bluuebunny/crossref_metadata_2025_split huggingface dataset:
New dot-blot method for evaluating the effect of inactivators on mite and Japanese cedar pollen allergens
Authors: Yoshida Megumi , Mizukami Keijiro , Kurata Keigo , Nasukawa Tadahiro , Uchiyama Jumpei , Sakaguchi Masahiro 
Published: August 2021

ABSTRACTAs a method of evaluating the effect of inactivators on allergens while suppressing the effect of inactivator on the assay, we developed new dot-blot method that combines immunostaining and protein detection methods. This method is useful for evaluating whether the inactivator can inactivate allergens rather than removing them from the assay.
GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field
Authors: Fan Yongxian , Chen Meijun , Pan Xiaoyong 
Published: August 2021

AbstractLong noncoding RNAs (lncRNAs) play important roles in various biological regulatory processes, and are closely related to the occurrence and development of diseases. Identifying lncRNA-disease associations is valuable for revealing the molecular mechanism of diseases and exploring treatment strategies. Thus, it is necessary to computationally predict lncRNA-disease associations as a complementary method for biological experiments. In this study, we proposed a novel prediction method GCRFLDA based on the graph convolutional matrix completion. GCRFLDA first constructed a graph using the available lncRNA-disease association information. Then, it constructed an encoder consisting of conditional random field and attention mechanism to learn efficient embeddings of nodes, and a decoder layer to score lncRNA-disease associations. In GCRFLDA, the Gaussian interaction profile kernels similarity and cosine similarity were fused as side information of lncRNA and disease nodes. Experimental results on four benchmark datasets show that GCRFLDA is superior to other existing methods. Moreover, we conducted case studies on four diseases and observed that 70 of 80 predicted associated lncRNAs were confirmed by the literature.
Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features
Authors: Dong Ji , Zhou Peijie , Wu Yichong , Chen Yidong , Xie Haoling , Gao Yuan , Lu Jiansen , Yang Jingwei , Zhang Xiannian , Wen Lu , Li Tiejun , Tang Fuchou 
Published: August 2021

Abstract
With the rapid development of single-cell sequencing techniques, several large-scale cell atlas projects have been launched across the world. However, it is still challenging to integrate single-cell RNA-seq (scRNA-seq) datasets with diverse tissue sources, developmental stages and/or few overlaps, due to the ambiguity in determining the batch information, which is particularly important for current batch-effect correction methods. Here, we present SCORE, a simple network-based integration methodology, which incorporates curated molecular network features to infer cellular states and generate a unified workflow for integrating scRNA-seq datasets. Validating on real single-cell datasets, we showed that regardless of batch information, SCORE outperforms existing methods in accuracy, robustness, scalability and data integration.
Distinctive wood anatomy of early-diverging Asteraceae: Barnadesioideae
Authors: Carlquist Sherwin , Stuessy Tod F , Urtubey Estrella 
Published: August 2021

AbstractAsteraceae subfamily Barnadesioideae (ten genera, c. 90 species), confined to South America, are sister to the remainder of the family. The relative antiquity of the barnadesioids might lead one to expect that they contain more wood features plesiomorphic for the family, but only one character clearly falls in that category. Pits on imperforate tracheary elements are bordered (except for annuals), whereas simple pits occur in two related families, Calyceraceae (part) and Stylidiaceae (all that have been examined); in Goodeniaceae bordered pits only occur. By attaining fully bordered pits in Chuquiraga, the imperforate tracheary elements qualify as an apomorphy, ‘neotracheids’, valuable for resisting embolism formation in dry and cold South American habitats. Neotracheids are found also in Loricaria (Asteraceae: Inuleae), also from these habitats. Neotracheids, like plesiomorphic tracheids, are conductive, unlike fibre tracheids and libriform fibres. Other barnadesioid wood characters adapted to cold and drought include grouping of vessels, high vessel density, shorter vessel elements and helical sculpture (including helical thickenings on lumen-facing walls) of secondary xylem vessels. In Chuquiraga and Dasyphyllum, these helical thickenings are bordered in some species (new report for angiosperms). Some of the barnadesioid adaptations to cold and drought can be found in North American Artemisia spp. (Asteraceae: Anthemideae), especially in montane and desert areas. Wood features of barnadesioids match their respective habits and habitats: a few trees; shrubs of humid, dry or desert areas; a distinctive rhizomatous succulent in the pampas (Schlechtendalia); a scree/gravel perennial (Huarpea) and two genera of annuals, one with succulent leaves (Duseniella) and one with rayless (at least at first) stems in arid and open soils (Doniophyton). Diversity is unusual considering the small size of the subfamily. Examples of endodermal crystals (Arnaldoa only), pith sclereids and primary xylem fibres are cited.
Short-Term Facilitation of Long-Range Corticocortical Synapses Revealed by Selective Optical Stimulation
Authors: Martinetti Luis E , Bonekamp Kelly E , Autio Dawn M , Kim Hye-Hyun , Crandall Shane R 
Published: August 2021

