bluuebunny/crossref_metadata_2025_split huggingface dataset:
PROTOSPACEJAM: AN OPEN-SOURCE, CUSTOMIZABLE AND WEB-ACCESSIBLE DESIGN PLATFORM FOR CRISPR/CAS9 INSERTIONAL KNOCK-IN
Authors: Peng Duo , Vangipuram Madhuri , Wong Joan , Leonetti Manuel D. 
Published: October 2023

ABSTRACTCRISPR/Cas9-mediated knock-in of DNA sequences enables precise genome engineering for research and therapeutic applications. However, designing effective guide RNAs (gRNAs) and homology-directed repair (HDR) donors remains a bottleneck. Here, we present protoSpaceJAM, an open-source algorithm to automate and optimize gRNA and HDR donor design for CRISPR/Cas9 insertional knock-in experiments. protoSpaceJAM utilizes biological rules to rank gRNAs based on specificity, distance to insertion site, and position relative to regulatory regions. protoSpaceJAM can introduce recoding mutations (silent mutations and mutations in non-coding sequences) in HDR donors to prevent re-cutting and increase knock-in efficiency. Users can customize parameters and design double-stranded or single-stranded donors. We validated protoSpaceJAM’s design rules by demonstrating increased knock-in efficiency with recoding mutations and optimal strand selection for single-stranded donors. An additional module enables the design of genotyping primers for next-generation sequencing of edited alleles. Overall, protoSpaceJAM streamlines and optimizes CRISPR knock-in experimental design in a flexible and modular manner to benefit diverse research and therapeutic applications. protoSpaceJAM is available open-source as an interactive web tool atprotospacejam.czbiohub.orgor as a standalone Python package atgithub.com/czbiohub-sf/protoSpaceJAM.
Ancestral genetic components are consistently associated with the complex trait landscape in European biobanks
Authors: Pankratov Vasili , Mezzavilla Massimo , Aneli Serena , Fusco Daniela , Wilson James F , Metspalu Mait , Provero Paolo , Pagani Luca , Marnetto Davide 
Published: October 2023

AbstractThe genetic structure in Europe was mostly shaped by admixture between the Western Hunter-Gatherer, Anatolian Neolithic and Steppe’s Yamnaya ancestral components. Such structure is regarded as a confounder in GWAS and follow-up studies, and gold-standard methods exist to correct for it. However, it is still poorly understood to which extent these ancestral components contribute to complex trait variation in present-day Europe.In this work we harness the UK Biobank to address this question. By extensive demographic simulations and incorporating previous results obtained using the Estonian Biobank, we carefully evaluate the significance and scope of our findings.Heart rate, platelet count, monocyte percentage and many other traits show stratification similar to height and pigmentation traits, likely targets of selection and divergence across ancestral groups. The consistency of our results across biobanks indicates that these ancestry-specific genetic predispositions act as a source of variability and as potential confounders in Europe as a whole.
A genome-wide CRISPR screen supported by human genetics identifies theTNRC18gene locus as a novel regulator of inflammatory signaling
Authors: Rahimov Fedik , Ghosh Sujana , Petiwala Sakina , Schmidt Mary , Nyamugenda Eugene , Tam Jason , Verduzco Daniel , Singh Sanjana , Avram Victor , Modi Apexa , Espinoza Celso A. , Lu Charles , Wang Jing , Keller Ashleigh , Macoritto Michael , Mahi Naim Al , Anton Tifani , Chung Namjin , Flister Michael J. , Katlinski Kanstantsin V. , Biswas Amlan , den Hollander Anneke I. , Waring Jeffrey F. , Stender Joshua D. 
Published: October 2023

