bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structures and implications of TBP–nucleosome complexes
Authors: Wang Haibo , Xiong Le , Cramer Patrick 
Published: July 2021

Significance
The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at the promoter of genes. We show here that TBP can interact with nucleosomes containing the Widom-601 sequence at two different positions. One position comprises a TATA box-like sequence near the end of nucleosomal DNA, and the other position is GC-rich and located near the nucleosome dyad. TBP–nucleosome complexes must be resolved before PIC assembly can occur but may persist during mitosis when chromatin is condensed, possibly explaining how TBP can act as a bookmarking factor that transfers transcriptional memory.
Masked form priming with newly-learned pseudo-L2 words in novice bilinguals
Authors: Tang Rongchao , Witzel Naoko , Qiao Xiaomei 
Published: July 2021

AbstractThis study explores whether novice bilinguals store newly-learned pseudo-L2 words together with or separately from the L1, by testing whether pseudo-L2 words compete with their formally-similar L1 words. Although we attempted to obtain a prime lexicality effect (PLE), with newly-trained pseudo-L2 words as primes and their formally-similar words in L1 as targets (stafe-STARE) showing an inhibitory effect, and untrained nonword primes with these targets (stace-STARE) showing a facilitatory effect, no such PLE was obtained. This was the case despite the fact that these newly-learned pseudo-L2 words yielded repetition priming (stafe-STAFE), suggesting that some form of representations were developed for these words. These results are discussed in terms of how to test newly-learned pseudo-L2 words, and whether competition can be exploited to test lexical integration.
Pseudomonas savastanoi var. fraxini
. [Distribution map].
Authors: UK, CAB International  
Published: July 2021

Abstract

A new distribution map is provided for
Pseudomonas savastanoi
var.
fraxini
(Brown) Dowson, 1957. Hosts: Ash (Fraxinus). This map has since been incorporated into Map No. 135, Pseudomonas syringae pv. savastanoi (E.F. Smith) Young, Dye & Wilkie.
A simple fabrication strategy for orientationally accurate twisted heterostructures
Authors: Debnath Rahul , Sett Shaili , Biswas Rabindra , Raghunathan Varun , Ghosh Arindam 
Published: July 2021

Abstract
Van der Waals (vdW) heterostructure is a type of metamaterial where multiple layers of 2D materials are vertically aligned at controlled misorientation. The relative rotation in between the adjacent layers, or the twist angle between them plays a crucial role in changing the electronic band structure of the superlattice. The assembly of multi-layers of precisely twisted two dimensional layered materials requires knowledge of the atomic structure at the edge of the flake. It may be artificially created by the ‘tear and stack’ process. Otherwise, the crystallographic orientation needs to be determined through invasive processes such as transmission electron microscopy or scanning tunneling microscopy, and via second-harmonic generation (SHG). Here, we demonstrate a simple and elegant transfer protocol using only an optical microscope as a edge identifier tool through which, controlled transfer of twisted homobilayer and heterobilayer transition metal dichalcogenides is performed with close to 100% yield. The fabricated twisted vdW heterostructures have been characterized by SHG, Raman spectroscopy and photoluminiscence spectroscopy, confirming the desired twist angle within ∼0.5° accuracy. The presented method is reliable, quick and prevents the use of invasive tools which is desirable for reproducible device functionalities.
An unsupervised learning approach to ultrasound strain elastography with spatio-temporal consistency
Authors: Delaunay Rémi , Hu Yipeng , Vercauteren Tom 
Published: July 2021

