic theories of questions face. The first is how to conceptualize and formally represent the semantic content of questions. This issue arises in particular because the standard truth-conditional notion of meaning, which has been fruitful in the analysis of declarative statements, is not applicable to questions. This is because questions are not naturally construed as being true or false. Instead, it has been proposed that the semantic content of a question must be characterized in terms of its answerhood or resolution conditions. This article surveys a number of theories which develop this basic idea in different ways, focusing on so-called proposition-set theories (alternative semantics, partition semantics, and inquisitive semantics).

The second issue that will be considered here concerns questions that are embedded within larger sentences. Within this domain, one important puzzle is why certain predicates can take both declarative and interrogative complements (e.g., Bill knows that Mary called / Bill knows who called), while others take only declarative complements (e.g., Bill thinks that Mary called / *Bill thinks who called) or only interrogative complements (e.g., Bill wonders who called / *Bill wonders that Mary called). We compare two general approaches that have been pursued in the literature. One assumes that declarative and interrogative complements differ in semantic type. On this approach, the fact that predicates like think do not take interrogative complements can be accounted for by assuming that such complements do not have the semantic type that think selects for. The other approach treats the two kinds of complement as having the same semantic type, and seeks to connect the selectional restrictions of predicates like think to other semantic properties (e.g., the fact that think is neg-raising).
Syncretism in Morphology
Authors: Caha Pavel
Published: October 2019

The term syncretism refers to a situation where two distinct morphosyntactic categories are expressed in the same way. For instance, in English, first and third person pronouns distinguish singular from plural (I vs. we, he/she/it vs. them), but the second person pronoun (you) doesn’t. Such facts are traditionally understood in a way that English grammar distinguishes between the singular and plural in all persons. However, in the second person, the two distinct meanings are expressed the same, and the form you is understood as a form syncretic between the two different grammatical meanings.

It is important to note that while the two meanings are different, they are also related: both instances of you refer to the addressee. They differ in whether they refer just to the addressee or to a group including the addressee and someone else, as depicted here.

a.you (sg) = addressee

b.you (pl) = addressee + others

The idea that syncretism reflects meaning similarity is what makes its study interesting; a lot of research has been dedicated to figuring out the reasons why two distinct categories are marked the same.

There are a number of approaches to the issue of how relatedness in meaning is to be modeled. An old idea, going back to Sanskrit grammarians, is to arrange the syncretic cells of a paradigm in such a way so that the syncretic cells would always be adjacent. Modern approaches call such arrangements geometric spaces (McCreight & Chvany, 1991) or semantic maps (Haspelmath, 2003), with the goal to depict meaning relatedness as a spatial proximity in a conceptual space. A different idea is pursued in approaches based on decomposition into discrete meaning components called features (Jakobson, 1962).

Both of these approaches acknowledge the existence of two different meanings, which are related. However, there are two additional logical options to the issue of syncretism. First, one may adopt the position that the two paradigm cells correspond to a single abstract meaning, and that what appear to be different meanings/functions arises from the interaction between the abstract meaning and the specific context of use (see, for instance, Kayne, 2008 or Manzini & Savoia, 2011). Second, it could be that there are simply two different meanings expressed by two different markers, which accidentally happen to have the same phonology (like the English two and too). The three approaches are mutually contradictory only for a single phenomenon, but each of them may be correct for a different set of cases.
American Descriptivist Morphology in the 1950s
Authors: Goldsmith John
Published: October 2019

The American descriptivist movement includes the work of Edward Sapir, Leonard Bloomfield, and their students, including Zellig Harris, Charles Hockett, and Kenneth Pike. Their work on morphology set the stage for much of the discussion of the subject in the years that followed, right up to today. In a number of ways they laid greater emphasis on the role of morphemes in morphological analysis when linguists in Europe focused more on the central role played by words in morphosyntactic paradigms.
Agroecology: Principles and Practices for Diverse, Resilient, and Productive Farming Systems
Authors: Altieri Miguel A.
Published: October 2019

Agroecology is a science that applies ecological concepts and principles to the design and management of sustainable agricultural ecosystems. Inspired by the diversified models of traditional agriculture, agroecologists promote crop diversification (polycultures, crop-livestock combinations, rotations, agroforestry systems, etc.) as an effective agroecological strategy for introducing more biodiversity into agroecosystems, which in turn provides a number of ecological services to farmers, such as natural soil fertility, pest regulation, pollination, and others. The agroecological approach involves the application of blended agricultural and ecological sciences with indigenous knowledge systems. A variety of agroecological and participatory approaches have shown in many rural areas very positive outcomes, even under adverse environmental and socioeconomic conditions. Potentials include raising crop yields and total farm output, increasing stability of production through diversification, enhancing resilience of farms to climate change, improving diets and income, and conservation of the natural resource base and biodiversity. Agroecological principles can also be applied to break the monoculture nature of modern mechanized farms. Strategies include complex crop rotations, cover cropping in vineyards and fruit orchards, strip intercropping, and so on. The ultimate goal is to develop integrated diversified and resilient agroecosystems with minimal dependence on external, off-farm inputs.
Risk factors for development of aminoglycoside resistance among gram-negative rods
Authors: Richter Stefan E , Miller Loren , Needleman Jack , Uslan Daniel Z , Bell Douglas , Watson Karol , Humphries Romney , McKinnell James A
Published: October 2019

Purpose

Development of scoring systems to predict the risk of aminoglycoside resistance and to guide therapy is described.

