bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fully Automatic Cell Segmentation with Fourier Descriptors
Authors: Hirling Dominik , Horvath Peter 
Published: December 2021

ABSTRACTCell segmentation is a fundamental problem in biology for which convolutional neural networks yield the best results nowadays. In this paper, we present FourierDist, a network, which is a modification of the popular StarDist and SplineDist architectures. While StarDist and SplineDist describe an object by the lengths of equiangular rays and control points respectively, our network utilizes Fourier descriptors, predicting a coefficient vector for every pixel on the image, which implicitly define the resulting segmentation. We evaluate our model on three different datasets, and show that Fourier descriptors can achieve a high level of accuracy with a small number of coefficients. FourierDist is also capable of accurately segmenting objects that are not star-shaped, a case where StarDist performs suboptimally according to our experiments.
The aphid BCR4 structure and activity uncover a new defensin peptide superfamily
Authors: Loth Karine , Parisot Nicolas , Paquet Françoise , Sivignon Catherine , Rahioui Isabelle , Lopes Mélanie Ribeiro , Gaget Karen , Duport Gabrielle , Delmas Agnès F. , Aucagne Vincent , Heddi Abdelaziz , Calevro Federica , da Silva Pedro 
Published: December 2021

ABSTRACTAphids (Hemiptera: Aphidoidea) are among the most injuring insects for agricultural plants and their management is a great challenge in agronomical research. A new class of proteins, called Bacteriocyte-specific Cysteine-Rich (BCR), provides an alternative to chemical insecticides for pest control. BCRs have been initially identified in the pea aphid Acyrthosiphon pisum. They are small disulfide bond-rich proteins expressed exclusively in aphid bacteriocytes, the insect derived cells that host intracellular symbiotic bacteria. Here, we show that one out of the A. pisum BCRs, BCR4, displays an outstanding insecticidal activity against the pea aphid, impairing insect survival and nymphal growth, providing evidence for its potential use as a new biopesticides. Our comparative genomics and phylogenetic analysis indicate that BCRs seem restricted to the aphid lineage. The 3D structure of the BCR4 reveals that this peptide belongs to a yet unknown structural class of peptides and defines a new superfamily of defensins.
Sibling rivalry among the ZBTB transcription factor family: homo vs. heterodimers
Authors: Piepoli Sofia , Nogay Liyne , Akkose Umit , Barakat Sarah , Taskiran Hakan , Tolay Nazife , Gezen Melike , Adebali Ogun , Atilgan Canan , Erman Batu 
Published: December 2021

AbstractThe BTB domain is an oligomerization domain found in over 200 proteins encoded in the human genome. In the family of BTB domain and Zinc Finger-containing (ZBTB) transcription factors, 49 members share the same protein architecture. The N-terminal BTB domain is structurally conserved among the family members and serves as the dimerization site while the C-terminal zinc finger motifs mediate DNA binding. The available BTB domain structures from this family reveal a natural inclination for homodimerization. In this study we investigated the potential for heterodimer formation in the cellular environment. We selected five BTB homodimers and four heterodimer structures. We performed in vitro binding assays with fluorescent protein-BTB domain fusions to assess dimer formation. We tested the binding of several BTB pairs, and we were able to confirm the heterodimeric physical interaction between the BTB domains of PATZ1 and PATZ2, previously reported only in an interactome mapping experiment. We also found this pair to be co-expressed in several immune system cell types. Finally, we used the available structures of BTB domain dimers and newly constructed models in extended molecular dynamics simulations (500 ns) to understand the energetic determinants of homo and heterodimer formation. We conclude that heterodimer formation, although frequently described as less preferred than homodimers, is a possible mechanism to increase the combinatorial specificity of this transcription factor family.
Drosophila hemocytes recognize lymph gland tumors of mxc mutants and activate the Toll pathway in reactive oxygen species-dependent manner
Authors: Kinoshita Suzuko , Takarada Kazuki , Inoue Yoshihiro H. 
Published: December 2021

