bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conceptual understanding procedure to elicit metacognition with pre-service physics teachers
Authors: Carpendale Jared , Cooper Rebecca 
Published: January 2021

Abstract
Contemporary views on physics education in high schools promote the need for students to develop their conceptual understanding about physics phenomena. However, teaching in this way requires specialized professional knowledge and for pre-service physics teachers, such knowledge needs to be scaffolded and developed. A strategy to support this knowledge development includes eliciting metacognition, where pre-service teachers have opportunities to explore and reconstruct their own knowledge, views, and attitudes about teaching physics. The conceptual understanding procedure (CUP) was developed in the late 1990s at Monash University, initially to support physics students in their first year at university. In particular, a CUP was used to support these students’ understanding of mechanics and highlight their potential alternate conceptions. Researchers found that two thirds of the students involved in this procedure reported that it had positive effects on their understanding and their ideas were clarified. In this paper, we investigate our own use of CUPs as physics teacher educators as a strategy to elicit metacognition with pre-service physics teachers to support their professional knowledge development. Our pre-service physics teachers act as high school physics students to complete the task, and then as physics teachers to explore the pedagogical purposes of the CUP. Ultimately, this process of working in these two roles, while reflecting on their immediate experiences, elicits metacognition in a meaningful way that scaffolds and supports the development of the specialized knowledge required for effective teaching. Thus, we recommend a CUP is a suitable and worthwhile pedagogical strategy to use when supporting pre-service physics teachers’ to elicit metacognition and support professional knowledge development to promote teaching for conceptual understanding.
The invisibility of time dilation
Authors: Hughes Theo , Kersting Magdalena 
Published: January 2021

Abstract
Recently, the physics education community has taken a keen interest in modernising physics education. However, while topics in modern physics have great potential to engage students, these topics are abstract and hard-to-visualise. Therefore, many students hold mistaken pictures and misconceptions, which can impede learning. In this article, we expose a pervasive misconception about relativistic time dilation by presenting a thought experiment illustrating the difference between visual observation and coordinate measurement. We also point out how existing language can mislead and confuse students. In response, we describe an instructional approach that introduces world-maps, world-pictures and event-diagrams to clarify the applicability of key equations in special relativity for improved understanding. By unpacking ‘the invisibility of time dilation’ from the perspectives of both physics and pedagogy, we aim to help teachers provide clearer instruction.
Feedback–feedforward control for high-speed trajectory tracking of an amplified piezoelectric actuator
Authors: Saleem Ashraf , Mesbah Mostefa , Shafiq Muhammad 
Published: January 2021

Abstract
Piezoelectric actuators (PAs) are increasingly used in industrial and research applications requiring high speed and accurate positioning at the micro and nano scales such as atomic force microscopy. This is due to their high positioning resolution, compactness, and fast response. There are, however, two main factors that significantly limit their performance, namely hysteresis and the structural resonance. To overcome these limitations, while avoiding using inversion-based feedforward compensators, we propose, a new learning controller for high speed amplified PA (APA) trajectory tracking. To further enhance the robustness of the APA against sensor noise and other disturbances, a simple proportional and integral (PI) controller is added in the feedback loop. The proposed feedback–feedforward controller compensates for the above-mentioned phenomena without requiring access to the ‘complex’ mathematical model of the APA. Using the notions of system passivity and finite gain stability, we show that the closed-loop system is stable, and the tracking error is bounded for continuous reference inputs. These results are experimentally confirmed using a sinusoidal reference input with varying frequencies. The controller is able to track reference signals with frequencies up to 500 Hz (very close to the resonance frequency of the APA) with relatively small tracking errors. To further assess the quality of the proposed controller, we compare its tracking performance against a previously proposed controller. We show that our controller consistently achieves smaller tracking errors and the performance gap between the two controllers increases with an increase in frequency. We finally show the advantage of using the feedforward learning controller by comparing the tracking performance of our feedforward–feedback controller against that of the PI. The results show a clear performance improvement and that this improvement becomes even more evident at higher frequencies.
Defects and dopants in zinc-blende aluminum arsenide: a first-principles study
Authors: Cao Jiangming , Huang Menglin , Liu Dingrong , Cai Zenghua , Wu Yu-Ning , Ye Xiang , Chen Shiyou 
Published: January 2021

