bluuebunny/crossref_metadata_2025_split huggingface dataset:
TopoRoot: A method for computing hierarchy and fine-grained traits of maize roots from X-ray CT images
Authors: Zeng Dan , Li Mao , Jiang Ni , Ju Yiwen , Schreiber Hannah , Chambers Erin , Letscher David , Ju Tao , Topp Christopher N. 
Published: August 2021

AbstractBackground3D imaging, such as X-ray CT and MRI, has been widely deployed to study plant root structures. Many computational tools exist to extract coarse-grained features from 3D root images, such as total volume, root number and total root length. However, methods that can accurately and efficiently compute fine-grained root traits, such as root number and geometry at each hierarchy level, are still lacking. These traits would allow biologists to gain deeper insights into the root system architecture (RSA).ResultsWe present TopoRoot, a high-throughput computational method that computes fine-grained architectural traits from 3D X-ray CT images of field-excavated maize root crowns. These traits include the number, length, thickness, angle, tortuosity, and number of children for the roots at each level of the hierarchy. TopoRoot combines state-of-the-art algorithms in computer graphics, such as topological simplification and geometric skeletonization, with customized heuristics for robustly obtaining the branching structure and hierarchical information. TopoRoot is validated on both real and simulated root images, and in both cases it was shown to improve the accuracy of traits over existing methods. We also demonstrate TopoRoot in differentiating a maize root mutant from its wild type segregant using fine-grained traits. TopoRoot runs within a few minutes on a desktop workstation for volumes at the resolution range of 400^3, without need for human intervention.ConclusionsTopoRoot improves the state-of-the-art methods in obtaining more accurate and comprehensive fine-grained traits of maize roots from 3D CT images. The automation and efficiency makes TopoRoot suitable for batch processing on a large number of root images. Our method is thus useful for phenomic studies aimed at finding the genetic basis behind root system architecture and the subsequent development of more productive crops.
A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes
Authors: Aardema Matthew L. , Campana Michael G. , Wagner Nicole E. , Ferreira Francisco C. , Fonseca Dina M. 
Published: August 2021

AbstractUnderstanding patterns of diversification, genetic exchange, and pesticide resistance in insect species of human health concern is necessary for effective population reduction and management. With the broad availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for large numbers of genetic markers from across the known genome. To this end, the targeting of gene sequences of known function or inheritance can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens that are detrimental to endangered vertebrate species such as bird malaria. Here we describe our development of a targeted gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we examined taxonomic divergence among samples from several members of the complex, as well as distinct populations of the relatively under-studied Culex quinquefasciatus, an urban pantropical species. We also examined the presence of known insecticide-resistance conferring alleles. Broadly, our developed gene-based assay proved effective for examining patterns of taxonomic and geographic clustering within the species complex, as well as for surveying genetic variants that have been associated with insecticide resistance. This assay will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of ubiquitous and increasingly damaging disease vectors.
Genomic screening of antimicrobial resistance markers in UK and US Campylobacter isolates highlights stability of resistance over an 18 year period
Authors: van Vliet Arnoud H.M. , Thakur Siddhartha , Prada Joaquin M. , Mehat Jai W. , La Ragione Roberto M. 
Published: August 2021

ABSTRACTCampylobacter jejuni and Campylobacter coli are important bacterial causes of human foodborne illness. Despite several years of reduced antibiotics usage in livestock production in the UK and US, high prevalence of antimicrobial resistance (AMR) persists in Campylobacter. Both countries have instigated genome sequencing-based surveillance programs for Campylobacter, and here we have identified AMR genes in 32,256 C. jejuni and 8,776 C. coli publicly available genome sequences to compare the prevalence and trends of AMR in Campylobacter isolated in the UK and US between 2001-2018. AMR markers were detected in 68% of C. coli and 53% of C. jejuni, with 15% of C. coli being multi-drug resistant (MDR) compared to only 2% of C. jejuni. The prevalence of aminoglycoside, macrolide, quinolone and tetracycline resistance remained fairly stable from 2001-2018 in both C. jejuni and C. coli, but statistically significant differences were observed between the UK and US. There was a statistically significant higher prevalence of aminoglycoside and tetracycline resistance for US C. coli and C. jejuni, and macrolide resistance for US C. coli. In contrast, UK C. coli and C. jejuni showed a significantly higher prevalence of quinolone resistance. Specific MLST clonal complexes (e.g. ST-353/464) showed >95% quinolone resistance. This large-scale comparison of AMR prevalence has shown that the prevalence of AMR remains stable for Campylobacter in the UK and the US. This suggests that antimicrobial stewardship and restricted antibiotic usage may help contain further expansion of AMR prevalence in Campylobacter, but are unlikely to reduce it in the short term.
The AIRE G228W mutation disturbs the interaction of AIRE with its partner molecule SIRT1
Authors: Santos Jadson C. , Dametto Mariangela , Masson Ana Paula , Faça Vitor M. , Bonacin Rodrigo , Donadi Eduardo A. , Passos Geraldo Aleixo 
Published: August 2021

