bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic classification error profoundly impacts inference in high-depth Whole Genome Shotgun Sequencing datasets
Authors: Johnson James , Sun Shan , Fodor Anthony A. 
Published: April 2022

AbstractThere is little consensus in the literature as to which approach for classification of Whole Genome Shotgun (WGS) sequences is best. In this paper, we examine two of the most popular algorithms, Kraken2 and Metaphlan2 utilizing four publicly available datasets. As expected from previous literature, we found that Kraken2 reports more overall taxa while Metaphlan2 reports fewer taxa while classifying fewer overall reads. To our surprise, however, Kraken 2 reported not only more taxa but many more taxa that were significantly associated with metadata. This implies that either Kraken2 is more sensitive to taxa that are biologically relevant and are simply missed by Metaphlan2, or that Kraken2’s classification errors are generated in such a way to impact inference. To discriminate between these two possibilities, we compared Spearman correlations coefficients of each taxa against each taxa with higher abundance from the same dataset. We found that Kraken2, but not Metaphlan2, showed a consistent pattern of classifying low abundance taxa that generated high correlation coefficients with higher abundance taxa. Neither Metaphlan2, nor 16S sequences that were available for two of our four datasets, showed this pattern. Simple simulations based on a variable Poisson error rate sampled from the uniform distribution with an average error rate of 0.0005 showed strikingly strong concordance with the observed correlation patterns from Kraken2. Our results suggest that Kraken2 consistently misclassifies high abundance taxa into the same erroneous low abundance taxa creating “phantom” taxa have a similar pattern of inference as the high abundance source. Because of the large sequencing depths of modern WGS cohorts, these “phantom” taxa will appear statistically significant in statistical models even with a low overall rate of classification error from Kraken. Our simulations suggest that this can occur with average error rates as low as 1 in 2,000 reads. These data suggest a novel metric for evaluating classifier accuracy and suggest that the pattern of classification errors should be considered in addition to overall classification error rate since consistent classification errors have a more profound impact on inference compared to classification errors that do not always result in assignment to the same erroneous taxa. This work highlights fundamental questions on how classifiers function and interact with large sequencing depth and statistical models that still need to be resolved for WGS, especially if correlation coefficients between taxa are to be used to build covariance networks. Our work also suggests that despite its limitations, 16S rRNA sequencing may still be useful as neither of the two most popular 16S classifiers showed these patterns of inflated correlation coefficients between taxa.
CHANGES IN LIFE EXPECTANCY BETWEEN 2019 AND 2021 IN THE UNITED STATES AND 21 PEER COUNTRIES
Authors: Masters Ryan K. , Aron Laudan Y. , Woolf Steven H. 
Published: April 2022

