bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics of ancient and modern Trichuris trichiura
Authors: Doyle Stephen R. , Søe Martin Jensen , Nejsum Peter , Betson Martha , Cooper Philip J. , Peng Lifei , Zhu Xing-Quan , Sanchez Ana , Matamoros Gabriela , Sandoval Gustavo Adolfo Fontecha , Cutillas Cristina , Tchuenté Louis-Albert Tchuem , Mekonnen Zeleke , Ame Shaali M. , Namwanje Harriet , Levecke Bruno , Berriman Matthew , Fredensborg Brian Lund , Kapel Christian Moliin Outzen 
Published: July 2022

AbstractThe neglected tropical disease trichuriasis is caused by the whipwormTrichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today,T. trichiurainfects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study ofT. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infectiveT. trichiuraand will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.
Estuarine plastisphere as an overlooked source of N2O production
Authors: Su Xiaoxuan , Yang Leyang , Yang Kai , Tang Yijia , Wen Teng , Wang Yingmu , Rillig Matthias C. , Rohe Lena , Pan Junliang , Li Hu , Zhu Yong-guan 
Published: July 2022

Abstract“Plastisphere”, microbial communities colonizing plastic debris, has sparked global concern for marine ecosystems. Microbiome inhabiting this novel human-made niche has been increasingly characterized; however, whether the plastisphere holds crucial roles in biogeochemical cycling remains largely unknown. Here we evaluate the potential of plastisphere in biotic and abiotic denitrification and nitrous oxide (N2O) production in estuaries. Biofilm formation provides anoxic conditions favoring denitrifiers. Comparing with surrounding bulk water, plastisphere exhibits a higher denitrifying activity and N2O production, suggesting an overlooked N2O source. Regardless of plastisphere and bulk water, bacterial and fungal denitrifications are the main regulators for N2O production instead of chemodenitrification. However, the contributions of bacteria and fungi in the plastisphere are different from those in bulk water, indicating a distinct N2O production pattern in the plastisphere. These findings pinpoint plastisphere as a N2O source, and provide insights into roles of the new biotope in biogeochemical cycling in the Anthropocene.
Atypical cyclic di-AMP signaling is essential for Porphyromonas gingivalis growth and regulation of cell envelope homeostasis and virulence
Authors: Moradali M. Fata , Ghods Shirin , Bähre Heike , Lamont Richard J. , Scott David A. , Seifert Roland 
Published: July 2022

AbstractMicrobial pathogens employ signaling systems through cyclic (di-) nucleotide monophosphates serving as second messengers to increase fitness during pathogenesis. However, signaling schemes via second messengers in Porphyromonas gingivalis, a key Gram-negative anaerobic oral pathogen, remain unknown. Here, we report that among various ubiquitous second messengers, P. gingivalis strains predominantly synthesize bis-(3′,5′)-cyclic di-adenosine monophosphate (c-di-AMP), which is essential for their growth and survival. Our findings demonstrate an unusual regulation of c-di-AMP synthesis in P. gingivalis. P. gingivalis c-di-AMP phosphodiesterase (PDE) gene (pdepg) positively regulates c-di-AMP synthesis and impedes a decrease in c-di-AMP concentration despite encoding conserved amino acid motifs for phosphodiesterase activity. Instead, the predicted regulator gene cdaR, unrelated to the c-di-AMP PDE genes, serves as a potent negative regulator of c-di-AMP synthesis in this anaerobe. Further, our findings reveal that pdepg and cdaR are required to regulate the incorporation of ATP into c-di-AMP upon pyruvate utilization, leading to enhanced biofilm formation. We show that shifts in c-di-AMP signaling change the integrity and homeostasis of cell envelope, importantly, the structure and immunoreactivity of the lipopolysaccharide layer. Additionally, microbe–microbe interactions and the virulence potential of P. gingivalis were modulated by c-di-AMP. These studies provide the first glimpse into the scheme of second messenger signaling in P. gingivalis and perhaps other Bacteroidetes. Further, our findings indicate that c-di-AMP signaling promotes the fitness of the residents of the oral cavity and the development of a pathogenic community.
Comparative analysis of human immune responses following SARS-CoV-2 vaccination with BNT162b2, mRNA-1273, or Ad26.COV2.S
Authors: Barbeau Dominique J. , Martin Judith M. , Carney Emily , Dougherty Emily , Doyle Joshua D. , Dermody Terence S. , Hoberman Alejandro , Williams John V. , Michaels Marian G. , Alcorn John F. , Paul Duprex W. , McElroy Anita K. 
Published: July 2022