Abstract
Quasi-static ultrasound elastography (USE) is an imaging modality that measures deformation (i.e. strain) of tissue in response to an applied mechanical force. In USE, the strain modulus is traditionally obtained by deriving the displacement field estimated between a pair of radio-frequency data. In this work we propose a recurrent network architecture with convolutional long-short-term memory decoder blocks to improve displacement estimation and spatio-temporal continuity between time series ultrasound frames. The network is trained in an unsupervised way, by optimising a similarity metric between the reference and compressed image. Our training loss is also composed of a regularisation term that preserves displacement continuity by directly optimising the strain smoothness, and a temporal continuity term that enforces consistency between successive strain predictions. In addition, we propose an open-access in vivo database for quasi-static USE, which consists of radio-frequency data sequences captured on the arm of a human volunteer. Our results from numerical simulation and in vivo data suggest that our recurrent neural network can account for larger deformations, as compared with two other feed-forward neural networks. In all experiments, our recurrent network outperformed the state-of-the-art for both learning-based and optimisation-based methods, in terms of elastographic signal-to-noise ratio, strain consistency, and image similarity. Finally, our open-source code provides a 3D-slicer visualisation module that can be used to process ultrasound RF frames in real-time, at a rate of up to 20 frames per second, using a standard GPU.
Design of quasi-axisymmetric stellarators with variable-thickness perpendicular permanent magnets based on a two-step magnet design strategy
Authors: Lu Z.Y. , Xu G.S. , Chen D.H. , Chen L. , Zhang X.Y. , Ye M.Y. , Wan B.N. 
Published: July 2021

Abstract
A new method for designing stellarators with variable-thickness perpendicular permanent magnets has been developed, based on a two-step magnet design strategy that we previously proposed for designing stellarators with standardized magnet blocks. Our design strategy uses a ‘local compensation’ method to obtain an initial magnet design and a ‘global fine-tuning’ method to further optimize the initial design. The new method is compared to the previously proposed Fourier decomposition method, and the results indicate that this new method can yield a similar magnet design for an N

fp
= 2 quasi-axisymmetric stellarator at a lower computational cost. High accuracy is achieved, as demonstrated by a normal magnetic field square on the plasma surface of

χ

B

2

=
3.43
×
1

0

−
8

T

2

m

2

, a maximum residual of

B

n

=
3.44

G
s

for a ∼1 T total field, and a flux-surface-averaged residual B

n
of

B

n

/
B

=
3.16
×
1

0

−
5

relative to the total field. Furthermore, the new method can automatically yield a magnet design with large areas of continuous vacancies for ports and plasma access, which is more flexible than the Fourier decomposition method. These results indicate that the new method is robust and effective when used to design stellarators with variable-thickness perpendicular permanent magnets, and, most importantly, that the two-step magnet design strategy has great potential to develop permanent magnet design methods suitable for various magnet layouts.
An anthropomorphic deformable phantom of the vaginal wall and cavity
Authors: Somerwil Philip C , Nout Remi A , Mens Jan-Willem M , Kolkman-Deurloo Inger-Karine K , van Beekhuizen Heleen J , Dankelman Jenny , van de Berg Nick J 
Published: July 2021

Abstract
Brachytherapy is a common treatment in cervical, uterine and vaginal cancer management. The technique is characterised by rapid developments in the fields of medical imaging, dosimetry planning and personalised medical device design. To reduce unnecessary burden on patients, assessments and training of these technologies should preferable be done using high-fidelity physical phantoms. In this study, anthropomorphic deformable phantoms of the vaginal wall and cavity were developed for image-guided adaptive brachytherapy, in which vaginal wall biomechanics were mimicked. Phantoms were produced from both silicone and polyvinyl alcohol materials. Material characterisations were performed with uniaxial tensile tests, via which Young’s moduli and toughness were quantified. In addition, the contrast between adjacent phantom layers was quantified in magnetic resonance images. The results showed that stress-strain curves of the silicone phantoms were within the range of those found in healthy human vaginal wall tissues. Sample preconditioning had a large effect on Young’s moduli, which ranged between 2.13 and 6.94 MPa in silicone. Toughness was a more robust and accurate metric for biomechanical matching, and ranged between 0.23 and 0.28 ·106 J·m−3 as a result of preconditioning. The polyvinyl alcohol phantoms were not stiff or tough enough, with a Young’s modulus of 0.16 MPa and toughness of 0.02 ·106 J·m−3. All materials used could be clearly delineated in magnetic resonance images, although the MRI sequence did affect layer contrast. In conclusion, we developed anthropomorphic deformable phantoms that mimic vaginal wall tissue and are well visible in magnetic resonance images. These phantoms will be used to evaluate the properties and to optimise the development and use of personalised brachytherapy applicators.
Androgen-dependent and DNA-binding-independent association of androgen receptor with chromatic regions coding androgen-induced noncoding RNAs
Authors: Sawada Takahiro , Nishimura Koichi , Mori Jinichi , Kanemoto Yoshiaki , Kouzmenko Alexander , Amano Rei , Hayakawa Akira , Tokiwa Suguru , Shimmura Hiroaki , Kato Shigeaki 
Published: July 2021