ABSTRACTMechanisms of cancer cell recognition and elimination by the innate immune system remains unclear. Circulating hemocytes are associated with the hematopoietic tumors in Drosophila mxcmbn1 mutant larvae. The innate immune signalling pathways are activated in the fat body to suppress the tumor growth by inducing antimicrobial peptides (AMP). Here, we investigated the regulatory mechanism underlying the activation in the mutant. Reactive oxygen species accumulated in the hemocytes due to induction of dual oxidase and its activator. The hemocytes were also localized on the fat body. These were essential for transmitting the information on tumors toward the fat body to induce AMP expression. Regarding to the tumor recognition, we found that matrix metalloproteinase 1 (MMP1) and MMP2 were highly expressed in the tumors. Ectopic expression of MMP2 was associated with AMP induction in the mutants. Furthermore, the basement membrane components in the tumors were reduced and ultimately lost. The hemocytes may recognize the disassembly in the tumors. Our findings highlight the underlying mechanism via which macrophage-like hemocytes recognize tumor cells and relay the information toward the fat body to induce AMPs. and contribute to uncover the immune system’s roles against cancer.SUMMARY STATEMENTDrosophila blood cells transmit information regarding the existence of tumor cells to the fat body and induce the production of anti-tumor peptides via the generation of reactive oxygen species.
Genome Assemblies of the Warthog and Kenyan Domestic Pig Provide Insights into Suidae Evolution and Candidate Genes for African Swine Fever Tolerance
Authors: Feng Wen , Zhou Lei , Zhao Pengju , Du Heng , Diao Chenguang , Zhang Yu , Liu Zhen , Jin Wenjiao , Yu Jian , Han Jianlin , Okoth Edward , Morode Raphael , Liu Jian-Feng 
Published: December 2021

AbstractAs warthog (Phacochoerus africanus) has innate immunity against African swine fever (ASF), it is critical to understand the evolutionary novelty of warthog to explain its specific ASF resistance. Here, we present two completed new genomes of one warthog and one Kenyan domestic pig, as the fundamental genomic references to decode the genetic mechanism on ASF tolerance. Our results indicated, multiple genomic variations, including gene losses, independent contraction and expansion of specific gene families, likely moulded warthog’s genome to adapt the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that, the warthog genome had a DNA sequence absence of the lactate dehydrogenase B (LDHB) gene on chromosome 2 compared to the reference genome. The overexpression and siRNA of LDHB indicated that its inhibition on the replication of ASFV. Combining with large-scale sequencing data of 123 pigs from all over the world, contraction and expansion of TRIM genes families revealed that TRIM family genes in the warthog genome were potentially responsible for its tolerance to ASF. Our results will help further improve the understanding of genetic resistance ASF in pigs.
CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data
Authors: Söylev Arda , Çokoglu Sevim Seda , Koptekin Dilek , Alkan Can , Somel Mehmet 
Published: December 2021

AbstractTo date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low coverage (<1 ×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We applied CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages 0.44×-26× (median 4×) and read lengths 52-121 bp (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are strongly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.
Kismet/CHD7/CHD8 affects gut biomechanics, the gut microbiome, and gut-brain axis in Drosophila melanogaster
Authors: Niosi Angelo , Võ Nguyên Henry , Sundar Punithavathi , Welch Chloe , Penn Aliyah , Yuldasheva Yelena , Alfareh Adam , Rausch Kaitlin , Rukhsar Takhmina , Cavanaugh Jeffery , Yadav Prince , Peterson Stephanie , Brown Raina , Hu Alain , Ardon-Castro Any , Nguyen Darren , Crawford Robert , Lee Wendy , Jensen Mikkel Herholdt , Morris Eliza J. , Mulligan Kimberly 
Published: December 2021

AbstractThe gut-brain axis may contribute to the pathophysiology of neurodevelopmental disorders, yet it is often unclear how risk genes associated with these disorders affect gut physiology in a manner that could impact microbial colonization. We addressed this question using Drosophila melanogaster with a null mutation in kismet, the ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, CHD7 and CHD8 are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. We found kismet mutant flies have a significant increase in gastrointestinal transit time, indicating functional homology of kismet with CHD7/CHD8 in vertebrates. To measure gut tissue mechanics, we used a high-precision force transducer and length controller, capable of measuring forces to micro-Newton precision, which revealed significant changes in the mechanics of kismet mutant guts, in terms of elasticity, strain stiffening, and tensile strength.
Using 16S rRNA metagenomic sequencing, we also found kismet mutants have reduced diversity of gut microbiota at every taxonomic level and an increase in pathogenic taxa. To investigate the connection between the gut microbiome and behavior, we depleted gut microbiota in kismet mutant and control flies and measured courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of gut microbiome in the control strain reduced courtship activity. This result demonstrated that antibiotic treatment can have differential impacts on behavior that may depend on the status of microbial dysbiosis in the gut prior to depletion. We propose that Kismet influences multiple gastrointestinal phenotypes that contribute to the gut-brain axis to influence behavior. Based on our results, we also suggest that gut tissue mechanics should be considered as an element in the gut-brain communication loop, both influenced by and potentially influencing the gut microbiome and neuronal development.
Evolution of cities in Borneo: a kaleidoscope of urban landscapes for planning future resilient cities
Authors: Kozlowski Marek , Ibrahim Rahinah , Zaini Khairul Hazmi 
Published: December 2021

