bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preventing Aspiration Complications
Authors: Wangen Tina , Hatlevig Janelle , Pifer Gina , Vitale Kirsten 
Published: August 2019

Aims:
The aim of this study was to decrease the number of patients with acquired aspiration mortality.

Design:
This was an evaluation research study. Data were collected on acutely ill hospitalized patients from January 2013 to December 2017.

Methods:
In 2016, a 1100-bed Midwestern quaternary care facility found an increasing trend in mortality rates of patients with acquired aspiration from 2013 to 2015. A need for improved detection of patients at risk of aspiration was identified. A multidisciplinary team analyzed this need and developed a screening process found on the American College of Chest Physicians practice guidelines and the Massey Bedside Swallowing Screen to reduce these rates. Nurses implemented the aspiration risk screening process on all hospitalized patients. Data were collected through nursing responses and chart reviews.

Results:
Initial implementation of the aspiration risk screening process yielded procedural concerns that were ameliorated through increased education and refinement of the screen. After refinement and reimplementation, mortality data from 2016 to 2017 revealed a decrease to zero aspiration-related events.

Conclusion:
Our findings suggest implementation of a nursing-led aspiration risk screening process with acutely ill patients is a factor in decreasing patient mortality from acquired aspiration. These clinical practice changes of identifying patients at risk of aspirating and involving dysphagia therapists prior to oral intake increase patient safety while decreasing acquired aspiration mortality.

Impact:
This study addressed upward trends in patient mortality with acquired aspiration. Mortality rates declined after implementation of the aspiration risk screening process on hospitalized patients. These findings have potential to impact healthcare personnel and all acutely ill hospitalized patients.
Postsurgical Opioid Prescriptions and Risk of Long-term Use
Authors: Young Jessica C. , Dasgupta Nabarun , Chidgey Brooke A. , Jonsson Funk Michele 
Published: August 2019

Objective:
The aim of this study was to evaluate differences in risk of long-term opioid therapy after surgery among an opioid-naive population using varying cutoffs based on days supplied (DS), total morphine milligram equivalents (MME) dispensed, and quantity of pills (QTY) dispensed.

Background:
In response to the US opioid crisis, opioid prescription (Rx) limits have been implemented on a state-by-state basis beginning in 2016. However, there is limited evidence informing appropriate prescribing limits, and the effect of these policies on long-term opioid therapy.

Methods:
Using the MarketScan claims databases, we identified all opioid-naive patients undergoing outpatient surgery between July 1, 2006 and June 30, 2015. We identified the initial postsurgical opioid prescribed, examining the DS, total MME, and QTY dispensed. We used Poisson to estimate adjusted risk differences and risk ratios of long-term opioid use comparing those receiving larger versus smaller volume of opioids.

Results:
We identified 5,148,485 opioid-naive surgical patients. Overall, 55.5% received an opioid for postoperative pain, with median days supply = 5 and median total MME = 240. The proportion of patients receiving prescriptions above 7 DS increased from 11% in 2006 to 19% in 2015. Among those receiving postoperative opioids, 8% had long-term opioid use, and risk of long-term use was 1.16 times [95% confidence interval (CI), 1.10–1.25] higher among those receiving >7 days compared with those receiving ≤7 days. Those receiving >400 total MME (15% of patients) were at 1.17 times (95% CI, 1.10–1.25) the risk of long-term use compared with those receiving ≤400 MME.

Conclusions:
Between 2005 and 2015, the amounts of opioids prescribed for postoperative pain increased dramatically, and receipt of larger volume of opioids was associated with increased risk of long-term opioid therapy.
Understanding the emergence of bacterial pathogens in novel hosts
Authors: Bonneaud Camille , Weinert Lucy A. , Kuijper Bram 
Published: August 2019

Our understanding of the ecological and evolutionary context of novel infections is largely based on viral diseases, even though bacterial pathogens may display key differences in the processes underlying their emergence. For instance, host-shift speciation, in which the jump of a pathogen into a novel host species is followed by the specialization on that host and the loss of infectivity of previous host(s), is commonly observed in viruses, but less often in bacteria. Here, we suggest that the extent to which pathogens evolve host generalism or specialism following a jump into a novel host will depend on their level of adaptation to dealing with different environments, their rates of molecular evolution and their ability to recombine. We then explore these hypotheses using a formal model and show that the high levels of phenotypic plasticity, low rates of evolution and the ability to recombine typical of bacterial pathogens should reduce their propensity to specialize on novel hosts. Novel bacterial infections may therefore be more likely to result in transient spillovers or increased host ranges than in host shifts. Finally, consistent with our predictions, we show that, in two unusual cases of contemporary bacterial host shifts, the bacterial pathogens both have small genomes and rapid rates of substitution. Further tests are required across a greater number of emerging pathogens to assess the validity of our hypotheses.
This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
Percolation models of pathogen spillover
Authors: Washburne Alex D. , Crowley Daniel E. , Becker Daniel J. , Manlove Kezia R. , Childs Marissa L. , Plowright Raina K. 
Published: August 2019