ABSTRACT
Androgen induces the binding of its receptor (AR) to androgen-responsive elements (AREs), while genome-wide studies showed that most androgen-induced AR binding sites on chromatin were unrelated to AREs. Enhancer RNAs (eRNAs), a class of noncoding RNAs (ncRNAs), are transcribed from superenhancers (SEs) and trigger the formation of large ribonucleoprotein condensates of transcription factors. By in silico search, an SE is found to be located on the locus of KLK3 that encodes prostate specific antigen. On the KLK3 SE, androgen-induced expression of ncRNAs was detected and designated as KLK3eRNAs in LNCaP cells, and androgen-induced association of AR and FOXA1 on the KLK3eRNA coding regions was detected. Such androgen-induced association of an AR mutant lacking DNA binding activity on the KLK3eRNA coding regions was undetectable on an exogenous ARE. Thus, the present findings suggest a molecular basis of androgen-induced association of AR with chromatin on ARE-unrelated sequences.
Random or handedness? Use of laterally paired penises inNalaearwigs (Insecta: Dermaptera: Labiduridae)
Authors: Kamimura Yoshitaka , Matsumura Yoko , Yang Chin-Cheng Scotty , Gorb Stanislav N 
Published: July 2021

AbstractAnimals can show bias in their use of laterally paired organs that do not have any conspicuous anatomical differentiation between the right and left organs. Like right handedness in humans, males of the giant earwig Labidura riparia (Labiduridae: Labidurinae) preferentially (~90%) use the right one of their laterally paired penises for copulation. To elucidate the evolutionary origin of this lateralization, patterns of penis use were examined for the related species of the genus Nala (Labiduridae: Nalinae). In multiple populations and broods of both Nala lividipes and Nala nepalensis, males that were ready to use the right or left penis were equally frequent, providing a striking contrast to Labidura. Surgical ablation of one of the two penises revealed that both penises are functionally competent in N. lividipes. Nevertheless, each male almost consistently used only one of the paired penises, either the right or the left one. Changes in penis use were estimated to occur only once per 64–143 days per male. The present study is the first report of individual-level lateralization for animal genitalia that do not show any conspicuous anatomical differentiation between the right and left organs. Possible advantages of lateralization are discussed in relationship to co-evolution of the genitalia between the sexes.
Beyond bridging and bonding: the role of social capital in organizations
Authors: Williams Teshanee , McCall Jamie , Berner Maureen , Brown-Graham Anita 
Published: July 2021

AbstractSocial capital has been described as a vital asset that can be used to improve communities. More recently, researchers have focused on how bonding and bridging social capital functions to aid organizations. Yet, the actual mechanisms associated with organizational social capital remain unclear. The literature posits that expressive and instrumental actions may help explain the effects of social capital. Merging these concepts, we examine the role of social capital in community development organizations (CDOs). We extend the resource-based view of network theory to demonstrate the role of social capital within organizations. Findings indicate that organizations vary in their ability to access the benefits of the network. Paradoxically, there may be an underlying minimal prerequisite capacity for CDOs to access benefits in the network. Such findings challenge some traditional theoretical narratives of social capital for smaller organizations.
Atypical Intrinsic Hemispheric Interaction Associated with Autism Spectrum Disorder Is Present within the First Year of Life
Authors: Rolison Max , Lacadie Cheryl , Chawarska Katarzyna , Spann Marisa , Scheinost Dustin 
Published: July 2021