ABSTRACTInterleukin-1β (IL-1β) is dysregulated in many chronic inflammatory diseases, yet the genetic factors influencing IL-1β production and signaling remain largely unknown. Myeloid-derived cells are the primary producers of IL-1β, prompting a genome-wide CRISPR knockout screen in the human myeloid-derived U937 cell model, treated with lipopolysaccharide (LPS) to mimic inflammatory conditions, and sorted for high and low intracellular IL-1β levels. A total of 295 genes were identified as regulators of IL-1β production, including known mediators, such as TLR4, JAK-STAT, IL-10 receptor, and the Cullin ring finger ligase complex. Notably, 57 out of the 295 genes overlapped with loci associated with human inflammatory diseases, including theTNRC18gene on chromosome 7p22.1 associated with multiple diseases in the Finnish population. U937 cells engineered with the homozygous rs748670681 risk allele associated with inflammatory bowel disease, demonstrated decreased levels of mRNA forTNRC18and an adjacent geneWIPI2, reduction in LPS-dependent gene activation and cytokine production, but elevation of interferon-responsive gene programs. Transcriptomic profiles for individual knockouts ofTNRC18andWIPI2attributed the loss of LPS-dependent signaling primarily toTNRC18while the exacerbation of interferon signaling is a hallmark of loss ofWIPI2. Collectively, these findings delineate the global regulatory mechanisms of IL-1β production and provide molecular insights to the role of the rs748670681 variant as a pleiotropic risk factor for inflammatory diseases.
Photoreceptor calyceal processes accompany the developing outer segment, adopting a stable length despite a dynamic core
Authors: Sharkova Maria , Aparicio Gonzalo , Mouzaaber Constantin , Zolessi Flavio R , Hocking Jennifer C 
Published: October 2023

AbstractVertebrate photoreceptors detect light through a large cilium-based outer segment, which is filled with photopigment-laden membranous discs. Surrounding the base of the outer segment are microvilli-like calyceal processes (CPs). While CP disruption has been associated with altered outer segment morphology and photoreceptor degeneration, the role of the processes remains elusive. Here, we used zebrafish as a model to characterize CPs. We quantified CP parameters and report a strong disparity in outer segment coverage between photoreceptor subtypes. CP length is stable across light and dark conditions, while heat shock inducible expression of tagged actin revealed rapid turnover of the CP actin core. Detailed imaging of the embryonic retina uncovered substantial remodeling of the developing photoreceptor apical surface, including a transition from dynamic tangential processes to vertically-oriented CPs immediately prior to outer segment formation. Remarkably, we also found a direct connection between apical extensions of the Müller glia and retinal pigment epithelium, arranged as bundles around the ultraviolet sensitive cones. In summary, our data characterize the structure, development, and surrounding environment of photoreceptor microvilli in the zebrafish retina.
Bioinformatic Analysis of Defective Viral Genomes in SARS-CoV-2 and Its Impact on Population Infection Characteristics
Authors: Xu Zhaobin , Peng Qingzhi , Song Jian , Zhang Hongmei , Wei Dongqing , Demongeot Jacques 
Published: October 2023

AbstractDVGs (Defective Viral Genomes) and SIP (Semi-Infectious Particle) are commonly present in RNA virus infections. In this study, we analyzed high-throughput sequencing data and found that DVGs or SIPs are also widely present in SARS-CoV-2. Comparison of SARS-CoV-2 with various DNA viruses revealed that the SARS-CoV-2 genome is more susceptible to damage and has greater sequencing sample heterogeneity. Variability analysis at the whole-genome sequencing depth showed a higher coefficient of variation for SARS-CoV-2, and DVG analysis indicated a high proportion of splicing sites, suggesting significant genome heterogeneity and implying that most virus particles assembled are enveloped with incomplete RNA sequences. We further analyzed the characteristics of different strains in terms of sequencing depth and DVG content differences and found that as the virus evolves, the proportion of intact genomes in virus particles increases, which can be significantly reflected in third-generation sequencing data, while the proportion of DVG gradually decreases. Specifically, the proportion of intact genome of Omicron was greater than that of Delta and Alpha strains. This can well explain why Omicron strain is more infectious than Delta and Alpha strains. We also speculate that this improvement in completeness is due to the enhancement of virus assembly ability, as the Omicron strain can quickly realize the binding of RNA and capsid protein, thereby shortening the exposure time of exposed virus RNA in the host environment and greatly reducing its degradation level. Finally, by using mathematical modeling, we simulated how DVG effects under different environmental factors affect the infection characteristics and evolution of the population. We can explain well why the severity of symptoms is closely related to the amount of virus invasion and why the same strain causes huge differences in population infection characteristics under different environmental conditions. Our study provides a new approach for future virus research and vaccine development.
Role of spirulina microalgae blends in the micro gas turbine on engine performance and emission characteristics
Authors: R. Gokulnath , Devi Booma 
Published: October 2023

Purpose
Diesel has traditionally been considered the best-suited and most widely used fuel in various sectors, including manufacturing industries, power production, automobiles and transportation. However, with the ongoing crisis of fossil fuel inadequacy, the search for alternative fuels and their application in these sectors has become increasingly important. One particularly interesting and beneficial alternative fuel is biodiesel derived from bio sources.