Predicting pathogen spillover requires counting spillover events and aligning such counts with process-related covariates for each spillover event. How can we connect our analysis of spillover counts to simple, mechanistic models of pathogens jumping from reservoir hosts to recipient hosts? We illustrate how the pathways to pathogen spillover can be represented as a directed graph connecting reservoir hosts and recipient hosts and the number of spillover events modelled as a percolation of infectious units along that graph. Percolation models of pathogen spillover formalize popular intuition and management concepts for pathogen spillover, such as the inextricably multilevel nature of cross-species transmission, the impact of covariance between processes such as pathogen shedding and human susceptibility on spillover risk, and the assumptions under which the effect of a management intervention targeting one process, such as persistence of vectors, will translate to an equal effect on the overall spillover risk. Percolation models also link statistical analysis of spillover event datasets with a mechanistic model of spillover. Linear models, one might construct for process-specific parameters, such as the log-rate of shedding from one of several alternative reservoirs, yield a nonlinear model of the log-rate of spillover. The resulting nonlinearity is approximately piecewise linear with major impacts on statistical inferences of the importance of process-specific covariates such as vector density. We recommend that statistical analysis of spillover datasets use piecewise linear models, such as generalized additive models, regression clustering or ensembles of linear models, to capture the piecewise linearity expected from percolation models. We discuss the implications of our findings for predictions of spillover risk beyond the range of observed covariates, a major challenge of forecasting spillover risk in the Anthropocene.This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
Spatial and temporal transcriptomics reveal microglia-astroglia crosstalk in the amyloid-β plaque cell niche of Alzheimer’s disease
Authors: Chen Wei-Ting , Lu Ashley , Craessaerts Katleen , Pavie Benjamin , Sala Frigerio Carlo , Mancuso Renzo , Qian Xiaoyan , Lalakova Jana , Kühnemund Malte , Voytyuk Iryna , Wolfs Leen , Snellinx An , Munck Sebastian , Jurek Aleksandra , Fernandez Navarro Jose , Saido Takaomi C , Lundeberg Joakim , Fiers Mark , De Strooper Bart 
Published: August 2019

SummaryThe linear cause-consequence relationship linking amyloid-β peptide (Aβ) accumulation to neuronal dysfunction in Alzheimer disease (AD) is gradually replaced by the concept that Aβ initiates complex inflammatory-like cellular alterations that progressively become Aβ independent and lead to brain dyshomeostasis. Little is known about the pathophysiology of this cellular phase of AD. We use here two orthogonal technologies, Spatial Transcriptomics and in situ sequencing, to analyse the transcriptome changes in cells in the amyloid-β plaque niche in a knock-in mouse model for AD. We identify a multicellular co-expressed gene network of 57 Plaque-Induced Genes (PIGs) that define a series of co-ordinated and spatially restricted microglia, astroglia and oligodendrocyte responses to progressing amyloid plaques encompassing complement, oxidative stress and inflammation. A separate oligodendrocyte network suggests abnormal myelination. Spatial Transcriptomics provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.
Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)
Authors: Cruz Mariana Vargas , Mori Gustavo Maruyama , Oh Dong-Ha , Dassanayake Maheshi , Zucchi Maria Imaculada , Oliveira Rafael Silva , de Souza Anete Pereira 
Published: August 2019

AbstractEnvironmental variation along the geographical space can shape populations by natural selection. In the context of global warming, accompanied by substantial changes in precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the Black-Mangrove (Avicennia germinans). Fifty-seven trees were sampled in seven sites differing markedly on precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the genotype association with the precipitation of the warmest quarter and the annual precipitation. We also found candidate loci for selection, based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci present within coding sequences were functionally associated with central aspects of drought-tolerance or plant response to drought. Complementarily, our results suggest the occurrence of rapid evolution of a population, likely in response to sudden and persistent limitation in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included reduction in tree size and changes in allele frequencies and in transcripts expression levels associated with increased drought-tolerance, through accumulation of osmoprotectants and antioxidants, biosynthesis of plant cuticle, protection against stress-induced proteins degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
Single-Cell RNA-Seq Reveals Naïve B cells Associated with Better Prognosis of HCC
Authors: He Jian , Lin Yingxin , Su Xianbin , Luo Qing , Ghazanfar Shila , Yang Jean Y H , Han Ze-guang 
Published: August 2019