Methods

Infections due to aminoglycoside-resistant gram-negative rods (AR-GNRs) are increasingly common and associated with adverse outcomes; selection of effective initial antibiotic therapy is necessary to reduce adverse consequences and shorten length of stay. To determine risk factors for AR-GNR recovery from culture, cases of GNR infection among patients admitted to 2 institutions in a major academic hospital system during the period 2011–2016 were retrospectively analyzed. Gentamicin and tobramycin resistance (GTR-GNR) and amikacin resistance (AmR-GNR) patterns were analyzed separately. A total of 26,154 GNR isolates from 12,516 patients were analyzed, 6,699 of which were GTR, and 2,467 of which were AmR.

Results

In multivariate analysis, risk factors for GTR-GNR were presence of weight loss, admission from another medical or long-term care facility, a hemoglobin level of <11 g/dL, receipt of any carbapenem in the prior 30 days, and receipt of any fluoroquinolone in the prior 30 days (C statistic, 0.63). Risk factors for AmR-GNR were diagnosis of cystic fibrosis, male gender, admission from another medical or long-term care facility, ventilation at any point prior to culture during the index hospitalization, receipt of any carbapenem in the prior 30 days, and receipt of any anti-MRSA agent in the prior 30 days (C statistic, 0.74). Multinomial and ordinal models demonstrated that the risk factors for the 2 resistance patterns differed significantly.

Conclusion

A scoring system derived from the developed risk prediction models can be applied by providers to guide empirical antimicrobial therapy for treatment of GNR infections.
The Leaky Pipeline of Women in Plastic Surgery: Embracing Diversity to Close the Gender Disparity Gap
Authors: Moak Teri N , Cress Phaedra E , Tenenbaum Marissa , Casas Laurie A
Published: October 2019

The Balance for Better campaign theme of the 2019 International Women’s Day prompted a closer look at diversity within the plastic surgery specialty. Gender balance in the United States has improved through many organizational efforts and enactment of laws. Unfortunately, despite these endeavors, statistics show that men still enjoy greater financial and career success. Within the field of medicine, a similar trend has been observed. Although women constitute 50% of medical school graduates, the majority still enter fields outside of surgical subspecialties. In comparison to other surgical subspecialties, women are most represented in plastic surgery. Unfortunately, significant gender discrepancies remain in postgraduate practice including academic practice rank, societal board membership, invited speaker opportunities, and compensation, to name a few. The “leaky pipeline” of women describes the precipitous decline in the numbers of women at each step up the professional ladder. We explore the multifaceted nature of this phenomenon and highlight factors that contribute to limiting female growth within the plastic surgery profession. We also emphasize the continued growth of female plastic surgeon presence in all sectors despite these existing obstacles. We submit that continued leadership, mentorship, and sponsorship provided by both male and female physicians in the field will facilitate future leadership, advance gender parity, and cultivate a sense of belonging within the plastic surgery community, allowing brilliant minds to flourish and the profession to thrive.
GenCLiP 3: mining human genes’ functions and regulatory networks from PubMed based on co-occurrences and natural language processing
Authors: Wang Jia-Hong , Zhao Ling-Feng , Wang Hua-Feng , Wen Yue-Ting , Jiang Kui-Kui , Mao Xiang-Ming , Zhou Zi-Ying , Yao Kai-Tai , Geng Qing-Shan , Guo Dan , Huang Zhong-Xi
Published: October 2019

We present a web server, GenCLiP 3, which is an updated version of GenCLiP 2.0 to enhance analysis of human gene functions and regulatory networks, with the following improvements: (i) accurate recognition of molecular interactions with polarity and directionality from the entire PubMed database; (ii) support for Boolean search to customize multiple-term search and to quickly retrieve function-related genes; (iii) strengthened association between gene and keyword by a new scoring method; and (iv) daily updates following literature release at PubMed FTP.

Availability and implementation

The server is freely available for academic use at: http://ci.smu.edu.cn/genclip3/.