AbstractThe autoimmune regulator (AIRE) protein functions as a tetramer, interacting with partner proteins to form the “AIRE complex,” which relieves RNA Pol II stalling in the chromatin of medullary thymic epithelial cells (mTECs). AIRE is the primary mTEC transcriptional controller, promoting the expression of a large set of peripheral tissue antigen genes implicated in the negative selection of self-reactive thymocytes. Under normal conditions, the SIRT1 protein temporarily interacts with AIRE and deacetylates K residues of the AIRE SAND domain. Once the AIRE SAND domain is deacetylated, the binding with SIRT1 is undone, allowing the AIRE complex to proceed downstream with the RNA Pol II to the elongation phase of transcription. Considering that the in silico and in vitro binding of the AIRE SAND domain with SIRT1 provides a powerful model system for studying the dominant SAND G228W mutation mechanism, which causes the autoimmune polyglandular syndrome-1, we integrated computational molecular modeling, docking, dynamics between the whole SAND domain with SIRT1, and surface plasmon resonance using a peptide harboring the 211 to 230 residues of the SAND domain, to compare the structure and energetics of binding/release between AIRE G228 (wild-type) and W228 (mutant) SAND domain to SIRT1. We observed that the G228W mutation in the SAND domain negatively influences the AIRE-SIRT1 interaction. The disturbed interaction might cause a disruption in the binding of the AIRE SAND domain with the SIRT1 catalytic site, impairing the AIRE complex to proceed downstream with RNA Pol II.
Plant Polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
Authors: Sundar G Vivek Hari , Swetha Chenna , Basu Debjani , Pachamuthu Kannan , Raju Steffi , Chakraborty Tania , Mosher Rebecca A. , Shivaprasad P. V. 
Published: August 2021

AbstractAcross eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein coding genes are poorly understood. Here we show that a plant specific paralogue of RNA polymerase (pol) II, named pol IV, is involved in avoidance of facultative heterochromatic marks in protein coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with larger genome with distributed heterochromatin when compared to Arabidopsis. Our results indicate the surprising division of labour among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation, but also in influencing chromatin boundaries.
VTA-projecting cerebellar neurons mediate stress-dependent depression-like behavior
Authors: Baek Soo Ji , Park Jinsung , Kim Jinhyun , Yamamoto Yukio , Tanaka-Yamamoto Keiko 
Published: August 2021

AbstractAlthough cerebellar alterations have been implicated in mental depression, the exact contribution of the cerebellum to depressive symptoms remains to be elucidated. Here, we demonstrated the crucial role of cerebellar neurons projecting to the ventral tegmental area (VTA) in the chronic stress-induced development of depression-like behavior. The combination of adeno-associated virus-based circuit mapping and electrophysiological recording identified network connections from crus I to the VTA via the dentate nucleus (DN) of the deep cerebellar nuclei. Chronic chemogenetic activation of inhibitory Purkinje cells in crus I suppressed c-Fos expression in the DN and depression-like behavior, which were triggered by chronic stress application. Furthermore, specific inhibition of neurons in the DN that project to the VTA prevented stressed mice from showing depression-like behavior, whereas specific activation of these neurons alone triggered depression-like behavior that was comparable with the one triggered by chronic stress application. Our results indicate that the VTA-projecting cerebellar neurons proactively regulate depression-like behavior, raising the possibility that cerebellum may be an effective target for the prevention of depressive disorders.
Key elements of green supply chain management drivers and barriers empirical study of solar energy companies in South Egypt
Authors: Yassin Ahmed Mostafa Mahmoud , Hassan Mohamed Ahmed , Elmesmary Hebatallah Mohamed 
Published: August 2021

Purpose
There are several important strategic projects in the field of renewable energy in Egypt. Benban project is considered as one of the largest solar generation facilities in the world, which aims to increase clean energy produced, provide electricity needs for citizens and help to increase the volume of Egypt's electricity exports. The purpose of this paper is to explore the most important drivers and barriers that affect the implementation of green supply chain management (GSCM) practices in the field of solar energy production.

