bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teachers’ pedagogical intentions while using motivational strategies
Authors: Yang Zening , Sanchez Hugo Santiago 
Published: October 2021

AbstractTeaching in a way that motivates students to learn and grow is a ubiquitous goal in language teaching and language teacher education. Although the existing literature has looked into various motivational strategies that can enhance or maintain L2 students’ motivation, there is currently little research on teachers’ mental lives behind their motivational teaching practices. This qualitative case study thus explored teachers’ pedagogical intentions while implementing motivational strategies. Drawing on data from semi-structured background interviews, classroom observations, and post-lesson stimulated recall interviews, this study shows that teachers’ enactment of motivational strategies was influenced by their awareness of the intentions to motivate as well as the intentions to facilitate student learning. Furthermore, the study provides evidence of the potential of stimulated recall for awareness-raising. Based on these findings, we provide practical recommendations for using stimulated recall for maximising the pedagogical potential of motivational strategies in the language classroom.
Knowledge gaps in the assessment of antimicrobial resistance in surface waters
Authors: Niegowska Magdalena , Sanseverino Isabella , Navarro Anna , Lettieri Teresa 
Published: October 2021

ABSTRACTThe spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on (i) the risk assessment in surface waters, (ii) selective pressures contributing to its transfer and propagation and (iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.
Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae)
Authors: Jiang Tao , Yin Zhiyong , Cai Renlian , Yu Hengmei , Lu Qin , Zhao Shuai , Tian Ying , Yan Yufang , Guo Jianjun , Chen Xiangsheng 
Published: October 2021

Abstract
The true bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae), is a fascinating insect with prolonged diapause and medicinal properties but also a notorious pest. However, because of the lack of genomic resources, an in-depth understanding of its biological characteristics is lacking. Here, we report the first genome assembly of A. chinensis anchored to 10 pseudochromosomes, which was achieved by combining PacBio long reads and Hi-C sequencing data. This chromosome-level genome assembly was 1.55 Gb in size with a scaffold N50 of 156 Mb. The benchmarking universal single-copy ortholog (BUSCO) analysis of the assembly captured 96.6% of the BUSCO genes. A total of 686,888,052 bp of repeat sequences, 18,511 protein-coding genes, and 1,749 noncoding RNAs were annotated. By comparing the A. chinensis genome with that of 8 homologous insects and 2 model organisms, 213 rapidly evolving gene families were identified, including 83 expanded and 130 contracted gene families. The functional enrichment of Gene Ontology and KEGG pathways showed that the significantly expanded gene families were primarily involved in metabolism, immunity, detoxification, and DNA/RNA replication associated with stress responses. The data reported here shed light on the ecological adaptation of A. chinensis and further expanded our understanding of true bug evolution in general.
The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation
Authors: Gilbert Kimberly J , Zdraljevic Stefan , Cook Daniel E , Cutter Asher D , Andersen Erik C , Baer Charles F 
Published: October 2021

Abstract
The distribution of fitness effects (DFE) for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the DFE from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, genome structure, and nonrandom mating. Although inference methods aim to control for population size changes, the influence of nonrandom mating remains incompletely understood, despite being a common feature of many species. We report the DFE estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection on linked sites can conspire to compromise estimates of the DFE from extant polymorphisms with existing methods. These factors together tend to bias inferences toward weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the DFE are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.
Inferring core processes using stochastic models of the geodynamo
Authors: Davis William , Buffett Bruce 
Published: October 2021

SUMMARYRecent studies have represented time variations in the Earth’s axial magnetic dipole field as a stochastic process, which comprise both deterministic and random elements. To explore how these elements are affected by the style and vigour of convection in the core, as well as the core–mantle boundary conditions, we construct stochastic models from a set of numerical dynamo simulations at low Ekman numbers. The deterministic part of the stochastic model, the drift term, characterizes the slow relaxation of the dipole back to its time average. We find that these variations are predominantly accommodated by the slowest decay mode, enhanced by turbulent diffusion to enable a faster relaxation. The random part—the noise term—is set by the amplitude and timescale of variations in dipole field generation, including contributions from both velocity and internal magnetic field variations. Applying these interpretations to the palaeomagnetic field suggest that reversal rates are very sensitive to rms variations in the field generation. Less than a 50 per cent reduction in rms field generation variations is sufficient to prevent reversals for the recent magnetic field.
Lis1 mutation prevents basal radial glia-like cell production in the mouse
Authors: Penisson Maxime , Jin Mingyue , Wang Shengming , Hirotsune Shinji , Francis Fiona , Belvindrah Richard 
Published: October 2021