Abstract
Autism spectrum disorder (ASD) is characterized by atypical connectivity lateralization of functional networks. However, previous studies have not directly investigated if differences in specialization between ASD and typically developing (TD) peers are present in infancy, leaving the timing of onset of these differences relatively unknown. We studied the hemispheric asymmetries of connectivity in children with ASD and infants later meeting the diagnostic criteria for ASD. Analyses were performed in 733 children with ASD and TD peers and in 71 infants at high risk (HR) or normal risk (NR) for ASD, with data collected at 1 month and 9 months of age. Comparing children with ASD (n = 301) to TDs (n = 432), four regions demonstrated group differences in connectivity: posterior cingulate cortex (PCC), posterior superior temporal gyrus, extrastriate cortex, and anterior prefrontal cortex. At 1 month, none of these regions exhibited group differences between ASD (n = 10), HR-nonASD (n = 15), or NR (n = 18) infants. However, by 9 months, the PCC and extrastriate exhibited atypical connectivity in ASD (n = 11) and HR-nonASD infants (n = 24) compared to NR infants (n = 22). Connectivity did not correlate with symptoms in either sample. Our results demonstrate that differences in network asymmetries associated with ASD risk are observable prior to the age of a reliable clinical diagnosis.
Genome assembly of a Mesoamerican derived variety of lima bean: a foundational cultivar in the Mid-Atlantic USA
Authors: Wisser Randall J , Oppenheim Sara J , Ernest Emmalea G , Mhora Terence T , Dumas Michael D , Gregory Nancy F , Evans Thomas A , Donofrio Nicole M 
Published: July 2021

Abstract
Lima bean, Phaseolus lunatus, is closely related to common bean and is high in fiber and protein, with a low glycemic index. Lima bean is widely grown in the state of Delaware, where late summer and early fall weather are conducive to pod production. The same weather conditions also promote diseases such as pod rot and downy mildew, the latter of which has caused previous epidemics. A better understanding of the genes underlying resistance to this and other pathogens is needed to keep this industry thriving in the region. Our current study sought to sequence, assemble, and annotate a commercially available cultivar called Bridgeton, which could then serve as a reference genome, a basis of comparison to other Phaseolus taxa, and a resource for the identification of potential resistance genes. Combined efforts of sequencing, linkage, and comparative analysis resulted in a 623 Mb annotated assembly for lima bean, as well as a better understanding of an evolutionarily dynamic resistance locus in legumes.
Promoting the get healthy information and coaching service (GHS) in Australian-Chinese communities: facilitators and barriers
Authors: O’Callaghan C , Tran A , Tam N , Wen L M , Harris-Roxas  
Published: July 2021

Summary
Obesity and being overweight are major public health concerns that health coaching can assist people to manage through encouraging self-management and behaviour change. The Get Healthy Information and Coaching Service (GHS) is a telephone health coaching service in Australia that has effectively improved the health of the general population but has had less participation of culturally and linguistically diverse (CALD) populations. The Chinese population is the largest migrant group in Australia with increased risk of diabetes but had reduced access to the GHS program due to communication barriers. The GHS developed a pilot program for Chinese (Mandarin and Cantonese-speaking) communities using bilingual coaches and translated material to address these barriers. Qualitative research was undertaken with Chinese stakeholders (14 interviews) and 11 program participants from the group which had completed the program (2 focus groups in Mandarin and Cantonese) to understand their experiences and the success of promotional activities. This research does not contain the experiences of the people that withdrew from the program. The bilingual program was culturally and linguistically appropriate and addressed risk factors for chronic conditions. Participants formed positive relationships with bilingual coaches who they preferred to interpreters. They felt the program promoted healthy eating, weight and physical activity. Although Chinese stakeholders had concerns about participants’ ability to goal set, participants said they met their health goals and were committed to the GHS program. Strategies to enhance the program included promoting the bilingual GHS to the communities and stakeholders. Factors to consider beyond language in adapting the program to the Australian Chinese communities include meeting the heterogenous needs of the older population, ensuring community engagement and addressing cultural beliefs and practices.
Constitutional rigidity: The Mexican experiment
Authors: Velasco-Rivera Mariana 
Published: July 2021