Abstract
AlAs is a semiconductor that can form heterostructure, superlattice, and ternary alloy with GaAs. We systematically investigate the formation energies, transition energy levels, as well as defect and carrier densities of intrinsic defects and extrinsic impurities in AlAs using first-principles simulations. Most of the intrinsic defects, including vacancies, antisites and interstitials, show similar features as those of GaAs. Intrinsic defects are found not to be the origin of the n-type or p-type conductivity due to their high formation energies. For extrinsic dopants (Si, C, Mg and Cu), Mg can be an effective p-type dopant under both As-rich and As-poor conditions. Si-doping can introduce either n-type or p-type, depending on the specific growth condition. C serves as a p-type dopant under As-poor and As-moderate conditions, and Cu-doping has little effect on the conductivity.
Disentanglement approach to quantum spin ground states: field theory and stochastic simulation
Authors: De Nicola Stefano 
Published: January 2021

Abstract
While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes.
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs
Authors: Han Xudong , Kong Qingfei , Liu Chonghui , Cheng Liang , Han Junwei 
Published: January 2021

Abstract

Summary
Cancer can be classified into various subtypes by its molecular, histological or clinical characteristics. Discovering cancer-subtype-specific drugs is a crucial step in personalized medicine. SubtypeDrug is a system biology R-based software package that enables the prioritization of subtype-specific drugs based on cancer expression data from samples of many subtypes. This provides a novel approach to identify the subtype-specific drug by considering biological functions regulated by drugs at the subpathway level. The operation modes include extraction of subpathways from biological pathways, identification of dysregulated subpathways induced by each drug, inference of sample-specific subpathway activity profiles, evaluation of drug-disease reverse association at the subpathways level, identification of cancer-subtype-specific drugs through subtype sample set enrichment analysis, and visualization of the results. Its capabilities enable SubtypeDrug to find subtype-specific drugs, which will fill the gaps in the recent tools which only identify the drugs for a particular cancer type. SubtypeDrug may help to facilitate the development of tailored treatment for patients with cancer.

Availability and implementation
The package is implemented in R and available under GPL-2 license from the CRAN website (https://CRAN.R-project.org/package=SubtypeDrug).

Supplementary information
Supplementary data are available at Bioinformatics online.
A rarefaction-based extension of the LDM for testing presence–absence associations in the microbiome
Authors: Hu Yi-Juan , Lane Andrea , Satten Glen A 
Published: January 2021

Abstract

Motivation
Many methods for testing association between the microbiome and covariates of interest (e.g. clinical outcomes, environmental factors) assume that these associations are driven by changes in the relative abundance of taxa. However, these associations may also result from changes in which taxa are present and which are absent. Analyses of such presence–absence associations face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias, but at the potential cost of information loss as well as the introduction of a stochastic component into the analysis. Currently, there is a need for robust and efficient methods for testing presence–absence associations in the presence of such confounding, both at the community level and at the individual-taxon level, that avoid the drawbacks of rarefaction.

Results
We have previously developed the linear decomposition model (LDM) that unifies the community-level and taxon-level tests into one framework. Here, we present an extension of the LDM for testing presence–absence associations. The extended LDM is a non-stochastic approach that repeatedly applies the LDM to all rarefied taxa count tables, averages the residual sum-of-squares (RSS) terms over the rarefaction replicates, and then forms an F-statistic based on these average RSS terms. We show that this approach compares favorably to averaging the F-statistic from R rarefaction replicates, which can only be calculated stochastically. The flexible nature of the LDM allows discrete or continuous traits or interactions to be tested while allowing confounding covariates to be adjusted for. Our simulations indicate that our proposed method is robust to any systematic differences in library size and has better power than alternative approaches. We illustrate our method using an analysis of data on inflammatory bowel disease (IBD) in which cases have systematically smaller library sizes than controls.

Availabilityand implementation
The R package LDM is available on GitHub at https://github.com/yijuanhu/LDM in formats appropriate for Macintosh or Windows.

Supplementary information
Supplementary data are available at Bioinformatics online.
Simulation of diffuse and stringy fibrosis in a bilayer interconnected cable model of the left atrium
Authors: Saliani Ariane , Irakoze Éric , Jacquemet Vincent 
Published: January 2021

Abstract

Aims
The aim of this study is to design a computer model of the left atrium for investigating fibre-orientation-dependent microstructure such as stringy fibrosis.

Methods and results
We developed an approach for automatic construction of bilayer interconnected cable models from left atrial geometry and epi- and endocardial fibre orientation. The model consisted of two layers (epi- and endocardium) of longitudinal and transverse cables intertwined-like fabric threads, with a spatial discretization of 100 µm. Model validation was performed by comparison with cubic volumetric models in normal conditions. Then, diffuse (n = 2904), stringy (n = 3600), and mixed fibrosis patterns (n = 6840) were randomly generated by uncoupling longitudinal and transverse connections in the interconnected cable model. Fibrosis density was varied from 0% to 40% and mean stringy obstacle length from 0.1 to 2 mm. Total activation time, apparent anisotropy ratio, and local activation time jitter were computed during normal rhythm in each pattern. Non-linear regression formulas were identified for expressing measured propagation parameters as a function of fibrosis density and obstacle length (stringy and mixed patterns). Longer obstacles (even below tissue space constant) were independently associated with prolonged activation times, increased anisotropy, and local fluctuations in activation times. This effect was increased by endo-epicardial dissociation and mitigated when fibrosis was limited to the epicardium.

