bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution and molecular evolution of the anti-CRISPR family AcrIF7
Authors: Figueroa Wendy , Cazares Adrián , Cazares Daniel , Wu Yi , de la Cruz Ana , Welch Martin , Kameyama Luis , Nobrega Franklin L. , Guarneros Gabriel 
Published: June 2021

ABSTRACTAnti-CRISPRs are proteins capable of blocking CRISPR-Cas systems and typically encoded in mobile genetic elements. Since their discovery, numerous anti-CRISPR families have been identified. However, little is known about the distribution and sequence diversity of members within a family, nor how these traits influence the anti-CRISPR’s function and evolution. Here we use AcrIF7 to explore the dissemination and molecular evolution of an anti-CRISPR family. We uncovered five sub-clusters and prevalent anti-CRISPR variants within the group. Remarkably, AcrIF7 homologs display high similarity despite their broad geographical, ecological and temporal distribution. Although mainly associated with Pseudomonas aeruginosa, AcrIF7 was identified in distinct genetic backgrounds indicating horizontal dissemination, primarily by phages. Using mutagenesis, we recreated variation observed in databases but also extended the sequence diversity of the group. Characterisation of the variants identified residues key for the anti-CRISPR function and other contributing to its mutational tolerance. Moreover, molecular docking revealed that variants with affected function lose key interactions with its CRISPR-Cas target. Analysis of publicly available data and the generated variants suggests that the dominant AcrIF7 variant corresponds to the minimal and optimal anti-CRISPR selected in the family. Our study provides a blueprint to investigate the molecular evolution of anti-CRISPR families.
Bacterial filamentation is an in vivo mechanism for cell-to-cell spreading
Authors: Tran Tuan D , Ali Munira Aman , Lee Davin , Félix Marie-Anne , Luallen Robert J 
Published: June 2021

ABSTRACTIntracellular pathogens are challenged with limited space and resources while replicating in a single host cell. Mechanisms for direct invasion of neighboring host cells have been discovered in cell culture, but we lack an understanding of how bacteria directly spread from cell-to-cell in vivo. Here, we describe the discovery of a bacterial species that uses filamentation as an in vivo mechanism for intracellular spreading between the intestinal epithelial cells of its host, the rhabditid nematodeOscheius tipulae. In vitro and in vivo filamentation by this bacterium,Bordetella atropi, requires a highly conserved nutrient-sensing pathway used by divergent bacteria to detect rich conditions and inhibit the divisome. Thus,B. atropiuses a distinct mechanism for cell-to-cell spreading by coopting a pathway that normally regulates bacterial cell size to trigger filamentation inside host cells.
Modified defence peptides from horseshoe crab target and kill bacteria inside host cells
Authors: Amiss Anna S. , von Pein Jessica B. , Webb Jessica R. , Condon Nicholas D. , Harvey Peta J. , Phan Minh-Duy , Schembri Mark A. , Currie Bart J. , Sweet Matthew J. , Craik David J. , Kapetanovic Ronan , Henriques Sónia Troeira , Lawrence Nicole 
Published: June 2021

ABSTRACTBacteria that occupy an intracellular niche can evade extracellular host immune responses and antimicrobial molecules. In addition to classic intracellular pathogens, other bacteria including uropathogenic Escherichia coli (UPEC) can adopt both extracellular and intracellular lifestyles. UPEC intracellular survival and replication complicates treatment, as many therapeutic molecules do not effectively reach all components of the infection cycle. In this study, we explored cell penetrating antimicrobial peptides from distinct structural classes as alternative molecules for targeting bacteria. We identified two β-hairpin peptides from the horseshoe crab, tachyplesin I and polyphemusin I, with broad antimicrobial activity toward a panel of pathogenic and non-pathogenic bacteria in planktonic form. Peptide analogues [I11A]tachyplesin I and [I11S]tachyplesin I maintained activity toward bacteria, but were less toxic to mammalian cells than native tachyplesin I. This important increase in therapeutic window allowed treatment with higher concentrations of [I11A]tachyplesin I and [I11S]tachyplesin I, to significantly reduce intramacrophage survival of UPEC in an in vitro infection model. Mechanistic studies using bacterial cells, model membranes and cell membrane extracts, suggest that tachyplesin I and polyphemusin I peptides kill UPEC by selectively binding and disrupting bacterial cell membranes. Moreover, treatment of UPEC with sublethal peptide concentrations increased zinc toxicity and enhanced innate macrophage antimicrobial pathways. In summary, our combined data show that cell penetrating peptides are attractive alternatives to traditional small molecule antibiotics for treating UPEC infection, and that optimization of native peptide sequences can deliver effective antimicrobials for targeting bacteria in extracellular and intracellular environments.
Genome-wide identification, expression and bioinformatic analyses of GRAS transcription factor genes in rice
Authors: Dutta Mouboni , Saha Anusree , Moin Mazahar , Kirti P.B. 
Published: June 2021