Supplementary information

Supplementary data are available at Bioinformatics online.
PRODIGY: personalized prioritization of driver genes
Authors: Dinstag Gal , Shamir Ron
Published: October 2019

Motivation

Evolution of cancer is driven by few somatic mutations that disrupt cellular processes, causing abnormal proliferation and tumor development, whereas most somatic mutations have no impact on progression. Distinguishing those mutated genes that drive tumorigenesis in a patient is a primary goal in cancer therapy: Knowledge of these genes and the pathways on which they operate can illuminate disease mechanisms and indicate potential therapies and drug targets. Current research focuses mainly on cohort-level driver gene identification but patient-specific driver gene identification remains a challenge.

Methods

We developed a new algorithm for patient-specific ranking of driver genes. The algorithm, called PRODIGY, analyzes the expression and mutation profiles of the patient along with data on known pathways and protein–protein interactions. Prodigy quantifies the impact of each mutated gene on every deregulated pathway using the prize-collecting Steiner tree model. Mutated genes are ranked by their aggregated impact on all deregulated pathways.

Results

In testing on five TCGA cancer cohorts spanning >2500 patients and comparison to validated driver genes, Prodigy outperformed extant methods and ranking based on network centrality measures. Our results pinpoint the pleiotropic effect of driver genes and show that Prodigy is capable of identifying even very rare drivers. Hence, Prodigy takes a step further toward personalized medicine and treatment.

Availability and implementation

The Prodigy R package is available at: https://github.com/Shamir-Lab/PRODIGY.

Supplementary information

Supplementary data are available at Bioinformatics online.
Transmural Histological Scoring Systems in Crohn’s Disease: A Systematic Review With Assessment of Methodological Quality and Operating Properties
Authors: Tavares de Sousa Helena , Estevinho Maria Manuela , Peyrin-Biroulet Laurent , Danese Silvio , Dias Cláudia Camila , Carneiro Fátima , Magro Fernando
Published: October 2019

Background

The relative proportion of inflammation and fibrosis in a stricture is highly relevant in defining the clinical approach for Crohn’s disease [CD] patients. Whereas transmural inflammation in CD can be accurately estimated by cross-sectional imaging, evaluating the extent and severity of fibrosis still requires surgical pathology of intestinal resection specimens. This study systematically reviewed all existing transmural histopathological scoring systems developed for the assessment of inflammation and/or fibrosis in CD.

Methods

A systematic review of histopathological scoring systems for the assessment of transmural inflammation and/or fibrosis in CD, focusing on originally developed scoring systems. Risk of bias, methodological quality, and operating or psychometric properties [validity, reliability, responsiveness, and feasibility] of each histological scoring system were analysed.

Results

A total of 29 original scoring systems were included in this review. Three scoring systems were highlighted as the most widely reproduced, one aimed at assessing inflammation only and two aimed at assessing inflammation and fibrosis. These scores were more widely reproduced probably due to their ease of application in clinical studies. Two highly comprehensive scores were identified, showing good operating properties and high methodological quality, as well as the lowest risk of bias; these should, therefore, be further validated in clinical research studies.

Conclusions

This study reviewed all existing transmural histopathological scoring systems for the assessment of inflammation and/or fibrosis in CD and identified the most reliable and accurate scores for clinical research and clinical practice settings.
The use of serial cardiac 18F-fluorodeoxyglucose– positron emission tomography imaging to diagnose, monitor, and tailor treatment of cardiac sarcoidosis patients with arrhythmias: a case series and review
Authors: Kersey Cooper B , Flaherty Kathleen R , Goldenthal Isaac L , Bokhari Sabahat , Biviano Angelo B
Published: October 2019

Background

Clinically evident cardiac involvement has been documented in 5% of sarcoidosis patients, primarily manifesting as heart block, ventricular arrhythmias, and heart failure. Heart Rhythm Society consensus guidelines recommend advanced cardiac imaging with fluorodeoxyglucose–positron emission tomography (FDG-PET) scan for diagnosis of cardiac sarcoidosis, given endomyocardial biopsy’s low sensitivity.

Case summary 

We describe four patients with cardiac sarcoidosis diagnosed with FDG-PET scan performed using a standardized imaging protocol for cardiac sarcoidosis. Serial FDG-PET scans were performed to monitor disease progression and response to therapy. Patients 1 and 2 presented with heart block, Patient 3 with heart failure and ventricular tachycardia (VT), and Patient 4 with VT. Patient 1 showed an initial decrease in standard uptake value (SUV) on immunosuppression, followed by an increase in SUV, necessitating steroid therapy. Patient 2’s SUV decreased on immunosuppression. Patient 3 required 3.5 years of immunosuppression for the SUV to decrease to inactive disease levels, with SUV increasing and decreasing at different times during treatment, and subsequently developed VT. For Patient 4, areas of inflammation on the initial scan matched low voltage areas on the patient’s EP study, confirming the arrhythmia’s pathophysiological basis.