Conclusion
Interconnected cable models enable the study of microstructure in organ-size models despite limitations in the description of transmural structures.
A qualitative study of VHA clinicians’ knowledge and perspectives on cannabis for medical purposes
Authors: Christensen Vivian A , Nugent Shannon M , Ayers Chelsea K , Morasco Benjamin J , Kansagara Devan 
Published: January 2021

Abstract

Background
The legalization of cannabis is expanding across the USA, and its use has increased significantly, including among Veterans. Although the Veterans Health Administration (VHA) abides by the classification of cannabis as a Schedule I substance, it recently recommended that clinicians discuss cannabis with their patients. Little is known about VHA clinicians’ perspectives on and knowledge of cannabis.

Objective
We sought to better understand clinicians’ attitudes, beliefs, knowledge and communication with patients regarding cannabis.

Methods
We conducted semi-structured phone interviews with 14 VHA clinicians. Interviews were audio-recorded, transcribed verbatim and analysed using qualitative thematic analysis.

Results
VA clinicians described ambivalence towards cannabis for therapeutic purposes and identified several factors that inhibit conversations about cannabis use with their patients including discomfort with the lack of product standardization; lack of research examining the effectiveness and risks of cannabis use; unfamiliarity with pharmacology, formulations, and dosing of cannabis; and uncertainty regarding VHA policy. Clinicians had differing views on cannabis in the context of the opioid crisis.

Conclusions
VA clinicians face challenges in navigating the topic of medical cannabis. Educational materials about cannabis products, dose and harms would be helpful to clinicians.
A GENETIC ANALYSIS OF TETRAHYMENA THAT HAVE ABORTED NORMAL DEVELOPMENT
Authors: Scholnick Steven B , Bruns Peter J 
Published: January 2021

ABSTRACT
Conjugating Tetrahymena can abort the sexual cycle before the production of progeny somatic (macro-) nuclei and return to vegetative growth. We have analyzed the germinal (micronuclear) genotypes of these cells in order to determine the stage at which they aborted conjugation. Our data demonstrate that nearly all of these cells attempt meiosis, but that very few reach the successful completion of cross-fertilization. The resulting micronuclear genotypes suggest that either germinal chromosomes or entire nuclei are lost during an unsuccessful attempt at meiosis or cross-fertilization. We conclude that the decision to develop progeny macronuclei is made during meiosis and is dependent on the completion of some step necessary for successful cross-fertilization.
TWO CELL DIVISION CYCLE MUTANTS OF SACCHAROMYCES CEREVISIAE ARE DEFECTIVE IN TRANSMISSION OF MITOCHONDRIA TO ZYGOTES
Authors: Dutcher Susan K 
Published: January 2021

ABSTRACT
Mutations in CDC genes of S. cerevisiae disrupt the cell cycle at specific stages. The experiments reported here demonstrate that two CDC genes, CDC5 and CDC27, are necessary for mitochondrial segregation as well as for nuclear division. The defect in the transmission of mitochondria was revealed by the examination of uninucleate and binucleate progeny of transient heterokaryons generated by using the kar1-1 mutation that disrupts nuclear fusion. One of the parents lacked mitochondrial DNA (?0) whereas the other parent had functional mitochondria (?+). When the parents of the heterokaryon were both wild-type (CDC), nearly all progeny received mitochondria at 21° and at 34°. Thirty-four of the 36 cdc mutations tested had no defect in transmission of mitochondria to zygotic progeny in crosses in which one parent was a cdc mutant and the other parent was not (CDC). However, the cdc5 and cdc27 mutations prevented the transmission of mitochondria to cdc progeny at 34° but not at 21°; CDC progeny received mitochondria at either temperature. This defect was observed in crosses of cdc5 or cdc27 by wild-type cells regardless of which parent donated mitochondria to the zygote. The defect in mitochondrial transmission cosegregated in meiotic tetrads with the defect in mitosis demonstrating that both are likely to be caused by the same temperature-sensitive mutation. These results indicate that the CDC5 and CDC27 gene products are essential in two motility-related processes: mitochondrial movement from the zygote to the progeny and in mitosis.—Furthermore, the results suggest that the function performed by the CDC5 and CDC27 gene products for mitochondrial transmission differ in some fundamental way from the function performed for mitosis. The function necessary for mitosis can be supplied to the cdc5 (or cdc27) nucleus by the CDC5 (or CDC27) nucleus in the same heterokaryon but the function necessary for mitochondrial transmission cannot. Perhaps the function needed for mitochondrial transmission must be performed in the cell cycle preceding the actual segregation of mitochondria whereas the function needed for nuclear segregation can be performed at the time that mitosis occurs.
DOSAGE COMPENSATION OF SERINE-4 TRANSFER RNA IN DROSOPHILA MELANOGASTER
Authors: Birchler James A , Owenby R Keith , Jacobson K Bruce 
Published: January 2021