Abstract
Human cerebral cortical malformations are associated with progenitor proliferation and neuronal migration abnormalities. Progenitor cells include apical radial glia, intermediate progenitors and basal (or outer) radial glia (bRGs or oRGs). bRGs are few in number in lissencephalic species (e.g. the mouse) but abundant in gyrencephalic brains. The LIS1 gene coding for a dynein regulator, is mutated in human lissencephaly, associated also in some cases with microcephaly. LIS1 was shown to be important during cell division and neuronal migration. Here, we generated bRG-like cells in the mouse embryonic brain, investigating the role of Lis1 in their formation. This was achieved by in utero electroporation of a hominoid-specific gene TBC1D3 (coding for a RAB-GAP protein) at mouse embryonic day (E) 14.5. We first confirmed that TBC1D3 expression in wild-type (WT) brain generates numerous Pax6+ bRG-like cells that are basally localized. Second, using the same approach, we assessed the formation of these cells in heterozygote Lis1 mutant brains. Our novel results show that Lis1 depletion in the forebrain from E9.5 prevented subsequent TBC1D3-induced bRG-like cell amplification. Indeed, we observe perturbation of the ventricular zone (VZ) in the mutant. Lis1 depletion altered adhesion proteins and mitotic spindle orientations at the ventricular surface and increased the proportion of abventricular mitoses. Progenitor outcome could not be further altered by TBC1D3. We conclude that disruption of Lis1/LIS1 dosage is likely to be detrimental for appropriate progenitor number and position, contributing to lissencephaly pathogenesis.
Trade-offs among spatio-temporal management actions for a mixed-stock fishery revealed by Bayesian decision analysis
Authors: Whitlock R E , Pakarinen T , Palm S , Koljonen M L , Östergren J , Dannewitz J 
Published: October 2021

Abstract
Management and conservation of populations that are harvested simultaneously present a unique set of challenges. Failure to account for differences in productivity and spatio-temporal abundance patterns can lead to over-exploitation of depleted populations and/or loss of potential yield from healthy ones. Mixed-stock fisheries (where a stock may comprise one or more populations of reared or wild origin) harvest multiple stocks, often in unknown proportions, and lack of tools for estimation of stock-specific harvest rates can hamper status evaluations and attainment of management goals. We present a method for evaluating stock-specific impacts of alternative harvest strategies, using coastal trap net fisheries for Atlantic salmon (Salmo salar) in the Baltic Sea as a case study. Our results demonstrate a large variation among stocks in coastal mixed fishery harvest rates, as well as large differences in harvest rates relative to stock-specific maximum sustainable yield (MSY) and recovery levels. Bayesian decision analysis showed that spatio-temporal management actions, such as delayed fishery opening and closed areas may be effective in improving probabilities of meeting management objectives for Baltic salmon. However, stocks did not respond uniformly to different management actions, highlighting the potential for trade-offs in reaching stock-specific targets that must be considered by managers.
Actual incidence of cerebral infarction after thoracic endovascular aortic repair: a magnetic resonance imaging study
Authors: Kotani Sohsyu , Inoue Yoshito , Oki Naohiko , Yashiro Hideki , Hachiya Takashi 
Published: October 2021

Abstract

OBJECTIVES
The actual incidence of cerebral infarction (CI), including asymptomatic infarction, owing to thoracic endovascular aortic repair (TEVAR) has not been reported in detail. This study was performed to investigate the incidence of post-TEVAR CI by using diffusion-weighted magnetic resonance imaging (DW-MRI) and to determine the risk factors for both symptomatic and asymptomatic CI.

METHODS
We examined 64 patients undergoing TEVAR at our institute between April 2017 and November 2020. Aortic atheroma was graded from 1 to 5 by preoperative computed tomography. Cerebral DW-MRIs were conducted 2 days after the procedure to diagnose postoperative CI.

RESULTS
A total of 44 new foci were detected by post-interventional cerebral DW-MRI in 22 patients (34.4%). Only one patient developed a symptomatic stroke (1.6%), and TEVAR was successfully completed in all cases. Debranching of the aortic arch and left subclavian artery occlusion with a vascular plug was performed in 19 (29.7%) and 12 (18.8%) patients, respectively. The number of patients with proximal landing zones 0–2 was significantly higher in the CI group than in the non-CI group (68.2% vs 11.9%; P &lt; 0.001). The following risk factors were identified for asymptomatic CI: aortic arch debranching (P &lt; 0.001), left subclavian artery occlusion (P = 0.001) and grade 4/5 aortic arch atheroma (P = 0.048).

CONCLUSIONS
Over one-third of the patients examined by cerebral DW-MRI after TEVAR were diagnosed with CI. High-grade atheroma and TEVAR landing in zone 0–2 were found to be positively associated with asymptomatic CI.