Abstract
Short-term plasticity regulates the strength of central synapses as a function of previous activity. In the neocortex, direct synaptic interactions between areas play a central role in cognitive function, but the activity-dependent regulation of these long-range corticocortical connections and their impact on a postsynaptic target neuron is unclear. Here, we use an optogenetic strategy to study the connections between mouse primary somatosensory and motor cortex. We found that short-term facilitation was strong in both corticocortical synapses, resulting in far more sustained responses than local intracortical and thalamocortical connections. A major difference between pathways was that the synaptic strength and magnitude of facilitation were distinct for individual excitatory cells located across all cortical layers and specific subtypes of GABAergic neurons. Facilitation was dependent on the presynaptic calcium sensor synaptotagmin-7 and altered by several optogenetic approaches. Current-clamp recordings revealed that during repetitive activation, the short-term dynamics of corticocortical synapses enhanced the excitability of layer 2/3 pyramidal neurons, increasing the probability of spiking with activity. Furthermore, the properties of the connections linking primary with secondary somatosensory cortex resemble those between somatosensory–motor areas. These short-term changes in transmission properties suggest long-range corticocortical synapses are specialized for conveying information over relatively extended periods.
Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults
Authors: Johnson Stuart , Lavergne Valéry , Skinner Andrew M , Gonzales-Luna Anne J , Garey Kevin W , Kelly Ciaran P , Wilcox Mark H 
Published: August 2021

Abstract
This clinical practice guideline is a focused update on management of Clostridioides difficile infection (CDI) in adults specifically addressing the use of fidaxomicin and bezlotoxumab for the treatment of CDI. This guideline was developed by a multidisciplinary panel representing the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA). This guideline is intended for use by healthcare professionals who care for adults with CDI, including specialists in infectious diseases, gastroenterologists, hospitalists, pharmacists, and any clinicians and healthcare providers caring for these patients. The panel’s recommendations for the management CDI are based upon evidence derived from topic-specific systematic literature reviews. Summarized below are the recommendations for the management of CDI in adults. The panel followed a systematic process which included a standardized methodology for rating the certainty of the evidence and strength of recommendation using the GRADE approach (Grading of Recommendations Assessment, Development, and Evaluation). A detailed description of background, methods, evidence summary and rationale that support each recommendation, and knowledge gaps can be found online in the full text.
The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis
Authors: Miller Steve , Chiu Charles 
Published: August 2021

Abstract

Background
Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms.

Content
We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing.

Summary
The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
Biotic habitats as refugia under ocean acidification
Authors: Falkenberg Laura J , Scanes Elliot , Ducker James , Ross Pauline M 
Published: August 2021

Abstract
Habitat-forming organisms have an important role in ameliorating stressful conditions and may be of particular relevance under a changing climate. Increasing CO2 emissions are driving a range of environmental changes, and one of the key concerns is the rapid acceleration of ocean acidification and associated reduction in pH. Such changes in seawater chemistry are anticipated to have direct negative effects on calcifying organisms, which could, in turn, have negative ecological, economic and human health impacts. However, these calcifying organisms do not exist in isolation, but rather are part of complex ecosystems. Here, we use a qualitative narrative synthesis framework to explore (i) how habitat-forming organisms can act to restrict environmental stress, both now and in the future; (ii) the ways their capacity to do so is modified by local context; and (iii) their potential to buffer the effects of future change through physiological processes and how this can be influenced by management adopted. Specifically, we highlight examples that consider the ability of macroalgae and seagrasses to alter water carbonate chemistry, influence resident organisms under current conditions and their capacity to do so under future conditions, while also recognizing the potential role of other habitats such as adjacent mangroves and saltmarshes. Importantly, we note that the outcome of interactions between these functional groups will be context dependent, influenced by the local abiotic and biotic characteristics. This dependence provides local managers with opportunities to create conditions that enhance the likelihood of successful amelioration. Where individuals and populations are managed effectively, habitat formers could provide local refugia for resident organisms of ecological and economic importance under an acidifying ocean.
Social Control of Intellect: Four Features of the Academic–Media Nexus
Authors: McDevitt Michael 
Published: August 2021