PurposeThis study aims to examine the trajectory of the urban growth of Borneo by portraying its resilient settlements in the pre-colonial times, tropical sensitive colonial architecture, the built environment of the post–independence period and finally the contemporary city image. This is followed by a comparative study of its major urban centres and determining how globalisation and neoliberalism impact the traditional urban settlements of this island and poses a threat to its rich biodiversity.Design/methodology/approachThis study uses case study research methodology involving selected cities on the Island of Borneo including Kota Kinabalu, Sandakan, Miri and Kuching (Sabah and Sarawak, Malaysia), Bandar Seri Begawan (Brunei), and major cities of the state of Kalimantan, Indonesia. Data collection includes a literature review, content analysis, field assessment and observations. The major research objectives would address past and current issues in the selected urban environment of Borneo. They address the historical evolution of major cities of Borneo, current urban development trends, the deterioration of the traditional urban fabric as a result of post–independence development and later globalisation.FindingsThis study found that the rich cultural tradition and climate-responsive architecture from the past have been discontinued to pave way for fast track and often speculative development. The results contribute in the convergence of existing shortcomings of cities from three nations on Borneo Island in guiding future sustainable urban planning agenda for achieving a resilient city status while reinstating the character and the sense of place. The study expects the recommendations to become prerequisites for future urban planning in sensitive tropical regions.Originality/valueThis research identified a new “Borneo approach” to urban development. The study strongly recommends top priorities for the central, state and local governments of Malaysia, Brunei and Indonesia allowing the planners and decision-makers to establish a new tropical urban planning initiative with the ample design practice for this unique region in Southeast Asia. The results of this study can serve as the guiding principles for other urban environments in fragile and sensitive tropical regions.
Effect of banana peel flour on rheological, physico-chemical, mineral content and sensory properties of chicken patties
Authors: Chappalwar Anita M. , Pathak Vikas , Goswami Meena , Verma Arun Kumar , Rajkumar V. , Singh Prashant 
Published: December 2021

PurposeThe present study was conducted to evaluate the effect of banana peel flour as fat replacer on rheological, physico-chemical, textural, mineral content and sensory properties of chicken patties.Design/methodology/approachUltra low fat chicken patties were prepared with incorporation of banana peel flour at 0% (C), 1% (BP1), 2% (BP2) and 3% (BP3) levels separately to replace 50% externally added vegetable fat in formulation and evaluated for various quality characteristics and sensory attributes.FindingsHighest G' and G''? modulus were observed in banana peel powder incorporated emulsion. No cross-point was observed at all ranges of frequency in meat emulsions prepared with banana peel. Among physico-chemical properties, control had significantly (p < 0.05) higher emulsion pH, emulsion stability, product pH, water activity values, fat and cholesterol content; however, cooking yield, moisture and ash content, fat retention and moisture retention values increased significantly (p < 0.05) in treatment patties. Mineral, textural and colour parameters had a significant (p < 0.05) effect except on manganese content and a* values. Various sensory scores decreased significantly (p < 0.05) with increased level of banana peel flour.Practical implicationsSensory scores of 3% banana peel powder incorporated patties were significantly (p < 0.05) lower than other treatments. There was no significant difference between 1 and 2% banana peel incorporated chicken patties. Therefore, an ultra low fat chicken patties incorporated with 2.0% banana peel flour to replace 50% vegetable fat were selected as the best treatment.Originality/valuePresent global trend and life style are currently driving ready-to-eat healthy meat products and factors include extended working hours, increasing number of single-person households and perception of food as reward. Fat is an important component of meat products and imparts tenderness, improving flavor and mouth feel to processed meat products, like chicken patties. However intake of excess energy in form of saturated and unsaturated fat may lead to various life style diseases in consumers. Hence development of ultra low fat chicken patties with incorporation of fruit waste without adverse effect on sensory properties may be a significant challenge.
Good soldier syndrome. Do organizational cynicism and work alienation matter?
Authors: Singh Sabia , Randhawa Gurpreet 
Published: December 2021