Clinical trial registration
02-014.
Subxiphoid thoracoscopic thymectomy for myasthenia gravis
Authors: Liu Yuanyuan , Zhang Jinghao , Wu Wenbin , Zhang Hui , Zhao Chen , Zhang Miao 
Published: October 2021

Abstract
We investigated the efficacy of subxiphoid thoracoscopic thymectomy in patients with myasthenia gravis. The data of 37 consecutive cases were reviewed. 2 cases of postoperative myasthenia gravis crisis and 4 cases of residual mediastinal fat tissue were recorded. Moreover, 29 patients presented the neurological outcomes, and complete stable remission was achieved in 5 (17.2%) cases. Subxiphoid thymectomy is technically feasible. High-quality evidence is warranted before this approach can be recommended.
The major histocompatibility complex: new insights from old molecules into the pathogenesis of autoimmunity
Authors: Arase Hisashi 
Published: October 2021

Abstract
The major histocompatibility complex (MHC) is a central molecule in the immune system. The MHC is also a highly polymorphic gene that is the most strongly involved in susceptibility to many autoimmune diseases. Therefore, the elucidation of the mechanism by which specific MHC alleles are involved in autoimmune disease susceptibility is important to our understanding of the pathogenesis of autoimmune diseases. Specific autoantibody production is observed in many autoimmune diseases, but the mechanism underlying their production remains unclear. We have found that MHC class II molecules exhibit a chaperone-like function to transport misfolded proteins in the endoplasmic reticulum to the outside of cells. Furthermore, misfolded proteins transported to the cell surface by MHC class II molecules of autoimmune disease risk alleles are major autoantibody targets. In this article, I propose a novel mechanism underlying autoimmune diseases mediated by misfolded proteins complexed with MHC class II molecules.
Activity of the combination of colistin and fosfomycin against NDM-1-producing Escherichia coli with variable levels of susceptibility to colistin and fosfomycin in a murine model of peritonitis
Authors: Le Menestrel Alice , Guerin François , Chau Françoise , Massias Laurent , Benchetrit Laura , Cattoir Vincent , Fantin Bruno , de Lastours Victoire 
Published: October 2021

Abstract

Background
Alternative treatments are needed against NDM-1-producing Escherichia coli. Colistin (COL) and fosfomycin (FOS) often remain active in vitro but selection of resistant mutants is frequent if used separately. We determined whether the combination of colistin and fosfomycin may be useful to treat infections with NDM-1-producing E. coli with varying levels of resistance.

Methods
Isogenic derivatives of E. coli CFT073 with blaNDM-1 and variable levels of resistance to colistin and fosfomycin (CFT073-NDM1, CFT073-NDM1-COL and CFT073-NDM1-FOS, respectively) were used. The combination (colistin + fosfomycin) was tested in vitro and in a fatal peritonitis murine model. Mortality and bacterial loads were determined and resistant mutants detected.

Results
Colistin MICs were 0.5, 16 and 0.5 mg/L and fosfomycin MICs were 1, 1 and 32 mg/L against CFT073-NDM1, CFT073-NDM1-COL and CFT073-NDM1-FOS, respectively. In time–kill curves, combining colistin with fosfomycin was synergistic and bactericidal against CFT073-NDM1 and CFT073-NDM1-FOS, with concentrations of 4× MIC (for both drugs), but not against CFT073-NDM1-COL (concentrations of colistin = 0.5× MIC), due to regrowth with fosfomycin-resistant mutants. Mice died less and bacterial counts were lower in spleen with the combination compared with monotherapy against all strains; the combination prevented selection of resistant mutants except for CFT073-NDM1-COL where fosfomycin-resistant mutants were found in all mice.

Conclusions
Combining colistin and fosfomycin was beneficial in vitro and in vivo against NDM-1-producing E. coli, even with strains less susceptible to colistin and fosfomycin. However, the combination failed to prevent the emergence of fosfomycin-resistant mutants against colistin-resistant strains. Combining colistin and fosfomycin constitutes an alternative for treatment of NDM-1 E. coli, except against colistin-resistant strains.
Aminoglycoside-resistance gene signatures are predictive of aminoglycoside MICs for carbapenem-resistant Klebsiella pneumoniae
Authors: Huang Yanqin , Rana Amisha P. , Wenzler Eric , Ozer Egon A. , Krapp Fiorella , Bulitta Jürgen B. , Hauser Alan R. , Bulman Zackery P. 
Published: October 2021

Abstract

Background
Aminoglycoside-containing regimens may be an effective treatment option for infections caused by carbapenem-resistant Klebsiella pneumoniae (CR-Kp), but aminoglycoside-resistance genes are common in these strains. The relationship between the aminoglycoside-resistance genes and aminoglycoside MICs remains poorly defined.