AbstractHepatocellular Carcinoma (HCC) is a type of malignant solid tumor, causing high morbidity and mortality around the world and the major portion of HCC patients is from China. Cancer immunotherapies have shown some clinical responses in treating some types of cancer but did not shown significant efficiency in HCC treatment. This in part due to the impact of immune cells in the tumor microenvironment. It is commonly believed that HCC is a heterogeneous solid tumor and the microenvironment of HCC plays an important role in tumorgenesis and development. Currently, the residents of the microenvironment of HCC is not well-defined and clarification, especially the immune cells, which we believe that paly pivotal roles in tumorgenesis and development. To depict the landscape of the composition, lineage and functional states of the immune cells in HCC, we performed single-cell RNA sequencing on Diethylnitrosamine (DEN)-induced mouse HCC model. We observed heterogeneity within the immune and hepatocytes both in the precancerous condition of tumorigenesis and cancerous condition of HCC. In this study we found that the disease-associated changes appeared early in pathological progression and were highly cell-type specific. Specific subsets of T and B cells preferentially enriched in HCC, and we identified signature genes for each subset. Additionally, we mapped this group of specific cells to the human TCGA database. We found a cluster of naïve B cells characterized by high expression of CD38 associated with better prognosis of human HCC. Our study demonstrates signaling interaction map based on receptor-ligand bonding on the single-cell level could broaden our comprehending of cellular networks in varies status. Our finding provides a new approach for patient stratification and will help further understand the functional states, dynamics and signaling interaction of B cells in hepatocellular carcinoma, and may provide a novel insight and therapeutics for the HCC.
Automated and rapid self-report of nociception in transgenic mice
Authors: Black Christopher J. , Allawala Anusha B. , Bloye Kiernan , Vanent Kevin N. , Edhi Muhammad M. , Saab Carl Y. , Borton David A. 
Published: August 2019

AbstractA time-resolved, conscious report of detected nociceptive stimuli in mice offers an opportunity to examine the relationship between higher order neural circuits and pain perception. We have developed a detection behavior in transgenic mice that leverages temporally precise and cell-specific stimulation to elicit self-reports of nociception. Conscious reporting of peripheral nociceptive input may help identify neural mechanisms that generate pain perception.
Identification of 15 new bypassable essential genes of fission yeast
Authors: Takeda Aoi , Saitoh Shigeaki , Ohkura Hiroyuki , Sawin Kenneth E. , Goshima Gohta 
Published: August 2019

AbstractEvery organism has a different set of genes essential for its viability. This indicates that an organism can become tolerant to the loss of an essential gene under certain circumstances during evolution, via the manifestation of ‘masked’ alternative mechanisms. In our quest to systematically uncover masked mechanisms in eukaryotic cells, we developed an extragenic suppressor screening method using haploid spores deleted of an essential gene in the fission yeastSchizosaccharomyces pombe. We screened for the ‘bypass’ suppressors of lethality of 92 randomly selected genes that are essential for viability in standard laboratory culture conditions. Remarkably, extragenic mutations bypassed the essentiality of as many as 20 genes (22%), 15 of which have not been previously reported. Half of the bypass-suppressible genes were involved in mitochondria function; we also identified multiple genes regulating RNA processing. 18 suppressible genes were conserved in the budding yeastSaccharomyces cerevisiae, but 13 of them were non-essential in that species. These trends are consistent with a recent independent bypass-of-essentiality (BOE) screening of 142 fission yeast genes conducted with more elaborate methodology (Liet al., 2019). Thus, our study reinforces the emerging view that BOE is not a rare event and that each organism may be endowed with secondary or backup mechanisms that can substitute for primary mechanisms in various biological processes. Furthermore, the robustness of our simple spore-based methodology paves the way for genome-scale BOE screening.
Fungal traits important for soil aggregation
Authors: Lehmann Anika , Zheng Weishuang , Ryo Masahiro , Soutschek Katharina , Rongstock Rebecca , Maaß Stefanie , Rillig Matthias C. 
Published: August 2019

AbstractSoil health and sustainability is essential for ecosystem functioning and human well-being. Soil structure, the complex arrangement of soil into aggregates and pore spaces, is a key feature of soils under the influence of soil life. Soil biota, and among them filamentous saprobic fungi, have well-documented effects on soil aggregation. However, it is unclear what fungal properties, or traits, contribute to the overall positive effect on soil aggregation. So far, we lack a systematic investigation of a broad suite of fungal species for their trait expression and the relation of these traits to their soil aggregation capability.Here, we apply a trait-based approach to a set of 15 traits measured under standardized conditions on 31 fungal strains including Ascomycota, Basidiomycota and Mucoromycota, all isolated from the same soil.We found a spectrum of soil aggregate formation capability ranging from neutral to positive and large differences in trait expression among strains. We identified biomass density (positive effects), leucine aminopeptidase activity (negative effects) and phylogeny as important modulators of fungal aggregate formation capability. Our results point to a typical suite of traits characterizing fungi that are good soil aggregators; this could inform screening for fungi to be used in biotechnological applications, and illustrates the power of employing a trait-based approach to unravel biological mechanisms of soil aggregation, which could now be extended to other organism groups.
A single TRPV1 amino acid controls species sensitivity to capsaicin
Authors: Chu Ying , Cohen Bruce E. , Chuang Huai-hu 
Published: August 2019