Design/methodology/approach
In this research, an attempt was made to use biodiesel in an unconventional micro gas turbine engine. It will remove the concentric use of diesel engines for power production by improving fuel efficiency as well as increasing the power production rate. Before the fuel is used enormously, it has to be checked in many ways such as performance, emission and combustion analysis experimentally.

Findings
In this paper, a detailed experimental study was made for the use of Spirulina microalgae biodiesel in a micro gas turbine. A small-scale setup with the primary micro gas turbine and secondary instruments such as a data acquisition system and AVL gas analyser. The reason for selecting the third-generation microalgae is due to its high lipid and biodiesel production rate. For the conduction of experimental tests, certain conditions were followed in addition that the engine rotating rpm was varied from 4,000, 5,000 and 6,000 rpm. The favourable and predicted results were obtained with the use of microalgae biodiesel.

Originality/value
The performance and combustion results were not exactly equal or greater for biodiesel blends but close to the values of pure diesel; however, the reduction in the emission of CO was at the appreciable level for the used spirulina microalgae biodiesel. The emission of nitrogen oxides and carbon dioxide was a little higher than the use of pure diesel. This experimental analysis results proved that the use of spirulina microalgae biodiesel is both economical and effective replacement for fossil fuel.
A critical review of cost-benefit analysis for business software investments
Authors: Sakthivel Sachidanandam 
Published: October 2023

PurposeCost-benefit (C/B) analysis helps to determine the economic feasibility of business software investments. Research literature and published practices do not recognize substantial software maintenance costs in C/B analysis. Current analyses emphasize the benefits of an initial investment but do not consider the recurring benefits of each enhancement during the software lifecycle. Such analyses could lead to incorrect investment decisions and lost business opportunities. This article aims to review current research on software lifecycle costs and develop a theoretically sound C/B analysis.Design/methodology/approachThis article reviews current C/B analyses and discusses their shortcomings in treating the significant recurring maintenance costs. It analyzes the findings of various studies on software maintenance and synthesizes these findings to identify the nature of various maintenance costs and their benefits. Based on the synthesis, it theorizes various cost and benefit elements for inclusion in a revised C/B analysis.FindingsThis article identifies each recurring maintenance cost relevant to C/B analysis. It also identifies recurring benefits from each enhancement that hitherto have been omitted. Finally, this article discusses how these costs and benefits should be treated in the revised C/Bs analysis.Research limitations/implicationsThis is a conceptual paper proposing a new C/B analysis and requires an empirical validation.Practical implicationsThis article provides a revision of the C/B analysis that is long overdue. It will help to justify a software investment correctly, rank software projects that compete for limited funds and help create a sound software project portfolio. Since 20% of software products may incur 80% of software investment, this analysis will help to make correct software investments and avoid lost business opportunities. This article also describes a practical method to use the revised C/B analysis.Originality/valueThis article provides a revision of the C/B analysis that is long overdue. It will help to justify a software investment correctly, rank software projects that compete for limited funds and help create a sound software project portfolio. Since 20% of software products may incur 80% of software investment, this analysis will help to make correct software investments and avoid lost business opportunities. This article also describes a practical method to use the revised C/B analysis.
The impacts of role commitment and pay-for-performance on proactive career behavior: an interactionist perspective
Authors: Chen Hui , Liu Jie , Wang Yu , Yang Ning , Wang Xiao-Hua (Frank) 
Published: October 2023

PurposeProactive career behavior (PCB) is an effective form of career self-management that has positive impacts on individual career development and career success, and therefore, the purpose of this paper is to explore the driving factors of PCB.Design/methodology/approachDrawing on the interactionist perspective and situational strength theory, this study examined the independent and joint effects of role commitment and pay-for-performance (PFP) on employees' PCB based on data collected from 298 Chinese private enterprise employees at two time points.FindingsThe authors found that occupational role commitment (ORC), parental role commitment (PRC) and PFP were positively related to PCB. Furthermore, PFP moderated the relationship between ORC/PRC and PCB, such that the two relationships were stronger when PFP was low.Originality/valueDrawing on the interactionist perspective, the authors contribute to the literature on PCB by revealing novel antecedents of PCB: ORC, PRC and PFP. The authors also contribute to the situational strength theory by examining how role commitment and PFP may interact to impact employees' PCB. Finally, the authors are among the first to consider the effects of role commitment on individual career behaviors, thus extending the nomological network of role commitment.
The moderating effects of positive thinking on the relationship between job stress and turnover intention
Authors: Na-Nan Khahan 
Published: October 2023