AbstractSARS-CoV-2 vaccines BNT162b2, mRNA-1273, and Ad26.COV2.S received emergency use authorization by the U.S. Food and Drug Administration in 2020/2021. Individuals being vaccinated were invited to participate in a prospective longitudinal comparative study of immune responses elicited by the three vaccines. In this observational cohort study, immune responses were evaluated using a SARS-CoV-2 spike protein receptor-binding domain ELISA, SARS-CoV-2 virus neutralization assays and an IFN- γ ELISPOT assay at various times over six months following initial vaccination. mRNA-based vaccines elicited higher magnitude humoral responses than Ad26.COV2.S; mRNA-1273 elicited the most durable humoral response, and all humoral responses waned over time. Neutralizing antibodies against the Delta variant were of lower magnitude than the wild-type strain for all three vaccines. mRNA-1273 initially elicited the greatest magnitude of T cell response, but this declined by 6 months. Declining immunity over time supports the use of booster dosing, especially in the setting of emerging variants.
A convolutional neural network based tool for predicting protein AMPylation sites from binary profile representation
Authors: Azim Sayed Mehedi , Sharma Alok , Noshadi Iman , Shatabda Swakkhar , Dehzangi Iman 
Published: July 2022

AbstractAMPylation is an emerging post-translational modification that occurs on the hydroxyl group of threonine, serine, or tyrosine via a phosphodiester bond. AMPylators catalyze this process as covalent attachment of adenosine monophosphate to the amino acid side chain of a peptide. Recent studies have shown that this post-translational modification is directly responsible for the regulation of neurodevelopment and neurodegeneration and is also involved in many physiological processes. Despite the importance of this post-translational modification, there is no peptide sequence dataset available for conducting computation analysis. Therefore, so far, no computational approach has been proposed for predicting AMPylation. In this study, we introduce a new dataset of this distinct post-translational modification and develop a new machine learning tool using a deep convolutional neural network called DeepAmp to predict AMPylation sites in proteins. DeepAmp achieves 77.7%, 79.1%, 76.8%, 0.55, and 0.85 in terms of Accuracy, Sensitivity, Specificity, Matthews Correlation Coefficient, and Area Under Curve for AMPylation site prediction task, respectively. As the first machine learning model, DeepAmp demonstrate promising results which highlight its potential to solve this problem. Our presented dataset and DeepAmp as a standalone predictor are publicly available at https://github.com/MehediAzim/DeepAmp.
Clinical pharmacist interventions in ambulatory psychogeriatric patients with excessive polypharmacy
Authors: Stuhec Matej , Zorjan Kaja 
Published: July 2022