ABSTRACTBACKGROUNDPrior studies reported large decreases in US life expectancy during 2020 as a result of the COVID-19 pandemic, disproportionately affecting Hispanic and Black populations and vastly exceeding the average change in life expectancy in other high-income countries. Life expectancy estimates for 2021 have not been reported. This study estimated changes in life expectancy during 2019-2021 in the US population, in US racial/ethnic groups, and in 21 peer countries. The study compared outcomes across five US racial/ethnic groups and is the first to estimate changes in life expectancy during the pandemic in non-Hispanic American Indian/Alaska Native and Asian populations.METHODSUS and peer country death data for 2019-2021 were obtained from the National Center for Health Statistics, the Human Mortality Database, and overseas statistical agencies. The 21 peer countries included Australia, Austria, Belgium, Canada, Denmark, England and Wales, Finland, France, Germany, Israel, Italy, Netherlands, New Zealand, Northern Ireland, Norway, Portugal, Scotland, South Korea, Spain, Sweden, and Switzerland. Life expectancy was calculated for 2019 and 2020 and estimated for 2021 using a previously validated modeling method.RESULTSUS life expectancy decreased from 78.85 years in 2019 to 76.98 years in 2020 and 76.44 years in 2021, a net loss of 2.41 years. In contrast, peer countries averaged a smaller decrease in life expectancy between 2019 and 2020 (0.55 years) and a 0.26-year increase between 2020 and 2021, widening the gap in life expectancy between the United States and peer countries to more than five years. The decrease in US life expectancy was highly racialized: whereas the largest decreases in 2020 occurred among non-Hispanic (NH) American Indian/Alaska Native, Hispanic, NH Black, and NH Asian populations, in 2021 the largest decreases occurred in the NH White population.DISCUSSIONThe US mortality experience during 2020 and 2021 was more severe than in peer countries, deepening a US disadvantage in health and survival that has been building for decades. Over the two-year period between 2019 and 2021, US NH American Indian/Alaska Native, Hispanic, and NH Black populations experienced the largest losses in life expectancy, reflecting the ongoing legacy of systemic racism as well as inadequacies in the US handling of the pandemic. The crossover in racialized outcomes between 2020 and 2021, in which the NH White population experienced the largest decreases, likely has multiple explanations.
Kidins220 promotes thymic iNKT cell development by reducing TCR signals, but enhances TCR signals in splenic iNKT cells
Authors: Herr Laurenz A. , Fiala Gina J. , Schaffer Anna-Maria , Raute Katrin , Velasco Cárdenas Rubí M.-H. , Hummel Jonas F. , Ebert Karolina , Tanriver Yakup , Minguet Susana , Schamel Wolfgang W. 
Published: April 2022

AbstractThe stepwise development of thymic invariant natural killer T (iNKT) cells is controlled by the TCR signal strength. The scaffold protein Kinase D interacting substrate of 220 kDa (Kidins220) binds to the TCR regulating TCR signaling. T cell-specific Kidins220 knock-out (T-KO) mice contain severely decreased iNKT numbers. Very early in iNKT development TCR signals are reduced in the T-KO. In later steps, TCR signaling is increased in the T-KO leading to enhanced apoptosis of iNKT cells. Kidins220’s absence affects the iNKT1 subset most as it requires the weakest TCR signals for development. We also show that in iNKT1 development, weak TCR signals promote the progressive loss of CD4. In the periphery, Kidins220 switches its role back to promoting TCR signaling as splenic T-KO iNKT cells produce less cytokines and show reduced TCR signaling after in vivo stimulation with α-galactosylceramide. In conclusion, Kidins220 promotes or inhibits TCR signaling depending on the developmental context.summary statementWe demonstrate that the transmembrane scaffold protein Kidins220 switches its role twice in iNKT cell biology: from a positive to a negative regulator of TCR signal strength during thymic development and back to a positive regulator in the periphery.
TransCRISPR - sgRNA design tool for CRISPR/Cas9 experiments targeting DNA sequence motifs
Authors: Woźniak Tomasz , Sura Weronika , Kazimierska Marta , Kasprzyk Marta Elżbieta , Podralska Marta , Dzikiewicz-Krawczyk Agnieszka 
Published: April 2022

ABSTRACTEukaryotic genomes contain several types of recurrent DNA motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial DNA motifs. We present transCRISPR, the first online tool dedicated to search for DNA sequence motifs in the user-provided genomic regions and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen DNA motifs, for up to tens of thousands of target regions in 30 genomes, either for the Cas9 or dCas9 system. TransCRISPR provides user-friendly tables and visualizations, summarizing features of identified motifs and designed sgRNAs such as genomic localization, quality scores, closest transcription start sites, and others. Experimental validation of sgRNAs for MYC binding sites designed with transCRISPR confirmed efficient disruption of the targeted motifs and effect on expression of MYC-regulated genes. TransCRISPR is available from https://transcrispr.igcz.poznan.pl/transcrispr/
Vulnerability, transgenerationality, parenting styles, and use of psychoactive substances by adolescents
Authors: Castello Ana Lucia , Silva Hugo Rafael , Areco Kelsy , Paiva Paulo , Da Silveira Dartiu 
Published: April 2022

Purpose
The purpose of this study was to investigate the relationship between parenting styles, family psychological vulnerability environment (FPVE) and drug use among adolescents.