PurposeThe purpose of this study is to examine the impact of organizational cynicism (OCyn) on organizational citizenship behavior (OCB) among bank employees with a focus on the role of work alienation (WA) as a potential mediator.Design/methodology/approachUsing standardized questionnaire, data were collected from 381 employees working in the banking sector of Punjab, a northern state of India. Statistical techniques such as hierarchical multiple regression and confirmatory factor analysis along with PROCESS macro were used for data analysis.FindingsResults reveal that OCyn has a significant negative effect on OCB. Further, WA is found to be significantly partially mediating the relationship between the aforementioned constructs.Research limitations/implicationsThis study pertains to a single sector i.e., banking sector restricting the generalizability to other industrial and vocational settings. Further, it may be difficult to draw any causal inferences as the research design adopted for this study is cross-sectional in nature.Practical implicationsIn order to promote OCBs among bank employees, the formation of negative workplace attitudes such as OCyn and WA needs to be regulated. This can be achieved through improving communications network, encouraging participative decision-making activities, conducting psychological counseling and stress management training sessions.Originality/valueThis study is one of the scarce empirical research works that have substantiated the direct impact along with the indirect impact of OCyn (through work alienation) on OCB among bank employees.
A matter of others' money: How cash holdings of other firms affect a firm’s cash holding?
Authors: Jinkrawee Jisaba , Lonkani Ravi , Suwanaphan Suchanphin 
Published: December 2021

PurposeThis study examines the effects of comparable companies, within the same industry, on cash-holding (CH) levels of a specific firm in the Stock Exchange of Thailand (SET). Peer effects are hypothesized to affect a firm's average CH levels.Design/methodology/approachThe authors use data of listed firms in the Thai stock markets from 1995 to 2018. The sample consists of 5,277 firm-year observations. The authors perform robustness tests by incorporating gross domestic product, economy and competitiveness.FindingsPeer firms' CH levels correspond positively to the specific firm's CH. This strengthens further for firms with high cash flow volatility during periods of high competition. Unfavorable economic periods also motivate the association between a firm's CH and peer firms' CH.Practical implicationsA policy on CH should account for cash held by peer firms. Firms can justify their CH policy as compatible with peers' cash flows, especially during periods of competitiveness and an unfavorable economy.Originality/valueThe authors provide novel evidence on how emerging markets' CH levels differ from those in developed markets and propose adjusted explanations for the rivalry- and information-based theories. The findings add substantial knowledge to corporate finance by arguing that CH policies are based on peer firms' strategic moves.
The impact of corporate social responsibility on firm financial performance: does audit quality matter?
Authors: Dakhli Anissa 
Published: December 2021

PurposeThe purpose of this paper is to investigate the relation between corporate social responsibility (CSR) and firm financial performance, and how audit quality moderates this relationship.Design/methodology/approachThis study uses panel dataset of 200 French firms listed during 2007–2018 period. The direct and moderating effects were tested by using multiple regression technique.FindingsThe authors find that CSR has a positive impact on firm financial performance proxy with return on assets (ROA), return on equity (ROE) and Tobin'sQ(TQ),suggesting that investment in social activities helps firms to achieve better financial results. The authors also find that the improvement effect of CSR on corporate financial performance is more pronounced for firms audited by Big 4 auditors.Research limitations/implicationsOne limit of this study is the selection of independent variables. We are limited to one variable, namely CSR engagement. Further studies may consider other independent variables, such as the age of the company, the type of industry, the composition of the board of directors, etc., in order to provide an in-depth analysis of corporate financial performance drivers.Practical implicationsThe findings have practical implications that may be useful to managers in their management of the firm. They encourage all board members to seriously weigh investing in developing strategies that promote the social behavior components in order to improve overall corporate performance.Originality/valueThe research adds to the current literature on CSR by revealing the impact of external auditor quality on the CSR–financial performance relationship. In addition, it investigates not only the overall CSR ratings but also each of CSR dimensions, namely environmental, social and governance.