Discussion 

Cardiac sarcoidosis progression and response to therapy are heterogeneous. Serial FDG-PET scans are useful to diagnose disease, tailor therapy, and monitor the clinical course of disease, allowing treatment decisions to be based on the quantitative level of inflammation seen on FDG-PET.
Treatment outcome with orthodontic aligners and fixed appliances: a systematic review with meta-analyses
Authors: Papageorgiou Spyridon N , Koletsi Despina , Iliadi Anna , Peltomaki Timo , Eliades Theodore
Published: October 2019

Background

The use of orthodontic aligners to treat a variety of malocclusions has seen considerable increase in the last years, yet evidence about their efficacy and adverse effects relative to conventional fixed orthodontic appliances remains unclear.

Objective

This systematic review assesses the efficacy of aligners and fixed appliances for comprehensive orthodontic treatment.

Search methods

Eight databases were searched without limitations in April 2019.

Selection criteria

Randomized or matched non-randomized studies.

Data collection and analysis

Study selection, data extraction, and risk of bias assessment was done independently in triplicate. Random-effects meta-analyses of mean differences (MDs) or relative risks (RRs) with their 95% confidence intervals (CIs) were conducted, followed by sensitivity analyses, and the GRADE analysis of the evidence quality.

Results

A total of 11 studies (4 randomized/7 non-randomized) were included comparing aligners with braces (887 patients; mean age 28.0 years; 33% male). Moderate quality evidence indicated that treatment with orthodontic aligners is associated with worse occlusal outcome with the American Board of Orthodontics Objective Grading System (3 studies; MD = 9.9; 95% CI = 3.6–16.2) and more patients with unacceptable results (3 studies; RR = 1.6; 95% CI = 1.2–2.0). No significant differences were seen for treatment duration. The main limitations of existing evidence pertained to risk of bias, inconsistency, and imprecision of included studies.

Conclusions

Orthodontic treatment with aligners is associated with worse treatment outcome compared to fixed appliances in adult patients. Current evidence does not support the clinical use of aligners as a treatment modality that is equally effective to the gold standard of braces.

Registration

PROSPERO (CRD42019131589).
Temporal relations between atrial fibrillation and ischaemic stroke and their prognostic impact on mortality
Authors: Camen Stephan , Ojeda Francisco M , Niiranen Teemu , Gianfagna Francesco , Vishram-Nielsen Julie K , Costanzo Simona , Söderberg Stefan , Vartiainen Erkki , Donati Maria Benedetta , Løchen Maja-Lisa , Pasterkamp Gerard , Magnussen Christina , Kee Frank , Jousilahti Pekka , Hughes Maria , Kontto Jukka , Mathiesen Ellisiv B , Koenig Wolfgang , Palosaari Tarja , Blankenberg Stefan , de Gaetano Giovanni , Jørgensen Torben , Zeller Tanja , Kuulasmaa Kari , Linneberg Allan , Salomaa Veikko , Iacoviello Licia , Schnabel Renate B
Published: October 2019

Aims

Limited evidence is available on the temporal relationship between atrial fibrillation (AF) and ischaemic stroke and their impact on mortality in the community. We sought to understand the temporal relationship of AF and ischaemic stroke and to determine the sequence of disease onset in relation to mortality.

Methods and results

Across five prospective community cohorts of the Biomarkers for Cardiovascular Risk Assessment in Europe (BiomarCaRE) project we assessed baseline cardiovascular risk factors in 100 132 individuals, median age 46.1 (25th–75th percentile 35.8–57.5) years, 48.4% men. We followed them for incident ischaemic stroke and AF and determined the relation of subsequent disease diagnosis with overall mortality. Over a median follow-up of 16.1 years, N = 4555 individuals were diagnosed solely with AF, N = 2269 had an ischaemic stroke but no AF diagnosed, and N = 898 developed both, ischaemic stroke and AF. Temporal relationships showed a clustering of diagnosis of both diseases within the years around the diagnosis of the other disease. In multivariable-adjusted Cox regression analyses with time-dependent covariates subsequent diagnosis of AF after ischaemic stroke was associated with increased mortality [hazard ratio (HR) 4.05, 95% confidence interval (CI) 2.17–7.54; P < 0.001] which was also apparent when ischaemic stroke followed after the diagnosis of AF (HR 3.08, 95% CI 1.90–5.00; P < 0.001).