Design/methodology/approach
The quantitative survey using paper and pencil was administered to collect data from 284 parents registered with a paediatric clinic in the city of São Paulo (Brazil), most of whom claimed that their children used drugs. FPVE was measured by eight scales: family relationship patterns and drug use habits; hereditary predisposition to drug use; transmission of moral values to children (reverse); parents’ hereditary predisposition; parental drug use; depression; impulsiveness; and anxiety.

Findings
Dimensions of FPVE that had effect on drug use by adolescents were: the family relationship and drug use patterns of the family of procreation, drug use by the parents and heredity in relation to drug use. Conversely, the family relationship and drug use patterns of the family of origin and the parents’ anxiety, symptoms of depression and impulsiveness did not affect their children’s drug use.

Research limitations/implications
One limit of this study is the sample of parents. These parents were parents of adolescents that were at psychological treatment. The authors do not know if part of parents who declared that their children are not drug users, because the treatment effect. Another limit is that this study did not compare the effect of parents’ drugs misuse with parents that do not use drugs on adolescent drug use. One other limit is that the parents were treated regardless of whether they were mothers or fathers.

Originality/value
This study expands the study of the antecedents of drug use by adolescents, considering FPVE as a construct. Regarding this construct when facing resources limitation, the practitioners can prioritize strategies to prevent adolescent drug use.
Is coolness important to luxury hotel brand management? The linking and moderating mechanisms between coolness and customer brand engagement
Authors: Khoi Nguyen Huu , Le Angelina Nhat-Hanh 
Published: April 2022

Purpose
This study aims to contribute by forming the concept of luxury hotel brand (four- and five-star hotel) coolness and revealing its promoting role to customer brand engagement with brand satisfaction and brand love as connecting components and materialism as a contingent factor.

Design/methodology/approach
A conditional model linking luxury hotel brand coolness and customer brand engagement is proposed and tested using the partial least squares structural equation modeling (PLS-SEM) technique on a data set of 284 customers.

Findings
Luxury hotel brand coolness reflecting various brand qualities fosters satisfaction and love, which facilitate CBE. Materialism positively moderates the impact of luxury hotel brand coolness on brand satisfaction and love.

Research limitations/implications
Future studies should further generalize the findings by extending the current research on different hospitality services and luxury consumption. Also, more personality traits and personal values should be investigated as moderators.

Practical implications
Luxury hotel brand management should place brand coolness at the center of luxury hotel brand strategies.

Originality/value
This study fills in the gap of unraveling the central role of luxury hotel brand coolness in fostering customer brand engagement with brand satisfaction and love as catalysts and materialism as a contingent condition.
Self-reported unmet health needs of adults with disabilities in Kurdistan, Iran
Authors: Azadnia Arian , Mohamadi Bolbanabad Amjad , Safari Hossein , Afkhamzadeh Abdorrahim , Piroozi Bakhtiar , Ghamari Darya , Khosravi Shiva , Banafshi Zhina , Ebrahimi Ramazan 
Published: April 2022

Purpose
Health is one of the most basic human rights. This study aims to examine the pattern of unmet health services needs and barriers to use health services among people with disabilities.

Design/methodology/approach
This cross-sectional study was conducted among people with disabilities in Sanandaj, the capital of a less economically developed province in western Iran in 2020. In total, 548 samples were selected using random sampling, and data were collected using a questionnaire. Chi-square test and Fisher's exact test were used to examine the relationship between independent variables including demographic variables and dependent variables. Statistical tests were performed using STATA software package.