AbstractOur group has previously identified the activation tagging of a GRAS transcription factor (TF)gene in the gain-of-function mutant population of rice (indicarice variety BPT 5204) screened for water use efficiency (Moin et al, 2016a). This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. OnlyOsGRAS23(here named asOsGRAS22) was reported to code for a TF that induces drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens,Xanthomonas oryzaepv.oryzaethat causes bacterial leaf blight andRhizoctonia solanithat causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in thirteen different developmental stages. We studied their spatio-temporal regulation and correlated them within-silicostudies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence ofcis-regulatory elements in a bioinformatics analysis. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants.OsGRAS39was found to be very highly expressive gene under sheath blight infection and both abiotic stress treatments whileOsGRAS8,OsSHR1andOsSLR1were also responsive. Our earlier functional characterization (Moin et al., 2016a) followed by the genome wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.
Robust integration of single-cell cytometry datasets
Authors: Pedersen Christina Bligaard , Dam Søren Helweg , Barnkob Mike Bogetofte , Leipold Michael D. , Purroy Noelia , Rassenti Laura Z. , Kipps Thomas J. , Nguyen Jennifer , Lederer James Arthur , Gohil Satyen Harish , Wu Catherine J. , Olsen Lars Rønn 
Published: June 2021

AbstractCombining single-cell cytometry datasets increases the analytical flexibility and the statistical power of data analyses. However, in many cases the full potential of co-analyses is not reached due to technical variance between data from different experimental batches. Here, we present cyCombine, a method to robustly integrate cytometry data from different batches, experiments, or even different experimental techniques, such as CITE-seq, flow cytometry, and mass cytometry. We demonstrate that cyCombine maintains the biological variance and the structure of the data, while minimizing the technical variance between datasets. cyCombine does not require technical replicates across datasets, and computation time scales linearly with the number of cells, allowing for integration of massive datasets. Robust, accurate, and scalable integration of cytometry data enables integration of multiple datasets for primary data analyses and the validation of results using public datasets.
Sparse connectivity for MAP inference in linear models using sister mitral cells
Authors: Tootoonian Sina , Schaefer Andreas , Latham Peter 
Published: June 2021

AbstractSensory processing is hard because the variables of interest are encoded in spike trains in a relatively complex way. A major goal in studies of sensory processing is to understand how the brain extracts those variables. Here we revisit a common encoding model in which variables are encoded linearly. Although there are typically more variables than neurons, this problem is still solvable because only a small number of variables appear at any one time (sparse prior). However, previous solutions require all-to-all connectivity, inconsistent with the sparse connectivity seen in the brain. Here we propose an algorithm that provably reaches the MAP (maximum a posteriori) inference solution, but does so using sparse connectivity. Our algorithm is inspired by the circuit of the mouse olfactory bulb, but our approach is general enough to apply to other modalities. In addition, it should be possible to extend it to nonlinear encoding models.SummarySensory systems must infer latent variables from noisy and ambiguous input. MAP inference – choosing the most likely latent variable given the sensory input – is one of the simplest methods for doing that, but its neural implementation often requires all-to-all connectivity between the neurons involved. In common sensory contexts this can require a single neuron to connect to hundreds of thousands of others, which is biologically implausible. In this work we take inspiration from the ‘sister’ mitral cells of the olfactory system – groups of neurons associated with the same input channel – to derive a method for performing MAP inference using sparse connectivity. We do so by assigning sister cells to random subsets of the latent variables and using additional cells to ensure that sisters correctly share information. We then derive the circuitry and dynamics required for the sister cells to compute the original MAP inference solution. Our work yields a biologically plausible circuit that provably solves the MAP inference problem and provides experimentally testable predictions. While inspired by the olfactory system, our method is quite general, and is likely to apply to other sensory modalities.
Identifying focus areas to decode the decision to litigate contractual disputes in construction
Authors: Jagannathan Murali , Delhi Venkata Santosh Kumar 
Published: June 2021