Conclusion

The temporal relations of ischaemic stroke and AF appear to be bidirectional. Ischaemic stroke may precede detection of AF by years. The subsequent diagnosis of both diseases significantly increases mortality risk. Future research needs to investigate the common underlying systemic disease processes.
Comparing the Slope–Area Threshold for Stream Initiation in Primeval and Managed Forests of Northern Michigan
Authors: Anderson Christopher J
Published: October 2019

Forest management and other land uses can alter hydrological pathways and affect stream initiation along draining hillslopes. To evaluate this potential effect, primeval forests at the Huron Mountain Club in northern Michigan were compared to surrounding forest lands historically logged. A total of 59 stream channel heads (19 in primeval forests and 40 in managed forests) were mapped using GPS. Per the slope–area method, channel heads were plotted within a digital elevation model to determine drainage area and local slope, which were used to discern a threshold of channel initiation. A watershed Hydrologic Soil Index (representing the tendency for surface runoff) was also determined and evaluated for its importance for channel formation. Consistent with the slope–area method, a significant relation was detected between drainage area and local slope for both managed (R2 = .29) and primeval forest watersheds (R2 = .56). However, no significant difference in relation was detected between forest types. This was noteworthy because soils mapped in the primeval forests had a significantly higher Hydrologic Soil Index indicating thinner soils more prone to surface runoff. Results suggest that forest management has likely varied throughout the region but has sustained forest drainage densities comparable to primeval forests.
Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints
Authors: Godden Grant T , Kinser Taliesin J , Soltis Pamela S , Soltis Douglas E
Published: October 2019

Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the non-uniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.
A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome
Authors: Varadharajan Srinidhi , Rastas Pasi , Löytynoja Ari , Matschiner Michael , Calboli Federico C F , Guo Baocheng , Nederbragt Alexander J , Jakobsen Kjetill S , Merilä Juha
Published: October 2019

The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the ‘ecology’s supermodel’, while the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
The Role of Ames Dwarfism and Calorie Restriction on Gut Microbiota
Authors: Wiesenborn Denise S , Gálvez Eric J C , Spinel Lina , Victoria Berta , Allen Brittany , Schneider Augusto , Gesing Adam , Al-Regaiey Khalid A , Strowig Till , Schäfer Karl-Herbert , Masternak Michal M
Published: October 2019

The gut microbiome (GM) represents a large and very complex ecosystem of different microorganisms. There is an extensive interest in the potential role of the GM in different diseases including cancer, diabetes, cardiovascular diseases, and aging. The GM changes over the lifespan and is strongly associated with various age-related diseases. Ames dwarf (df/df) mice are characterized by an extended life- and healthspan, and although these mice are protected from many age-related diseases, their microbiome has not been studied. To determine the role of microbiota on longevity animal models, we investigated the changes in the GM of df/df and normal control (N) mice, by comparing parents before mating and littermate mice at three distinct time points during early life. Furthermore, we studied the effects of a 6-month calorie restriction (CR), the most powerful intervention extending the lifespan. Our data revealed significant changes of the GM composition during early life development, and we detected differences in the abundance of some bacteria between df/df and N mice, already in early life. Overall, the variability of the microbiota by genotype, time-point, and breeding pair showed significant differences. In addition, CR caused significant changes in microbiome according to gastrointestinal (GI) location (distal colon, ileum, and cecum), genotype, and diet. However, the overall impact of the genotype was more prominent than that of the CR. In conclusion, our findings suggest that the gut microbiota plays an important role during postnatal development in long-living df/df mice and CR dietary regimen can significantly modulate the GM.
Uncontrolled Diabetes as an Associated Factor with Dynapenia in Adults Aged 50 Years or Older: Sex Differences
Authors: Nebuloni Clarice Cavalero , Máximo Roberta de Oliveira , de Oliveira Cesar , Alexandre Tiago da Silva
Published: October 2019

Background

Epidemiological studies demonstrate an association between diabetes and low neuromuscular strength (NMS). However, none have grouped participants into nondiabetics (ND), undiagnosed diabetics (UDD), controlled diabetics (CD), and uncontrolled diabetics (UCD) or investigated what glycated hemoglobin levels (HbA1c) are associated with low NMS (dynapenia) by sex.

Methods

We analyzed the association between UDD, CD, and UCD and dynapenia, the extent to which the different groupings of these individuals modifies this association and the association between HbA1c levels and NMS, by sex, in a cross-sectional study involving 5,290 participants ≥50 years from the ELSA study. In the first two analyses, logistic regression models were used with dynapenia (grip strength <26 kg in men and <16 kg in women) as outcome and diabetes (ND, UDD, CD, and UCD) as exposure. Next, linear regression was performed with grip strength as the outcome, and the participants were classified based on HbA1c level as exposure. The models were adjusted by sociodemographic, behavioral, and clinical characteristics.

Results

Compared to ND, only UCD was associated with dynapenia (men OR = 2.37 95% CI 1.36–4.14; women OR = 1.67 95% CI 1.01–2.79). This association was less clear, particularly in women, when CD and UCD groups were merged. HbA1c ≥6.5% in men and ≥8.0% in women were associated with lower NMS.