Findings
About 64% and 23% of participants needed outpatient and inpatient services, respectively. The gap between the perceived need and using health services for outpatient and inpatient services was reported to be 55% and 30%, respectively. The main reasons for not seeking the required health care were “insufficient coverage of costs by insurance” and “lack of physical access.” Having supplementary insurance and better economic status were significantly correlated with using outpatient care and having supplementary insurance and type of disability had a significant relationship with using inpatient care.

Originality/value
There was a big gap between the perceived need, seeking for and receiving health services in people with disabilities. Designing and implementing appropriate interventions to reduce barriers on the way of transforming, the need for health services into demand in the population of people with disabilities should be on the agenda of policymakers and relevant managers in the country.
Ethical leadership and sustainability of agro-allied firms: moderating role of environmental dynamism
Authors: Ogaga Ida Austin , Ezenwakwelu Charity A. , Isichei Ejikeme Emmanuel , Olabosinde Taiwo Samuel 
Published: April 2022

Purpose
This paper aims to account for the direct effect of ethical leadership on the sustainability of agro-allied firms and the moderating effect of environmental dynamism on ethical leadership–organisational sustainability relation.

Design/methodology/approach
A total of 215 managers participated in the survey, which covered agro-allied firms from the 6 geo-political zones of the country, Nigeria. Partial least square structural equation model was conducted with the aid of SmartPLSv3.

Findings
The result confirms that ethical leadership positively affects the sustainability of firms in the agro-allied sector and also supports that environmental dynamism strengthens the relation between ethical leadership and sustainability of firms.

Originality/value
The study advances ethical leadership literature through a nuanced examination of its relevance in the agricultural sector, while also validating the integrative social contract theory as a theoretical lens used in exploring the relationship. The specific focus on “ethical” leadership and a specific sector of the economy – agro allied firms is a new ground by not just looking at leadership but the ethical consideration part in relation to a specific industry where competition is a key driver to management/leadership performance.
A state-of-art review of circular economy in the supply chain management: scientometric mapping
Authors: Majiwala Hardik , Kant Ravi 
Published: April 2022

PurposeThis study aims to summarize the trend and overall aspect of Circular Economy (CE) in supply chain management research as a contribution of the previous research towards the CE concept narrowed in perspective, without presenting a specific application. Further, it is explored to identify the research hotspot, knowledge base, topic, landmark and pivot point in this research.Design/methodology/approachThe scientometric mapping of CE in supply chain research papers is analyzed using VOSviewer and CiteSpace software to cover the broader field spectrum and overcome a manual review. The Research papers are extracted from the Web of Science core collection comprising keywords “Circular Economy*” and “Supply Chain*”. A number of 1,092 papers are selected from the reputed journals over 20 years (2001–2021) for review.FindingsThe co-operation visualization network analysis initially identifies the descriptive analysis of overall publications, leading authors, countries, institutions and journal sources. The co-occurrences of keywords present the research hotspot. Moreover, the co-citation cluster analysis identifies knowledge base, research topic, landmark and pivot point. Industry 4.0 integrated supply chain, their driver, barrier, challenges and risks need further investigation.Research limitations/implicationsThe findings are based on networks visualization analysis principles, which indicate connection, quality and impact of academic works that might be open to accusations. The methodology chosen for the research and findings interpretations are based on researchers' perceptive limitations and subjective judgment.Originality/valueThis review paper covers a diverse view to attain sustainable development goals due to considerable attention from researchers, practitioners and policymakers. Also is expected to set the future direction of the CE in the supply chain research.
Soil carbon and microbes in the warming tropics
Authors: Nottingham Andrew T. , Gloor Emanuel , Bååth Erland , Meir Patrick 
Published: April 2022

Abstract

Climate warming could destabilise the Earth's largest terrestrial store of reactive carbon (C), by accelerating the decomposition of soil organic matter. A third of that C store resides in the tropics. The potential for tropical soils to sequester C, or to act as an additional source of CO2, will depend on the balance of C inputs and outputs, mediated by the response of soil microbial communities and their activity to perturbation.