AbstractChili peppers produce capsaicin, the principle chemical that accounts for the culinary sensations of heat. Capsaicin activates the transient receptor potential cation channel subfamily V member 1 (TRPV1) on sensory neurons to alter the membrane potential to induce pain. While structural studies have identified residues important for the binding of capsaicin to rat TRPV1, there is still no clear understanding of differential capsaicin sensitivity of TRPV1 between birds and mammals. To determine the residues dictating relative capsaicin sensitivity among species, we have used intracellular Ca2+imaging to characterize chimeras composed of capsaicin-sensitive rat TRPV1 (rTRPV1) and capsaicin-insensitive chicken TRPV1 (cTRPV1) with a series of capsaicinoids. We find that chimeras containing rat E570-V686 swapped into chicken receptors displays capsaicin sensitivity, and that a single amino acid substitution in the S4-S5 helix, changing the alanine at position 578 in the chick receptor to a glutamate, is sufficient to endow micromolar capsaicin sensitivity. Moreover, introduction of lysine, glutamine or proline at A578 also install capsaicin sensitivity in cTRPV1. Comparing the derivatives Cap-EA and Cap-EMA with capsaicin, these two compounds with the hydrophilic vanilloid-like moiety affect the protein-ligand interaction. The ability of 10 μM Cap-EA to activate cTRPV1-A578E and the differential response of mutants to the analogs suggests that chick A578 may participate in vanilloid binding, as does the corresponding rTRPV1 site. The hydrophilic vanilloid agonist zingerone 500 μM failed to activate any A578 mutants that retained capsaicin sensitivity, suggesting that the vanilloid group alone is not sufficient for receptor activation. Replacing the rTRPV1-E570 residue with K, Q shows a similar tendency to maintain the receptor capsaicin sensitivity. Our study demonstrates a subtle modification on different species TRPV1 globally alter their capsaicin response.
Effectiveness of bilateral and multilateral concessional debts on economic growth in Africa
Authors: Ezeaku Hillary Chijindu , Egbo Obiamaka P. , Nwakoby Ifeoma , Onwumere Josaphat U.J. 
Published: August 2019

PurposeThe purpose of this paper is to assess the relative effectiveness of bilateral and multilateral concessional debts on economic growth in 32 sub-Saharan African (SSA) countries over the period 1985–2016.Design/methodology/approachThe recently developed dynamic panel autoregressive distributed lag models which comprise three different estimators, the mean group, pooled mean group (PMG) estimator and dynamic fixed effect, were applied to estimate the model. Following these estimators, the Hausman test was employed to determine the efficient and consistent estimator.FindingsThe results showed that bilateral concessional debts had a negative impact on growth. From the findings, a 1 percent increase in bilateral concessional debts induced economic growth to decline by 38.1 percent points in the short run, and by 7.1 percent points in the long run; convergence to long-run equilibrium adjusted at the speed of 90 percent on an annual basis. Multilateral concessional debts were found to have a positive impact on growth both in the short and long run. The coefficient of the error term was negatively signed and indicates that deviations from the long-run equilibrium path were being corrected at the speed of 89.4 percent annually.Originality/valueTo the authors’ best knowledge, empirical studies that specifically seek to examine how bilateral and multilateral concessional debts impacted on growth are yet to attract the attention of researchers. As a result, this study will complement related extant growth studies, especially in the case of SSA.
Public libraries as public sphere institutions
Authors: Audunson Ragnar , Aabø Svanhild , Blomgren Roger , Hobohm Hans-Christoph , Jochumsen Henrik , Khosrowjerdi Mahmood , Mumenthaler Rudolf , Schuldt Karsten , Rasmussen Casper Hvenegaard , Rydbeck Kerstin , Tóth Máté , Vårheim Andreas 
Published: August 2019

Purpose
The purpose of this paper is to analyze the role of public libraries as institutions underpinning a democratic public sphere as reasons legitimizing libraries compared to reasons that are more traditional and the actual use of libraries as public sphere arenas.

Design/methodology/approach
A survey of representative samples of the adult population in six countries – Denmark, Sweden, Norway, Germany, Hungary and Switzerland – was undertaken.

Findings
Legitimations related to the libraries role as a meeting place and arena for public debate are ranked as the 3 least important out of 12 possible legitimations for upholding a public library service. Libraries are, however, used extensively by the users to access citizenship information and to participate in public sphere relevant meetings.

Originality/value
Few studies have empirically analyzed the role of libraries in upholding a democratic and sustainable public sphere. This study contributes in filling that gap.