Conclusions

UCD increases the chance of dynapenia in both sexes. The different groupings based on diabetes status modify the association between UCD and dynapenia. The threshold of HbA1c associated with reduced NMS is lower in men compared to women.
Turbidity alters estuarine biodiversity and species composition
Authors: Lunt Jessica , Smee Delbert L
Published: October 2019

Turbidity is widely regarded for modulating primary production and influencing the distribution of submerged aquatic vegetation. Although less well studied, turbidity can also have significant effects on trophic interactions and food webs by modifying light penetration and scattering, influencing foraging ability of visual-hunting predators such as fishes. By interfering with visual foragers, turbidity may shift food webs towards predators that forage with other sensory modalities (e.g. chemoreception and mechanoreception), consequently altering food web structure. We analysed turbidity effects on estuarine community composition and biodiversity in the Gulf of Mexico by analysing an 18-year fisheries-independent data set and assessing communities inhabiting contemporary oyster reefs (Crassostrea virginica). In the long-term data set, elevated turbidity was associated with decreased fish species richness and diversity and higher abundances of benthic species that rely more on chemoreception for foraging and predator avoidance (e.g. crabs). High turbidity may provide a predation refuge for crabs and other benthic organisms that visually oriented fish prey upon. On oyster reefs, crabs readily consume suspension-feeding organisms including newly settled oysters and porcelain crabs (Petrolisthes armatus). Both were significantly less abundant in high turbidity. Human practices that increase turbidity may indirectly influence trophic interactions, species distributions, ecosystem function, and biodiversity.
Trends in the prevalence of cognitive impairment in Chinese older adults: based on the Chinese Longitudinal Healthy Longevity Survey cohorts from 1998 to 2014
Authors: Kuang Weihong , Gao Mingyue , Tian Liantian , Wan Yang , Qiu Peiyuan
Published: October 2019

In the context of a rapidly ageing Chinese population, this study aims to examine trends in the prevalence of cognitive impairment among people ≥65 y of age in China. Our sample is 72 821 adults aged 65–105 y from the seven waves of the Chinese Longitudinal Healthy Longevity Survey, a national mixed longitudinal cohort. The Chinese version of the Mini-Mental State Examination was used to measure CI. Risk factor-adjusted prevalence trend was examined using multilevel regression models. Age-standardized prevalence of cognitive impairment increased from 11.00% in 1998 to 11.84% in 2008 and decreased to 8.88% in 2014. Older age, female gender, less education, rural residence, not married, lack of physical and cognitive activities, suffering from stroke, vision and hearing impairment, and activities of daily living disability were negatively associated with cognitive impairment. Our study suggests a decreasing trend of cognitive impairment prevalence in China. However, whether decreasing prevalence will contribute to a reduced burden of cognitive impairment given the ageing of the population is unknown.
Supplemental effects of dietary nucleotides on intestinal health and growth performance of newly weaned pigs
Authors: Jang Ki Beom , Kim Sung Woo
Published: October 2019

Intestinal challenges upon weaning would increase the needs of nucleotides for enterocyte proliferation, whereas de novo synthesis maybe insufficient. This study aimed to evaluate supplemental effects of dietary nucleotides on intestinal health and growth performance in newly weaned pigs. Fifty newly weaned pigs (19-d-old, 25 barrows and 25 gilts, 4.76 ± 0.42 kg BW) were individually housed and allotted to 5 treatments with increasing nucleotide supplementation (0, 50, 150, 250, and 500 mg/kg) based on a randomized complete block design with the initial BW and sex as blocks. Dietary nucleotides were provided from YT500 (Hinabiotech, Guangzhou, China). Pigs were fed for 21 d based on 2 phases (phase 1: 11 d and phase 2: 10 d) and experimental diets were formulated to meet or exceed nutrient requirements suggested by NRC (2012). Feed intake and BW were recorded. Titanium oxide (0.4%) was added as an indigestible marker from day 17. Plasma collected on day 18 was used to measure tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and malondialdehyde (MDA). Pigs were euthanized on day 21 to collect tissues to evaluate TNF-α, IL-6, MDA, morphology, and crypt cell proliferation rate in the jejunum. Ileal digesta were collected to measure ileal nutrient digestibility. Data were analyzed using contrasts in the MIXED procedure of SAS. Nucleotide supplementation increased (P < 0.05) ADFI in phase 1. Nucleotide supplementation at 50 and 150 mg/kg increased (P < 0.05) ADG in phase 1, whereas increased (P < 0.05) ADFI and tended to increase (P = 0.082) ADG in overall. Increasing nucleotide supplementation changed (quadratic, P < 0.05) villus height-crypt ratio (at 247 mg/kg) and decreased (linear, P < 0.05) crypt cell proliferation rate in the jejunum. Increasing nucleotide supplementation reduced (P < 0.05) jejunal IL-6 (at 50 and 150 mg/kg) and tended to change (quadratic, P = 0.074) plasma MDA (at 231 mg/kg). Nucleotide supplementation at 50 and 150 mg/kg increased (P < 0.05) ileal digestibility of energy and ether extract. In conclusion, nucleotide supplementation at a range of 50 to 250 mg/kg in the diets seems to be beneficial to newly weaned pigs by enhancing growth performance possibly due to reduced intestinal inflammation and oxidative stress as well as improved intestinal villi structure and energy digestibility.
Diarrhea-Predominant Irritable Bowel Syndrome: Medical Management Update
Authors: Andrews Christopher N , Bradette Marc
Published: October 2019

Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder, which impacts the quality of life, work productivity and social activities of patients. Diarrhea-predominant IBS (IBS-D) is one of several subtypes, and accounts for approximately one third of all cases. Currently available treatments are typically unable to alleviate the cardinal symptoms of IBS-D, including abdominal pain and diarrhea, and a clinical unmet need remains for an effective treatment which simultaneously relieves multiple symptoms. Patients may benefit from a multipronged, individualized approach, including dietary modifications, and psychological and pharmacological therapies. The aim of this review is to provide an update on the available and upcoming treatment options for IBS-D in Canada, with reference to the recently updated Canadian IBS consensus guidelines. Initial treatment approaches include lifestyle modifications, dietary modifications, and non-prescription therapies such as peppermint oil. While some medications such as tricyclic antidepressants are also used to treat IBS-D symptoms, eluxadoline and rifaximin are the only two pharmacological therapies approved for the treatment of IBS-D in Canada. Key clinical trial data for the currently available pharmacological options are presented to provide an overview of the efficacy and safety of these agents
Evaluating Soybean Aphid-Resistant Varieties in Different Environments to Estimate Financial Outcomes
Authors: Dean Ashley N , Pritchard Shelby , Tyndall John C , Hodgson Erin W , O’Neal Matthew E
Published: October 2019

Farmers face many choices when selecting seed for soybean (Glycine max (L.) Merr.) production, including highly desired herbicide tolerance traits. Despite the convenience of herbicide tolerance, resistant weeds and technology fees may reduce utility and profitability of these varieties, especially when commodity prices are low. Sporadic outbreaks of soybean aphid (Aphis glycines Matsumura, Hemiptera: Aphididae) that require insecticide use for optimal yield can be a further complication for farmers in Iowa. Soybean aphid-resistant varieties are commercially available, but in limited genetic backgrounds without herbicide tolerance. We hypothesized yield and value of resistance traits will vary based on the environment. We established plots at two locations with different risks of soybean aphid outbreaks and used two planting dates at each location to mimic different yield environments. In 2016 and 2017, we planted four varieties that varied in their susceptibility to soybean aphids and glyphosate, and applied insecticides if aphid populations reached an economic threshold. Regardless of genetic background, aphid-resistant varieties prevented populations from reaching the economic threshold at all environments. We observed no significant difference in yield between resistant and susceptible varieties, revealing this trait is as effective at protecting yield as an insecticide application on susceptible varieties at the high-risk location. We also explored the value of each variety in different environments. Resistant varieties produced greater potential net revenue than susceptible varieties at the high-risk location, while the opposite occurred at the low-risk location. Resistant varieties with herbicide tolerance, if made available, would be the most valuable across all environments.
Integrating Probability and Nonprobability Samples for Survey Inference
Authors: Wiśniowski Arkadiusz , Sakshaug Joseph W , Perez Ruiz Diego Andres , Blom Annelies G
Published: October 2019

Survey data collection costs have risen to a point where many survey researchers and polling companies are abandoning large, expensive probability-based samples in favor of less expensive nonprobability samples. The empirical literature suggests this strategy may be suboptimal for multiple reasons, among them that probability samples tend to outperform nonprobability samples on accuracy when assessed against population benchmarks. However, nonprobability samples are often preferred due to convenience and costs. Instead of forgoing probability sampling entirely, we propose a method of combining both probability and nonprobability samples in a way that exploits their strengths to overcome their weaknesses within a Bayesian inferential framework. By using simulated data, we evaluate supplementing inferences based on small probability samples with prior distributions derived from nonprobability data. We demonstrate that informative priors based on nonprobability data can lead to reductions in variances and mean squared errors for linear model coefficients. The method is also illustrated with actual probability and nonprobability survey data. A discussion of these findings, their implications for survey practice, and possible research extensions are provided in conclusion.
Bringing the city to the country: relationships between streetscape vegetation type and bird assemblages in a major regional centre
Authors: Champness Brendan S , Palmer Grant C , Fitzsimons James A
Published: October 2019