Design/methodology/approach
It is an exploratory research that conducts a case study about solar energy companies operating in Benban, south Egypt. It adopts a mixed approach; qualitative and quantitative research strategy to test the relationship between dependent and independent variables through a survey.

Findings
This research concluded that normative drivers involving stakeholder pressure are of the greatest drivers of GSCM practice, while external barriers including lack of government regulations and government support, poor supplier commitment, customers’ unawareness of sustainable green products, lack of markets receiving and manufacturing recycled materials, lack of renewal or technological innovation in markets and lack of human resources or expertise in market are among the biggest barriers to GSCM implementation.

Research limitations/implications
The researchers collected 30 responses during the field survey, which is a nonrandom sample that does not allow generalization. In addition, samples are only from companies in the solar energy sector only.

Originality/value
As there is a need for research that addresses sustainability practices and solutions in developing countries, especially in Egypt, this paper theoretically contributes to literature by proposing a conceptual framework that identifies the drivers and barriers of GSCM from the existing literature, then investigates and measures their impact on the implementation of GSCM on an Egyptian case study. As regards the practical contribution, this research is a trial to experimentally test the importance of top management’s role in motivating and training employees to improve the brand image of their company and making them aware of the benefits of the successful GSCM implementation.
Limited liability companies in Jordan: another story for piercing the corporate veil
Authors: Alawamleh Kamal Jamal , Al-Qaisi Abeer Hassan , Alfaouri Fathi Tawfiq 
Published: August 2021

Purpose
In different recent judgments, the Jordanian Court of Cassation, among many other Jordanian Courts, has found that a limited liability company's shareholder may be held liable in addition to the company itself as to claims related to the company's debits and different obligations. While the aforementioned approach does constitute a departure from the well-established former approach that the same Court has followed for a long period, the Court have unsurprisingly brought up different interpretations to the insufficient provisions that the Jordanian Companies' Law no. 22 of the year 1997 does contain pertaining this specific area of law. Accordingly, this paper aims to attempt to point out and critically examine the aforementioned Courts' decisions and law provisions to demonstrate the extent to which limited liability companies in Jordan are truly limited in liability and whether such Courts have pierced the corporate veil for adequate reasons.

Design/methodology/approach
To examine the extent to which limited liability companies in Jordan are truly limited in liability, this work uses the most relevant secondary data available in this relation as the main method to complete such examination and this shall include different interrelated law provisions, case law and jurisprudence. Through critically analyzing and comparing such data, this work will identify the problems connected to this specific area of law and accordingly proposes different recommendations and conclusions.

Findings
This work submits that the aforementioned Courts and Legislator have not dealt with such a matter in an adequate and comprehensive manner and that they should have addressed this area of law in a different and more specific way. Furthermore, this work argues that while the reasons behind the Courts' decisions shall be respected, the distinct characteristics that brought up limited liability companies into practice shall be also respected and left intact.

Originality/value
Taking into consideration the recent different approach followed by the Jordanian Courts to this specific area of law, and as far as the author is aware, it would not be surprising to say that there is no comprehensive and updated scholarly work which has either examined such an issue or addressed its implications from technical and legal standpoints. This paper receives its originality and value from being the first work that examines and addresses such important matter.
Familial occurrence of follicular keratosis of the chin
Authors: Egawa Kiyofumi 
Published: August 2021

AbstractFollicular keratosis of the chin is a rare and poorly understood pediatric disorder with a characteristic presentation of multiple follicular papules on the chin. Although prolonged friction or pressure over the chin is considered an etiology, such history is not present in most cases. It sometimes occurs within families without any evidence of physical trauma, suggesting a genetic predisposition of the patients to develop the disease. In the present study, we report two brothers with the disease, in whom no definite physical trauma was identified but comedo formation was evident. The clinical presentation of follicular keratosis of the chin is unique, particularly owing to its specific location on the chin with an age predilection from late childhood to puberty. We assume that the hormone status is an etiology of the disease since the chin is an area where androgenic hormones target at puberty and comedogenesis is a well‐known biological function of the hormone. We also assumed that the susceptibility to the hormone may involve in the development of the familial follicular keratosis of the chin.
PrbP modulates biofilm formation in Liberibacter crescens
Authors: Pan Lei , Gardner Christopher L. , Beliakoff Reagan , da Silva Danilo , Zuo Ran , Pagliai Fernando A. , Padgett‐Pagliai Kaylie A. , Merli Marcelo L. , Bahadiroglu Erol , Gonzalez Claudio F. , Lorca Graciela L. 
Published: August 2021