Objectives
To identify genotypic signatures capable of predicting aminoglycoside MICs for CR-Kp.

Methods
Clinical CR-Kp isolates (n = 158) underwent WGS to detect aminoglycoside-resistance genes. MICs of amikacin, gentamicin, plazomicin and tobramycin were determined by broth microdilution (BMD). Principal component analysis was used to initially separate isolates based on genotype. Multiple linear regression was then used to generate models that predict aminoglycoside MICs based on the aminoglycoside-resistance genes. Last, the performance of the predictive models was tested against a validation cohort of 29 CR-Kp isolates.

Results
Among the original 158 CR-Kp isolates, 91.77% (145/158) had at least one clinically relevant aminoglycoside-resistance gene. As a group, 99.37%, 84.81%, 82.28% and 10.76% of the CR-Kp isolates were susceptible to plazomicin, amikacin, gentamicin and tobramycin, respectively. The first two principal components explained 72.23% of the total variance in aminoglycoside MICs and separated isolates into four groups with aac(6′)-Ib, aac(6′)-Ib′, aac(6′)-Ib+aac(6′)-Ib′ or no clinically relevant aminoglycoside-resistance genes. Regression models predicted aminoglycoside MICs with adjusted R2 values of 56%–99%. Within the validation cohort, the categorical agreement when comparing the observed BMD MICs with the predicated MICs was 96.55%, 89.66%, 86.21% and 82.76% for plazomicin, gentamicin, amikacin and tobramycin, respectively.

Conclusions
Susceptibility to each aminoglycoside varies in CR-Kp. Detection of aminoglycoside-resistance genes may be useful to predict aminoglycoside MICs for CR-Kp.
Design and evaluation of a Women in American Medical Informatics Association (AMIA) leadership program
Authors: Grando Adela , Ancker Jessica S , Tao Donghua , Howe Rachael , Coonan Clare , Johns Merida , Chapman Wendy 
Published: October 2021

AbstractThe objective is to report on the design and evaluation of the inaugural Women in AMIA Leadership Program. A year-long leadership curriculum was developed. Survey responses were summarized with descriptive statistics and quotes selected. Twenty-four scholars participated in the program. There was a significant increase in perceived achievement of learning objectives after the program (P &lt; .0001). The largest improvement was in leadership confidence and presence in work interactions (modal answer Neutral in presurvey from 21 responses rose to Agree in postsurvey from 24 responses). Most (92% of 13) scholars clarified leadership vision and goals and (83% of 18) would be Very Likely to recommend the program to others. The goals of the program—developing women’s leader identity, increasing networks, and accumulating experience for future programs—were achieved. The second leadership program is on its way in the United States and Australia. This study may benefit organizations seeking to develop leadership programs for women in informatics and digital health.
Can Native Plants Mitigate Climate-related Forage Dearth for Honey Bees (Hymenoptera: Apidae)?
Authors: Zhang Ge , St. Clair Ashley L , Dolezal Adam G , Toth Amy L , O’Neal Matthew E 
Published: October 2021

Abstract
Extreme weather events, like high temperatures and droughts, are predicted to become common with climate change, and may negatively impact plant growth. How honey bees (Apis mellifera L. [Hymenoptera: Apidae]) will respond to this challenge is unclear, especially when collecting pollen, their primary source of protein, lipids, and micro-nutrients. We explored this response with a data set from multiple research projects that measured pollen collected by honey bees during 2015–2017 in which above-average temperatures and a drought occurred in 2017. We summarized the abundance and diversity of pollen collected from July to September in replicated apiaries kept at commercial soybean and corn farms in Iowa, in the Midwestern USA. The most commonly collected pollen was from clover (Trifolium spp. [Fabales: Fabaceae]), which dramatically declined in absolute and relative abundance in July 2017 during a period of high temperatures and drought. Due to an apparent lack of clover, honey bees switched to the more drought-tolerant native species (e.g., Chamaecrista fasciculata [Michx.] Greene [Fabales: Fabaceae], Dalea purpurea Vent. [Fabales: Fabaceae], Solidago spp. [Asterales: Asteraceae]), and several species of Asteraceae. This was especially noticeable in August 2017 when C. fasciculata dominated (87%) and clover disappeared from bee-collected pollen. We discuss the potential implications of climate-induced forage dearth on honey bee nutritional health. We also compare these results to a growing body of literature on the use of native, perennial flowering plants found in Midwestern prairies for the conservation of beneficial insects. We discuss the potential for drought resistant-native plants to potentially promote resilience to climate change for the non-native, managed honey bee colonies in the United States.