PurposeStrong and independent judiciary symbolizes transparency and impartiality in the dispute resolution process. However, litigation is often time-consuming and affects the working relationship between the disputants. In the construction context, where projects typically have a short life span of three to four years, dispute resolution through litigation induces unaffordable process delays. Despite the inherent challenges associated with litigation, it is observed that disputing parties resort to litigation. This behavior, called the litigation dilemma, ostensibly appears counterintuitive to rational decision-making.Design/methodology/approachThe study identifies 35 “decision to litigate” (DTL)-triggers from a review of the literature and court cases followed by expert interviews and groups them into thematic research domains using Exploratory Factor Analysis (EFA) followed by Confirmatory Factor Analysis (CFA).FindingsDTL studies in construction stands benefited through interdisciplinary research. “Presumptuous decision-making,” “construction project characteristics,” “milieu influence,” “interest in amicable resolution,” “positional focus” and “opportunism” are the six focus areas to decode the DTL in construction.Research limitations/implicationsThe study identifies factors that consolidate the knowledge from various fields with the substantive experience of construction professionals from across the world to help understand the dynamics behind the DTL in the context of contract-linked disputes in construction.Originality/valueThe findings from the domains of law, behavior, sociology and economics can help understand the above dilemma in the context of contractual disputes in construction. However, studies that explore the “decision to litigate” (DTL) contractual disputes in construction are limited, providing a vast scope for further research. The current study addresses a part of this gap.
Women founders in a high-tech incubator: negotiating entrepreneurial identity in the Indian socio-cultural context
Authors: Gupta Namrata , Etzkowitz Henry 
Published: June 2021

PurposeThis study aims to understand the socio-cultural context of Indian women's high-tech entrepreneurial experience. Despite a small proportion of women entrepreneurs, and the traditional gender dynamics among the educated middle-classes that appears to be antithetical to female entrepreneurship; women-led high-tech start-ups are on the rise.Design/methodology/approachSemi-structured interviews were conducted with women founders at an academic incubator in an elite Indian Institute of Technology. The study was based on the post-structural feminist approach that women entrepreneurs are embedded in their socio-cultural and institutional context. During data collection, the Coronavirus lockdown provided a natural experiment, highlighting entrepreneurial response to unforeseen obstacles.FindingsIt finds that the context is significant in constructing opportunity, and in navigating challenges of gender and entrepreneurship. Further, in the process of construction of an entrepreneurial identity, women innovators not only reproduce, but also modify their context. Also, the experiences with academic incubator indicate positive results both for gender dynamics and enhancing an emergent entrepreneurial culture.Practical implicationsThe study highlights that women's high-tech entrepreneurship has considerable potential for enhancing women's status in society through the support of academic incubator. This has certain implications for policy.Originality/valueIt provides an insight in to the hitherto neglected issue of women's high-tech entrepreneurship in India, and argues that a study of “social embeddedness” not only highlights constraints for women entrepreneurs unique to that context, but also the potential of women's entrepreneurship in advancing women's agency and gender equality.
The impact of intangible intensity on relevance of R&D information: evidence from India
Authors: Kumari Pooja , Mishra Chandra Sekhar 
Published: June 2021

PurposeThis paper aims to examine the impact of the intangible intensity of the firm on the relevance of research and development (R&D) information to determine equity values in India. Additionally, the study compares the association of input information on R&D investment (the reported R&D cost) and output information on R&D investment (patent count) with equity values. Further, the study also examines the operational nature of the firm and patent count, which is the better proxy to measure the intangible intensity of the firm.Design/methodology/approachThe authors compared the explanatory power of R&D information between intangible and non-intangible intensive firms. To estimate the value relevance of R&D information, the authors followed the statistical model based on the theoretical framework of the residual income model.FindingsThe results indicate that there is a significant moderating impact of the intangible intensity of the firm on the relevance of R&D information to determine equity values in India over the 25 years study period (from 1991 to 2016). Further, in India, the study finds that the input information of R&D outlay is more relevant than output information on R&D outlay to determine equity values, irrespective of the proxy measure of intangible intensity. Moreover, the study finds that the operational nature of the firm is a better proxy of the intangible intensity of the firm compared to patent counts.Research limitations/implicationsIn this study, pooled cross-sectional data were used for analysis. In the future, longitudinal and panel data can be used for more insightful results.Practical implicationsThe findings of the study provide direction to investors and creditors to find the intrinsic value of the investments in internally developed intangible assets, which will reduce the asymmetry between the market value and accounting value of equity.Originality/valueThe paper offers insights into the impact of intangible intensity on the relevance quality of R&D information in an emerging country.
Bank earnings management using loan loss provisions: comparing the UK, France, South Africa and Egypt
Authors: Ozili Peterson K. 
Published: June 2021