Abstract
Intellect in social theory is often presented as an ideal type—the critical, iconoclastic side of the mind—but it must anticipate an audience in mediated contexts, unlike in the Kantian realm of transcendent reason. The terrain in which academia and media meet, consequently, is ripe for exploration into the fate of intellect when transgressive. This article explicates four features of the academic–media nexus that contribute to social control of intellect: instrumental rationalism of faculty, strategic management of university communication, journalistic appropriation of the “public intellectual” role, and surveillance of academic discourse. The article situates the features in a framework to recognize whether they originate primarily in academia or media, and whether the controlling process occurs through internalized norms or calculated practice. While social control is understood as recursive and reinforcing, reflexivity induced in an inter-field dynamic implies the possibility of reconciling intellect with news work.
Atherothrombotic factors and atherosclerotic cardiovascular events: the multi-ethnic study of atherosclerosis
Authors: DeFilippis Andrew P , Trainor Patrick J , Thanassoulis George , Brumback Lyndia C , Post Wendy S , Tsai Michael Y , Tsimikas Sotirios 
Published: August 2021

Abstract

Aims
Traditional atherosclerotic cardiovascular disease (ASCVD) risk factors fail to address the full spectrum of the complex interplay of atherosclerotic and atherothrombotic factors integral to ASCVD events. This study sought to examine the association between atherothrombotic biomarkers and ASCVD events.

Methods and results
The association between atherothrombotic biomarkers and 877 ASCVD events with and without adjustment for traditional risk factors was evaluated via Cox proportional hazards models and factor analysis in 5789 Multi-Ethnic Study of Atherosclerosis participants over a median follow-up of 14.7 years. Factor analysis accounted for multidimensional relationship and shared variance among study biomarkers, which identified two new variables: a thrombotic factor (Factor 1), principally defined by shared variance in fibrinogen, plasmin–antiplasmin complex, factor VIII, D-dimer, and lipoprotein(a), and a fibrinolytic factor (Factor 2), principally defined by shared variance of plasminogen and oxidized phospholipids on plasminogen. In a model including both factors, the thrombotic factor was associated with the higher risk of ASCVD events [hazard ratio (HR) 1.57, 95% confidence interval (CI) 1.45, 1.70], while the fibrinolytic factor was associated with the lower risk of ASCVD events (HR 0.76, 95% CI 0.70, 0.82), with estimated ASCVD free survival highest for low atherothrombotic Factor 1 and high atherothrombotic Factor 2.

Conclusion
Two atherothrombotic factors, one representative of thrombotic propensity and the other representative of fibrinolytic propensity, were significantly and complementarily associated with incident ASCVD events, remained significantly associated with incident ASCVD after controlling for traditional risk factors, and have promise for identifying patients at high ASCVD event risk specifically due to their atherothrombotic profile.
(Geo)Politics of Universal Periodic Review: Why States Issue and Accept Human Rights Recommendations?
Authors: Burger Anze , Kovac Igor , Tkalec Stasa 
Published: August 2021

AbstractThe research identifies geographic proximity as the crucial driving force behind state behavior in the Universal Periodic Review (UPR). Looking at both stages of the UPR mechanism, we pose two questions: what best explains states issuing human rights recommendations and what best explains states accepting those recommendations? Our model controls for a variety of alternative explanations—state capacity, international structure, and international institutions. The results show that the closer the states are, the more likely it is that they will issue each other recommendations; however, the closer the states are, the less likely it is that they will accept recommendations from one another. We also find an important caveat: the logic of issuance and acceptance of recommendations is reversed when it comes to neighboring states. The latter speaks against general international relations literature, where sharing a border and geographic proximity are both associated with increasing the likelihood of conflict.
Use of Benzodiazepines and Risk of Incident Dementia: A Retrospective Cohort Study
Authors: Gerlach Lauren B , Myra Kim Hyungjin , Ignacio Rosalinda V , Strominger Julie , Maust Donovan T 
Published: August 2021