AbstractPsychogeriatric primary care patients are frequently treated with excessive polypharmacy (≥ 10 medications), leading to complications and increased costs. Such cases are rarely included in treatment guidelines and randomized controlled trials. This paper evaluates the impact of clinical pharmacist medication reviews on the quality of pharmacotherapy in primary care psychogeriatric patients with excessive polypharmacy. The retrospective observational multicentric pre-post study included patients (aged 65 or above) treated with at least one psychotropic and ten or more medications. Clinical pharmacists’ recommendations were retrieved from medication review forms for the period 2012⁠–⁠2014. The study outcome measures were the number of medications, potentially inappropriate medications in the elderly (PIMs), potential drug-drug interactions which should be avoided (pXDDIs), and adherence to treatment guidelines. The study included 246 patients receiving 3294 medications, of which 14.6% were psychotropics. The clinical pharmacists proposed 374 interventions in psychopharmacotherapy. The general practitioners accepted 45.2% of them (169). Accepting clinical pharmacist recommendations reduced the total number of medications by 7.5% from 13.4 to 12.4 per patient (p < 0.05), the total number of prescribed PIMs by 21.8% from 312 to 244 (p < 0.05), the number of pXDDIs by 54.9% from 71 to 31 (p < 0.05) and also improved treatment guidelines adherence for antidepressants and antipsychotics (p < 0.05). Clinical pharmacist interventions significantly improved the quality of psychopharmacotherapy by reducing the total number of medications, PIMs, and pXDDIs. Accepting clinical pharmacist interventions led to better treatment guidelines adherence.
In vitro bacteriological effect of tri-beveled needle electrolysis against Staphylococcus aureus
Authors: García-Vidal José Antonio , Salinas Jesús , Ortega Nieves , Escolar-Reina Pilar , Camacho-Alonso Fabio , Medina-Mirapeix Francesc 
Published: July 2022

AbstractPercutaneous needle electrolysis using tri-beveled needles with a specific protocol (5 mA applied for 25 s) has demonstrated to provoke a clinical reduction of recurrent bacterial infections in mammary fistulas. However, the bactericidal effect of needle electrolysis in this pathology remains theoretical. This in vitro study evaluated the bactericidal effect of this protocol and whether it changed when introducing small variations. Staphylococcus aureus were generated in saline solution (9 Log10 CFU/mL) and treated in three different experiments including the main protocol and introducing variations in needle gauge, intensity, and total dosage, respectively. After 24 h, the viable cell count showed that the protocol had an average reduction of 5 log10 CFU/ml compared to the control group. While variations in needle gauge did not modify this effect, variations in current intensity or dosage did. This study demonstrated that the bacterial effect was greater by increasing either current intensity or total dosage, and it decreased with substantial reductions of these parameters.
Multivariate analysis methods improve the selection of strawberry genotypes with low cold requirement
Authors: Barth Eneide , de Resende Juliano Tadeu Vilela , Mariguele Keny Henrique , de Resende Marcos Deon Vilela , da Silva André Luiz Biscaia Ribeiro , Ru Sushan 
Published: July 2022

AbstractMethods of multivariate analysis is a powerful approach to assist the initial stages of crops genetic improvement, particularly, because it allows many traits to be evaluated simultaneously. In this study, heat-tolerant genotypes have been selected by analyzing phenotypic diversity, direct and indirect relationships among traits were identified, and four selection indices compared. Diversity was estimated using K-means clustering with the number of clusters determined by the Elbow method, and the relationship among traits was quantified by path analysis. Parametric and non-parametric indices were applied to selected genotypes using the magnitude of genotypic variance, heritability, genotypic coefficient of variance, and assigned economic weight as selection criteria. The variability among materials led to the formation of two non-overlapping clusters containing 40 and 154 genotypes. Strong to moderate correlations were found between traits with direct effect of the number of commercial fruit on the mass of commercial fruit. The Smith and Hazel index showed the greatest total gains for all criteria; however, concerning the biochemical traits, the Mulamba and Mock index showed the highest magnitudes of predicted gains. Overall, the K-means clustering, correlation analysis, and path analysis complement the use of selection indices, allowing for selection of genotypes with better balance among the assessed traits.
Arterial Thrombotic Events in Hospitalized COVID-19 Patients: A Short Review and Meta-Analysis
Authors: Candeloro Matteo , Schulman Sam 
Published: July 2022