SummaryIn Liberibacter asiaticus, PrbP is a transcriptional regulatory protein involved in survival and persistence during host infection. Tolfenamic acid was previously found to inhibit interactions between PrbP and the promotor region of rplK, resulting in reduced survival of L. asiaticus in the citrus host. In this study, we performed transcriptome analyses to elucidate the PrbP regulon in L. crescens, as it is phylogenetically the closest related species to L. asiaticus that can be grown in laboratory conditions. Chemical inhibition of PrbP with tolfenamic acid revealed that PrbP is involved in the regulation of diverse cellular processes, including stress response, cell motility, cell cycle and biofilm formation. In vitro DNA binding and bacterial two‐hybrid assays also suggested that PrbP is a global regulator of multiple transcription factors (RpoH, VisN, PleD, MucR, MocR and CtrA) at both transcriptional and/or post‐transcriptional levels. Sub‐lethal concentrations of tolfenamic acid significantly reduced the attachment of L. crescens during biofilm formation and decreased long‐term persistence in biofilm structures. Overall, our findings show the importance of PrbP in regulating diverse biological processes through direct and indirect interactions with other transcriptional regulators in L. crescens.
Applying Kolb's experiential learning framework to investigate the safety of energy drinks in a critical thinking general education course
Authors: Rath Danielle Robertson , Rock Cheryl Rosita 
Published: August 2021

AbstractThrough a collaboration between a professor in academia and an industry professional, entry‐level food science students were given the opportunity to critically evaluate the safety of energy drinks. This evaluation occurred through a General Education (Category A3) course designated “Critical Thinking” at California State University – Long Beach (CSULB), where students were introduced to a variety of controversial issues in food science. The goal of the course was for students to apply critical thinking skills to formulate conclusions that are factual, rather than judgmental and biased. Using Kolb's experiential learning framework, students completed exercises in an active‐learning classroom (ALC) environment, which encouraged exploration, reflection, and application. For the exploration phase, students were presented with six commercially available caffeinated beverages and were asked to categorize them as “energy drink” or “not energy drink.” For the reflection phase, students were presented with news articles, as well as peer‐reviewed scientific research articles. Students were tasked with reflecting on how the information in the research articles confirmed or disproved the information in the news articles. Finally, for the application phase, students were asked whether they believed energy drinks should be banned and why or why not. In conclusion, through Kolb's exploration‐reflection‐application framework and through the ALC environment, students learned how to use critical thinking to identify fallacies in news coverage of controversial products, such as energy drinks.
Climate shapes the spatiotemporal variation in color morph diversity and composition across the distribution range ofChrysomela lapponicaleaf beetle
Authors: Kozlov Mikhail V. , Oudendijk Zowi , Forsman Anders , Lanta Vojtěch , Barclay Maxwell V. L. , Gusarov Vladimir I. , Gustafsson Bert , Huang Zheng‐Zhong , Kruglova Oksana Y. , Marusik Yuri M. , Mikhailov Yuri E. , Mutanen Marko , Schneider Alexander , Sekerka Lukáš , Sergeev Maksim E. , Zverev Vitali , Zvereva Elena L. 
Published: August 2021

AbstractColor polymorphism offers rich opportunities for studying the eco‐evolutionary mechanisms that drive the adaptations of local populations to heterogeneous and changing environments. We explored the color morph diversity and composition in aChrysomela lapponicaleaf beetle across its entire distribution range to test the hypothesis that environmental and climatic variables shape spatiotemporal variation in the phenotypic structure of a polymorphic species. We obtained information on 13 617 specimens of this beetle from museums, private collections, and websites. These specimens (collected from 1830–2020) originated from 959 localities spanning 33° latitude, 178° longitude, and 4200 m altitude. We classified the beetles into five color morphs and searched for environmental factors that could explain the variation in the level of polymorphism (quantified by the Shannon diversity index) and in the relative frequencies of individual color morphs. The highest level of polymorphism was found at high latitudes and altitudes. The color morphs differed in their climatic requirements; composition of colour morphs was independent of the geographic distance that separated populations but changed with collection year, longitude, mean July temperature and between‐year temperature fluctuations. The proportion of melanic beetles, in line with the thermal melanism hypothesis, increased with increasing latitude and altitude and decreased with increasing climate seasonality. Melanic morph frequencies also declined during the past century, but only at high latitudes and altitudes where recent climate warming was especially strong. The observed patterns suggest that color polymorphism is especially advantageous for populations inhabiting unpredictable environments, presumably due to the different climatic requirements of coexisting color morphs.