We review the impact of warming on microbial communities and C storage in humid tropical forest soils over multiple time‐scales.

Recent in situ experiments indicate high sensitivity of tropical forest soil C mineralisation to warming in the short term. However, whether this will translate into long‐term soil C decline remains unclear. At decadal time‐scales, high sensitivity of soil C mineralisation to warming is consistent with the correlation between the inter‐annual variation in the tropical land surface temperature and atmospheric CO2 growth rate, and with simulations using the Carnegie‐Ames‐Stanford Approach biosphere model. This observed sensitivity may further contribute to climatic change over millennial time‐scales, suggested by radiocarbon dating of organic matter in river basins showing a twofold acceleration in tropical soil C release during the late‐glacial warming period. However, counter to this evidence, long‐term stability of tropical soil C is suggested by observed steady‐state soil C turnover across temperature gradients with elevation, and by the presence of C in tropical soils that pre‐dates the Holocene Thermal Maximum and late‐glacial warming periods.

To help reconcile these recent experimental findings and long‐term observations, we propose mechanisms to explain tropical soil C and microbial responses to warming across multiple time‐scales. Combined in situ experimental and monitoring approaches—large‐scale and cross‐site—are urgently needed to resolve the interplay of these mechanisms across spatial and temporal scales, to shape a better understanding of the relationship between soil microbes and C storage in tropical soils.

Read the free Plain Language Summary for this article on the Journal blog.
How signals interact in multimodal displays: Insights from a robotic frog
Authors: Willink Beatriz 
Published: April 2022

AbstractIn Focus: Caldart, M. V., M. B. dos Santos & G. Machado (2021). Function of a multimodal signal: a multiple hypothesis test using a robot frog Journal of Animal Ecology, https://doi.org/10.1111/1365‐2656.13620. Animals can communicate using signals perceived by different sensory systems, and many combine multiple sensory modalities in their display repertoires. Why these multimodal displays evolve and how they function to transmit information between individuals are crucial questions in behavioural and evolutionary research. Most empirical studies addressing these questions assume, even if implicitly, that signals of different modalities have independent effects on receiver responses. Nonetheless, the potential for interactions between signals as an explanation for the function of multimodal displays has been recognized for over two decades. Caldart et al. (2021) use a robotic frog and a receiver‐based approach to test four alternative hypotheses for the function of multimodal (acoustic + visual) displays in the stream‐dwelling frog Crossodactylus schmidti. Their results lend support to an inter‐signal interaction mechanism, whereby inclusion of visual signals modifies the context in which an acoustic display is interpreted. In contrast, the results in Caldart et al. (2021) are less consistent with the hypotheses that emphasize the quality‐related information encoded in different signal modalities and a hypothesis that focuses on signal transmission across heterogeneous environments. These results showcase how experimental manipulation of different signal modalities and tests of multiple alternative hypotheses are key to clarifying the function of multimodal displays.
The market distortion effects of mortgage tightening and transaction taxes: Evidence from Hong Kong residential resale market
Authors: Ho Lok Sang , Hu Mengna , Wei Xiangdong , Wong Gary Wai Chung 
Published: April 2022

AbstractBy using transaction‐level data, we study if two popular policies intended to cool an overheated housing market would serve their intended purposes. We found both mortgage tightening and Special Stamp Duties (SSD) actually led to higher starter home prices in Hong Kong. Mortgage tightening shifted the demand for bigger homes to that for smaller ones. The SSD that applies to resales within a specified period of the original purchase lowered turnover across the housing market. The decline in turnover is, as expected, sharpest for small flats, implying a dramatic shrinkage in second‐hand supply of such homes, driving their prices up. We also found transactions bunching as many homes are held till the SSD is no longer applicable, indicating lock‐in effects. Relative to those that are not subject to the SSD, the prices of properties subject to the levy are found to be lower by 6.8%.