AbstractIt is well established that the risk of venous thromboembolism is high in coronavirus disease 19 (COVID-19). The frequency of arterial thromboembolic events (ATEs) in hospitalized patients with COVID-19 is unclear, as is the magnitude of these events in comparison with other infections. We searched MEDLINE from February 2020 to February 2022 for prospective or retrospective cohort studies and randomized clinical trials that reported the number of acute myocardial infarction (AMI), acute ischemic stroke (AIS), acute limb ischemia (ALI), or other ATE as defined by the original authors in hospitalized patients with COVID-19. The pooled frequencies were calculated through meta-analysis using random effects model with logit transformation and presented with relative 95% prediction intervals (95% PI). We retrieved a total of 4,547 studies, 36 of which (28 retrospective cohorts, five prospective cohorts and three randomized trials) were finally included in our analysis. The resulting cohort counted 100,949 patients, 2,641 (2.6%) of whom experienced ATE. The pooled ATE frequency was 2.0% (95% PI, 0.4–9.6%). The pooled ATE frequency for AMI, AIS, ALI, and other ATE was 0.8% (95% PI, 0.1–8.1%), 0.9% (95% PI, 0.3–2.9%), 0.2% (95% PI, 0.0–4.2%), and 0.5% (95% PI, 0.1–3.0%), respectively. In comparison with the ATE incidence reported in three studies on non-COVID viral pneumonia, we did not detect a significant difference from the results in our analysis. In conclusion, we found a non-negligible proportion of ATE in patients hospitalized for COVID-19. Our results are similar to those found in hospitalized patients with influenza or with non-COVID viral pneumonia.
Lab-scale chemical vapor deposition onto powders
Authors: Wang Jun , Obrovac M. N. 
Published: July 2022

In this paper, a laboratory chemical vapor deposition (CVD) reactor is described, which features an opposing screw rotating fluidized bed. The reactor efficiently concentrates powdered reactants in the reaction zone while maintaining fluidization independent of powder properties. This allows for lab-scale CVD processing of many small powder samples at high yields and without the need for re-adjustment of fluidization parameters for different samples. Alumina and graphite were carbon-coated and characterized in lithium batteries. The deposited carbon layer had a density of 1.84 g/ml and a capacity of 225 mA h/g when cycled between 7 mV and 0.9 V in lithium cells. Carbon coatings applied by this CVD reactor onto graphite particles were found to be effective at reducing surface reactions during cycling in lithium cells. We suggest that utilization of this opposing screw rotating fluidized bed reactor can effectively apply CVD coatings to small laboratory powder samples, with particular utility for Li-ion battery materials.
The distribution of dioecious plant pollination, sex ratio and seed dispersal research by climate type in Australia
Authors: Draper J. T. , Stanhope J. , Simpson B. S. , Weinstein P. 
Published: July 2022

Dioecious-plant life-history characteristics and reproduction vary greatly among species, and have been linked to certain climate and habitat types, particularly tropical and island habitats. Australia is a large, predominantly arid continent, although it also contains mediterranean, temperate and tropical climates. Dioecious plants occupy each of these climate types, with their respective habitats and evolutionary pressures. As a result, dioecious species demonstrate great variation in key reproductive characteristics (pollination mechanism, sex ratio, and seed dispersal), which require understanding so as to conserve dioecious species effectively among climate types. Therefore, to understand dioecious-plant ecology across Australia, research must include all climate types, and investigate reproductive traits in each to better focus conservation strategies. An external factor which could prevent equal study effort across climate types would be geoclimatic preference of study location or biases in researcher interest, causing gaps in practical understanding and less effective dioecious-plant conservation management in understudied systems. To assess the prevalence and nature of dioecious plant research in Australia, we conducted a systematic mapping and scoping review to answer the following questions: (1) what climate zones have been captured by dioecious-plant research in Australia, focusing on pollination, sex ratio and seed dispersal; and (2) what is the distribution of dioecious-plant pollination, sex ratio and seed dispersal research by climate type; of the 43 studies that met the inclusion criteria, 27 (62.8%) studies were conducted in temperate climates, 8 (18.6%) in dry climates, 6 (13.9%) in tropical climates, and 5 (11.6%) in continental climates. Of the three focal areas, pollination studies (n = 24, 75% studies of entomophily) were most common, whereas sex ratio (n = 17, 41% studies of sex ratio over more than one population) and seed dispersal studies (n = 13, 54% of studies investigated abiotic dispersal) were less frequently researched. Considering the climate classification distribution in Australia, studies of dioecious species in dry climates are less prevalent than those in temperate climates. Of the focal areas of research, particularly under-investigated areas were anemophily, biotic seed dispersal, and study of female-biased species. Further studies addressing these gaps would be beneficial to inform conservation initiatives for Australian dioecious plant species. Additionally, it would be informative to investigate whether similar patterns are found in dioecious plant research in other countries with diverse climate types.
Transformation of soil phosphorus fractions: the role of time and fertilisation
Authors: Wang Qiujun , Guo Dejie , Xu Yehong , Ma Yan 
Published: July 2022