ABSTRACT
A dosage series of the X chromosome site for serine-4 transfer RNA consisting of one of three copies in females and one to two in males was constructed to test whether transfer RNA expression is governed by dosage compensation. A dosage effect on the level of the serine-4 isoacceptor was observed in both females and males when the structural locus was varied. However, in males, each dose had a relatively greater expression so the normal one dose was slightly greater than the total female value and the duplicated male had the highest relative expression of all the types examined. Serine-4 levels in males and females from an isogenic Oregon-R stock were similar. Thus the transfer RNA levels conform to the expectations of dosage compensation.
METHYL METHANESULFONATE MUTAGENESIS IN BACTERIOPHAGE T4
Authors: Drake John W 
Published: January 2021

ABSTRACT
MMS induces diverse rII mutations from a wild-type background in bacteriophage T4. About 56% are base pair substitutions, about 30% are frameshift mutations, and the remainder is a miscellaneous set of rapidly reverting or leaky mutants of unknown composition; but deletions were not detected. MMS-induced forward mutation is sharply reduced by the mutations px and y, which also reduce ultraviolet, photodynamic and γ-ray mutagenesis and increase killing by all of these agents. Thus, many of the mutations arise via the T4 WXY system. The induction of G:C → A:T transitions was detected even in a px or y background using sensitive reversion tests, and the few forward rII mutations that were induced from this background also behaved like transition mutations. Thus, some MMS-induced mutations arise independently of the WXY system, perhaps as a result of the (rather weak) ability of MMS to alkylate the O6 position of guanine.
GENETIC PROPERTIES OF MUTATIONS AT THE PEP4 LOCUS IN SACCHAROMYCES CEREVISIAE
Authors: Zubenko George S , Park Frances J , Jones Elizabeth W 
Published: January 2021

ABSTRACT
Yeast cells that inherit mutations at the PEP4 locus exhibit a pronounced phenotypic lag in the expression of the mutant phenotype imparted by these mutations. This lag appears to extend to all of the enzymes that are affected by the pep4-3 mutation. For at least two of the enzymatic activities, phenotypic lag shows mitotic cosegregation. Phenotypic lag is found for meiotic progeny and for mitotic segregants from heterokaryons. The phenotypic lag in the expression of the carboxypeptidase Y deficiency is abolished by nonsense mutations in either PRC1, the structural gene for carboxypeptidase Y, or PRB1, the structural gene for proteinase B. Models to explain these observations are proposed.
CHROMOSOME REARRANGEMENTS IN DICTYOSTELIUM DISCOIDEUM
Authors: Welker Dennis L , Metz Birgit A , Williams Keith L 
Published: January 2021

ABSTRACT
A tandem duplication (D350(III,III)) of the whiB to radB interval of linkage group III has been characterized. The gene order on the duplication-bearing chromosome is: centromere, whiB500, radB+, whiB+, radB24, bsgA5, acrC4. Slow-growing, duplication-bearing strains (yellow-spored, radiation-resistant) produced four classes of faster growing sectors involving the whiB and radB loci: white-spored, radiation-sensitive (whiB500, radB24); white-spored, radiation-resistant (whiB500, radB+); yellow-spored, radiation-sensitive (whiB+, radB24); and yellow-spored, radiation-resistant. The first three classes can be explained as the products of single recombination events in which one copy of the whiB to radB interval was lost. The yellow-spored, radiation-resistant sectors probably arose by mutation elsewhere in the genome, but alternatively may represent multiple recombination events or deletion of part of one copy of the duplicated region. Loss of the duplicated segment was enhanced by irradiation with ultraviolet light (254 nm). Heterozygosity for a DNA repair mutation at the radB locus may have been involved in the formation of the duplication. It is proposed that translocations are a major cause of nonrandom segregation patterns such as the cosegregation of unlinked markers in Dictyostelium discoideum. Translocations involving all known linkage groups are tabulated and DNA damage by N-methyl-N′-nitro-N-nitrosoguanidine is implicated in the formation of translocations in D. discoideum.