AbstractBackgroundPrevious findings regarding the association between benzodiazepine exposure and dementia have conflicted, though many have not accounted for anticholinergic exposure. The goal of this study was to evaluate the association of benzodiazepine exposure with the risk of developing dementia, accounting for the anticholinergic burden.MethodsUsing a retrospective cohort design, we identified veterans 65 or older without dementia during a 10-year baseline period and then followed participants for 5 years to evaluate the risk of dementia diagnosis. The primary exposure was cumulative benzodiazepine exposure. Cox proportional hazards survival model was used to examine the association between benzodiazepine exposure and dementia, adjusting for anticholinergic burden and other demographic and clinical characteristics associated with increased dementia risk.ResultsOf the 528 006 veterans in the study cohort, 28.5% had at least one fill for a benzodiazepine. Overall, 7.9% developed a diagnosis of dementia during the observation period. Compared to veterans with no exposure to benzodiazepines, the adjusted hazard ratios for dementia risk were 1.06 (95% confidence interval [CI] 1.02–1.10) for low benzodiazepine exposure, 1.05 (95% CI 1.01–1.09) for medium benzodiazepine exposure, and 1.05 (95% CI 1.02–1.09) for high benzodiazepine exposure.ConclusionsCumulative benzodiazepine exposure was minimally associated with increased dementia risk when compared with nonuse but did not increase in a dose-dependent fashion with higher exposure. Veterans with low benzodiazepine exposure had essentially the equivalent risk of developing dementia as veterans with high exposure. While benzodiazepines are associated with many side effects for older adults, higher cumulative use does not appear to increase dementia risk.
Intra- and inter-temporal effort allocation and profit-maximizing strategy of trawl fishery
Authors: Alizadeh Ashrafi Tannaz , Abe Keita 
Published: August 2021

AbstractBottom trawlers are engaged in multi-species fisheries and fish for profit. In quota-regulated fisheries, intra- and inter-temporal substitutions of fishing effort is regarded as a key mechanisms that influences the profitability of the fishing portfolio. The feeding and spawning migration patterns of the available fish species in the fishing portfolio alter the bio-economic conditions of the different fishing areas. In addition, the spatial heterogeneity among different fishing areas in terms of the fuel costs and travel distance, accessibility to other fishing fleets, and sea ice extent affects the relative attractiveness of the fishing areas and further complicates the decisions underlying the effort allocation, such as when and where to fish what and how much to fish to maximize the profit. In this regard, the aim of this article is to identify the key drivers of intra- and inter-temporal effort allocation in a multi-species trawl fishery consisting of 61 Norwegian trawl vessels targeting cod, saithe, and haddock, the aim being to maximize the fishing profit within the quota constraints. We adopted a two-step Heckman estimator that incorporates the relative attractiveness of three heavily trawled areas, the southern and northern parts of the west coast of Norway and the high sea areas of the Arctic. The relative attractiveness is specified by the fish availability, measured using the catch per unit of effort, prices of the target species, fuel cost, intensity of the coastal fleet's participation in winter fishery, and seasonal sea ice extent in the Barents Sea during the period 2011–2016. Our results show that region-specific attributes and spatial margins have a profound impact on the intra-temporal and inter-temporal allocation of fishing effort to maximize the seasonal profit. Furthermore, we found evidence of economically rational behaviour of the Norwegian trawlers in constantly reallocating their fishing effort in response to the changes in the relative attractiveness of the selected fishing areas over the course of a fishing year.
“According to the Polls…” Opinion Poll Coverage in Network Evening News during the 2020 U.S. Election Campaign
Authors: Beckers Kathleen 
Published: August 2021

Abstract
After news media and pollsters were unsuccessful in predicting recent political outcomes such as the 2016 U.S. election, opinion polls came under scrutiny. Journalists were accused of not providing audiences the tools to correctly interpret poll information. Using a content analysis of all evening news items from CBS, ABC, and NBC from the final two months before the 2020 U.S. general election, we analyzed the quality of poll coverage. We find that half of the references to election polls are “diffuse,” in which journalists refer to “the polls” in a general manner. When news items do cover specific poll results, media often disclose the absolute minimal essential information (e.g., population and error margin), but fail to provide additional methodological details.