Urbanisation is a leading cause of biodiversity loss and habitat fragmentation internationally, and the conservation of representative native assemblages is a challenge confronting environmental managers in expanding urban landscapes. This study investigates the bird assemblages occurring in a rapidly growing regional centre, Ballarat, southeastern Australia. It aims to examine the relationships between urbanisation and bird communities in a regional city by investigating the differences in bird assemblage composition related to the type of vegetation (native or exotic) in urban streetscapes. Bird surveys were completed across four broad habitat types: remnant vegetation, exotic streetscapes, native streetscapes and newly developed streetscapes. Each habitat type had three 1 ha replicate sites. Results show that remnant vegetation fringing residential areas and native streetscapes supported around 60% more native bird species than exotic and newly developed streetscapes. Avian species composition was significantly different between broad habitat types, with remnant vegetation and native streetscapes maintaining representative native bird assemblages, but exotic streetscapes and newly developed streetscapes were dominated by introduced birds. Our results show that, for representative native bird assemblages to be maintained in urban areas, the maintenance of remnant and native vegetation is essential.
Management of Melanoma Patients by Non-Dermatologists in the Military Health System: A Retrospective Observational Study
Authors: Helmandollar Kenneth J , Lorei Nathan C , Clement Barak C , Hoverson Kara R , Logemann Nicholas F
Published: October 2019

Introduction

Compared to their civilian counterparts, military personnel can have more exposure to sunlight and, as recent studies have shown, do have an increased incidence of melanoma. Given the inherent challenges service members may face in getting appropriate care whether because of operational tempo, deployments, and/or austere locations, many are initially diagnosed by specialties other than dermatology. In this study, we sought to determine if patients within the military health system were receiving appropriate follow-up management after biopsies by non-dermatologists led to the diagnosis of melanoma by pathology.

Materials and Methods

Using the Co-Path system, 1,000 patients were identified who had first time biopsies positive for melanoma. Of these, 73 were originally biopsied by non-dermatologists. Retrospective medical record review was performed to determine specialties of the non-dermatologists, staging of melanoma at diagnosis, referrals to specialists and dermatologists, and adherence to National Comprehensive Cancer Network guidelines. The study protocol was approved by the Walter Reed National Military Medical Center Institutional Review Board, protocol number WRNMMC-EDO-2017-0030, in compliance with all applicable federal regulations governing the protection of human subject research.

Results

Family medicine physicians made up the majority of non-dermatologists involved in performing biopsies that led to the diagnosis of melanoma in this study. Most patients were Stage I (pT1a), and the average time from initial biopsy to further wide excision biopsy was 18 days. Sixty-seven of the 73 patients biopsied by non-dermatologists received referrals to dermatologists, and 55 of the 67 patients followed through with being seen. Follow-up full body skin exams were performed on 55 of the 73 patients, with dermatologists conducting the majority of them. National Comprehensive Cancer Network guidelines were followed in 45 of the 73 patients, with an additional 24 patients having insufficient evidence to determine if guidelines were adhered to.

Conclusion

Our study demonstrated that a number of different specialties outside of dermatology are involved in performing biopsies on patients in which melanoma is a concern. Although the results show that the majority of patients biopsied by non-dermatologists received appropriate follow-up care, there is still room to improve to ensure that all melanoma patients receive referrals to and are seen by dermatologists after a diagnosis of melanoma.
Revealing the cosmic evolution of boxy/peanut-shaped bulges from HST COSMOS and SDSS
Authors: Kruk Sandor J , Erwin Peter , Debattista Victor P , Lintott Chris
Published: October 2019

Vertically thickened bars, observed in the form of boxy/peanut (B/P) bulges, are found in the majority of massive barred disc galaxies in the local Universe, including our own. B/P bulges indicate that their host bars have suffered violent bending instabilities driven by anisotropic velocity distributions. We investigate for the first time how the frequency of B/P bulges in barred galaxies evolves from z = 1 to z ≈ 0, using a large sample of non-edge-on galaxies with masses M⋆ > 1010 M⊙, selected from the HST COSMOS survey. We find the observed fraction increases from $0^{+3.6}_{-0.0}{{\ \rm per\ cent}}$ at z = 1 to $37.8^{+5.4}_{-5.1}$ per cent at z = 0.2. We account for problems identifying B/P bulges in galaxies with low inclinations and unfavourable bar orientations, and due to redshift-dependent observational biases with the help of a sample from the Sloan Digital Sky Survey, matched in resolution, rest-frame band, signal-to-noise ratio and stellar mass and analysed in the same fashion. From this, we estimate that the true fraction of barred galaxies with B/P bulges increases from ∼10 per cent at z ≈ 1 to $\sim 70{{\ \rm per\ cent}}$ at z = 0. In agreement with previous results for nearby galaxies, we find a strong dependence of the presence of a B/P bulge on galaxy stellar mass. This trend is observed in both local and high-redshift galaxies, indicating that it is an important indicator of vertical instabilities across a large fraction of the age of the Universe. We propose that galaxy formation processes regulate the thickness of galaxy discs, which in turn affect which galaxies experience violent bending instabilities of the bar.