PurposeThis paper aims to investigate bank earnings management using loan loss provision. The paper examines income smoothing, which is a type of earnings management. It compares the income smoothing behaviour of banks in the UK, France, South Africa and Egypt.Design/methodology/approachThe study uses the panel fixed effect regression methodology to analyse bank income smoothing.FindingsThe findings show that bank income smoothing is present in the UK and Egypt and absent in France and South Africa. Banks in Egypt used LLPs to smooth income before the global financial crisis. Meanwhile, bank income smoothing is pronounced in France during and after the financial crisis but was absent in the pre-crisis period. Also, bank income smoothing is reduced in countries that (1) have strict banking supervision, (2) adopt common law particularly the United Kingdom, and by countries that adopt civil law, particularly France and Egypt. Bank earnings management is greater in countries that (3) adopt a mixed legal system, particularly South Africa, and in countries that adopt International Financial Reporting Standards accounting standards.Research limitations/implicationsThe implication of the findings is that country differences may affect banks' incentive to smooth income using loan loss provision.Originality/valueThe novelty of this paper is that it explicitly analyses specific countries that have different supervisory regimes, different structure and accounting rules.
Differential effects of online signals on sales performance of local brand clothing products
Authors: Srivastava Praveen Ranjan , Sharma Dheeraj , Kaur Inderjeet 
Published: June 2021

PurposeBusinesses need to make quick decisions and adjustments to fulfill the growing online demand. Previous studies examined various factors affecting the online sales performance of products such as books, electronics and movies; however, they paid limited attention toward the local brand clothing products. The current study investigates the importance of different kinds of seller-generated and consumer-generated signals such as price, discount, product ratings, review volume, review sentiment, number of questions and interaction between some of these factors for predicting the sales performance of clothing products.Design/methodology/approachThe multiple linear regressions has been employed to investigate the influence of various predictor variables on sales performance. The study also examines the importance of these predictor variables by using different machine learning models, including random forest (RF), neural networks and support vector regression (SVR).FindingsThe findings of the study emphasize the importance of price and discount rates offered on the product. The quantitative characteristics of reviews, such as review volume and average rating, have been found to be more important predictors than sentiment strengths. However, the sentiment strength of reviews with higher helpfulness scores plays a significant role in predicting sales performance.Originality/valueThe study highlights the varying importance of seller-based and consumer-based signals in predicting sales performance. It also investigates the interaction effect of these two kinds of signals. The consumer-generated signals have been further divided into two components based on social influence theory, and the interaction effects of these components have also been examined.
The idiosyncratic characteristics of Turkish REITs: evidence from financial ratios
Authors: Çelik Emre , Arslanli Kerem Yavuz 
Published: June 2021

PurposeThis paper aims to determine the specific financial ratio's effects on market value and return of assets for Turkish real estate investment trusts (REITs) traded at Istanbul Stock Exchange (ISE). The paper intends to define liquidity ratios, financial structure ratios, return ratios and stock performance ratios related to market value and return of asset.Design/methodology/approachThe study includes 17 REITs traded in ISE. The period of study is specified as the year from 2009 to 2018. Panel data analysis is applied in this study. Dependent variables are current market value and return of assets, independent variables are 12 financial ratios, which are considered to explain the model significantly. These ratios will be calculated from audited year-end balance sheets for specific periods throughout at least ten years as time series. Two different models and hypotheses have been established to identify the financial ratios that affect the market value and return of assets for REITs.FindingsAccording to the results, long-term financial loans/total assets, return of equity and working capital ratio are negatively correlated with market value, while market value/book value and total assets are correlated positively. On the other hand, market value/book value ratio, price/earning ratio, long-term financial loans/total assets and earnings per share are correlated with return of assets. REITs have high levels of financial leverage, especially in foreign currency. The striking point is that REITs hardly ever do not use financial derivatives to hedge their position again currency and interest rate risk. This approach makes the financial structures of REITs vulnerable and fragile against market volatility.Originality/valueIn Turkey, as an example of an emerging market, financial borrowing does not increase the return rates and market value for REITs due to market's idiosyncratic properties. This finding provides substantial insight into how the debt and equity allocation of Turkish REITs should be structured. Also, it has been observed that forward-looking expectations are considered more than the current situation in the market.
Virtue ethics, situationism and casuistry: toward a digital ethics beyond exemplars
Authors: Vanacker Bastiaan 
Published: June 2021

Purpose
This paper aims to propose an ethical approach best suited to dealing with the issues of digital ethics in general and internet research ethics in particular.

Design/methodology/approach
This article engages with the existing literature on virtue ethics, situationism and digital (research) ethics.

Findings
A virtue-based casuistic method could be well-suited to deal with issues relating to digital ethics in general and internet research ethics in particular as long as it can take place in communities with shared practices and traditions.

Originality/value
These insights could add and further deepen the rich debate about research ethics that is already ongoing within the internet research community.