Context Organic fertilisation may increase soil phosphorus (P) availability and increase risk of P loss to groundwater. Aims To understand the effect of continuously applying organic fertilisers on formation of P fractions. Methods A field experiment was conducted to investigate the effect of different fertilisation (CF, chemical fertiliser; COF, cow dung compost with chemical fertiliser; POF, pig manure compost with chemical fertiliser) on different soil P fractions for five growing seasons. Key results Compared with CF, the COF and POF treatments had significantly higher total P and available P contents in each season. The COF treatment showed the highest concentration of NaOH-Pi; however, POF showed the highest concentration of HCl-Pi in all seasons. There were significant positive correlations between concentrations of total P (r = 0.863, P = 0.001), available P (r = 0.590, P = 0.006), each P fraction (r = 0.447 to 0.862, P = 0.048 to 0.001) and organic carbon concentration. Concentrations of total P (r = −0.473, P = 0.035), available P (r = −0.589, P = 0.006) and each P fraction (except HCl-Pi) (r = −0.711 to −0.476, P = 0.001 to 0.034) showed significant negative correlations with soil pH. Available P concentration showed the highest correlation with concentrations of residual P (r = 0.665, P = 0.007), HCl-Pi (r = 0.413, P = 0.126) and NaOH-Pi (r = 0.282, P = 0.309) in CF, COF and POF treatments, respectively. Conclusions Continuous application of organic fertiliser can significantly improve P availability through impacting distribution of P fractions. Implications Further studies are needed to establish the release risk of each P fraction in soils.
Important challenges in the study of metaphors
Authors: Gibbs Raymond W. 
Published: July 2022

Abstract
The world of metaphor scholarship is amazingly diverse, involving a myriad of empirical methods and theoretical frameworks. This diversity is greatly appealing, given the enormous complexity of metaphorical thinking, language, and human action. This chapter identifies some challenges for metaphor scholars both in doing particular empirical work and in offering theoretical accounts of metaphor and its role in human life. These challenges focus on issues with metaphor identification, the meanings of metaphor in discourse, online metaphor processing, and the metaphorical character of source domains. I see these challenges as “matters for all of us to think about” as we try to explain both the regularities and variations in metaphorical thinking, language, and multimodal action.
Being in the same boat, in two ways
Authors: Kuna Agnes , Bochatay Naike , Kim Sara , Csabai Márta 
Published: July 2022

Abstract
In research on conflicts, the systematic study of metaphors is playing an increasingly prominent role. In the context of a U.S. – Swiss–Hungarian international collaboration investigating conflicts through interviews with healthcare professionals, the present chapter analyzes linguistic and conceptual metaphors in Hungarian interviews. The theoretical background for the analysis is provided by the cognitive theory of metaphor, while its methodology is based on MIPVU.
Moving away from linguistic representations, this study aims to analyze the role of metaphors in the conceptualization, interpretation, and management of conflicts. The chapter presents general, conventionalized orientational and ontological metaphors of conflict, also exploring the core metaphors of the metaphor families of competition and cooperation as well as correlations between conflicts and power structures.
Number of states with given spin I and isospin T for n fermions in a j orbit*
Authors: Yin X. , Zhao Y. M. 
Published: July 2022

Abstract
In this study, we investigate formulas of the number of states with a given total spin I and isospin T for n nucleons in a single-j shell denoted by

. Talmi's recursion formulas for the number of states with a given z-axis projection of total spin are generalized by further considering the isospin couplings and are applied to derive explicit formulas of

.