Abstract
The constitutional amendment mechanism of the Mexican Constitution of 1857 (reproduced in the Constitution of 1917) and Article V of the US Constitution are very similar in design. Both require a two-thirds majority of each of the houses of a bicameral Congress and ratification by the states (half of the state legislatures in Mexico and three-fourths in the United States). Both articles were the result of an experiment aiming at striking the right balance between rigidity and flexibility. Yet, while characterized by similar levels of formal rigidity, these experiments have had the exact opposite effect. While the US Constitution has been described as one of the world’s most rigid and has only been amended twenty-seven times, the Mexican Constitution of 1917 has gone through over 700 amendments. Why are the amendment rates so divergent? This article argues that Mexico’s amendment practice offers an opportunity to deepen our knowledge about how non-institutional factors condition the way amendment provisions work and, thus, to dispel the idea that amendment difficulty is institutionally determined. In particular, there are at least three lessons that may be drawn from the Mexican case: (i) constitutional scholarship needs to shift its attention to political parties and party systems; (ii) unwritten rules influencing the behavior of party members need further study; and (iii) we must carefully look at the agency of constitutional decision-makers, specifically regarding the choices they make among different means to advance their interests and agendas.
Is greener better? Associations between greenness and birth outcomes in both urban and non-urban settings
Authors: Xiao Xiang , Gao Meng , Zhou Yang , Xu Shu-Li , Knibbs Luke D , Heinrich Joachim , Dharmage Shyamali C , Morawska Lidia , Lin Shao , Jalaludin Bin , Shen Xubo , Zhou Yuanzhong , Dong Guang-Hui 
Published: July 2021

Abstract

Background
Beneficial effects of greenness on birth outcomes have been reported, but few studies have investigated the associations in both urban and non-urban settings. We aimed to evaluate and compare linear and nonlinear associations between greenness and birth outcomes in urban and non-urban settings.

Methods
From October 2015 to December 2018, participants were recruited into the Maoming Birth Cohort Study. A total of 11 258 live birth records were obtained. Greenness exposure was assessed using the normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI). Linear regression and nonlinear restricted cubic spline models were implemented to investigate the associations between greenness and birthweight, birth length, gestational age, preterm birth, low birthweight, small for gestational age and the potential for effect variation under urban or non-urban settings, after adjusting for covariates.

Results
A 0.1-unit increase in NDVI-500m was significantly associated with an increase of 35.4 g in birthweight [95% confidence interval (CI): 13.2, 57.7], 0.15 cm in birth length (95% CI: 0.03, 0.26), 0.88 days in gestational age (95% CI: 0.05, 1.71) and lower odds of low birthweight [odds ratio (OR) = 0.69, 95% CI: 0.56, 0.85] and preterm birth (OR = 0.70, 95% CI: 0.58, 0.85). No association with head circumference was observed. For all outcomes, no significant linear associations were observed among non-urban dwellers. Inversed ‘U-shaped’ associations between greenness exposure and birth outcomes were observed in the total study population.

Conclusions
Greenness exposure was associated with increased gestational age, birthweight and birth length in urban dwellers. Nonlinear associations assessed by restricted cubic splines suggested that health benefits could be larger when increasing greenness levels from low to medium compared with increasing greenness from medium to high levels. Further studies adopting nonlinear methods are warranted to verify our findings.
Corruption Perception and Attitude Towards Taxation in Africa
Authors: Boly Amadou , Konte Maty , Shimeles Abebe 
Published: July 2021

Abstract
This paper analyses the effect of the quality of governance (proxied by perceived corruption) on attitudes towards paying taxes, using the Afrobarometer surveys from thirty-six African countries over the period 2011–2015. Specifically, we find that perceived corruption in the president’s office has a significant and negative effect on reported attitude towards taxation, even after controlling for individuals’ experiences with bribe payments. Such a result indicates that improving perception about the quality of governance at the highest level of authority in a sovereign country can help promote more positive attitudes towards taxation, thereby resulting in higher tax revenues.