PurposeThe purpose of this study was to test the moderating effects of positive thinking (PT) on the relationship between job stress (JS) and turnover intention (TI).Design/methodology/approachThe study was based on a questionnaire distributed among 275 employees at a convenience store business. The validity and reliability of the questionnaire were tested before the data were collected, and hierarchical regression analysis was used to test the moderating effects.FindingsJS had negative effects on employee TI with statistical significance, while PT functioned to moderate the relationship between JS and employee TI with statistical significance.Research limitations/implicationsThe moderating effects of PT among employees in the convenience store business were explained clearly. This research supports and expands the broaden-and-build theory in explaining the effects of PT or attitudes to help employees cope with problems and obstacles, create new things and perceive problems as challenges to be overcome.Practical implicationsManagers with an awareness of PT can help employees lower JS, increase organizational commitment and improve employees' PT to reduce the turnover rate.Originality/valueThis study contributes to the literature about organizational behavior and human resource management in dealing with job turnover by clarifying the moderating effects of PT on the relationship between JS and TI.
Does control of corruption play its role in enhancing the innovation? Empirical evidence from Asian region
Authors: Farooq Umar , Tabash Mosab I. , Hamouri Basem , Daniel Linda Nalini 
Published: October 2023

Purpose
In the current competitive era of industrialization, a significant level of innovation is necessary to meet the growing competition. There are many economic forces that determine the pace of innovation within a country. Among others, this study aims to focus on exploring the relevant role of corruption control (CC) in determining the innovation level.

Design/methodology/approach
For empirical analysis, the authors sample the 24 years of data (1996–2019) of Asian economies and use the fully modified ordinary least square (OLS) and dynamic OLS models to check the regression among variables. The selection of both techniques is based upon the empirical suggestions offered by unit root testing and the Johansen cointegration test.

Findings
The empirical findings infer the positive and statistically significant role of CC in boosting innovation. Strengthening the corruption-free environment encourages innovation activities within the country. In addition, foreign direct investment has a negative relationship with CC while financial development, economic growth, export volume and government subsidies positively determine the innovation level.

Practical implications
Based on empirical analysis, it is suggested that the policy officials should do more focus on CC to enhance the competitiveness of the country through more innovation.

Originality/value
The empirical analysis robust the findings of existing literature in an alternative data set and offers innovative views regarding the role of other factors in boosting the innovation level.
Investigating the effectiveness of tourism pricing strategies in mitigating post-COVID-19 economic challenges: an attribution theory perspective
Authors: Hassan Thowayeb , Saleh Mahmoud Ibraheam 
Published: October 2023

PurposeThe study aims to investigate how attribution theory in the context of pricing strategies can help tourism destinations recover from the negative impacts of the COVID-19 pandemic.Design/methodology/approachThe study adopted a qualitative research design using semi-structured interviews to address the lack of research in this area. Interview participants included tourists and tourism customers. The interview responses were then analyzed using “Nvivo” qualitative data analysis software to identify critical themes regarding applying attribution theory to pricing strategies.FindingsThe findings revealed that tourists prefer bundled and hedonic pricing strategies that integrate the service providers' pricing strategies' locus of control, stability and controllability. Tourists do not favor dual pricing strategies unless the reasons for price controllability or stability are justified. Tourists also prefer the controllable pay-what-you-want pricing strategy. Although tourists accept dynamic pricing, certain conditions related to price locus, stability and controllability must be met.Practical implicationsThe research shows tourists prefer pricing strategies that give them control and flexibility, like bundled packages and pay-what-you-want models. Service providers should integrate pricing strategies that transparent costs and justify price fluctuations. While dynamic pricing is accepted if necessitated by external factors, tourists are wary of unnecessary price changes. Providers can build trust and satisfaction by explaining pricing rationale and offering controllable options like bundles.Originality/valueThe study contributes to the theory by applying attribution theory to the context of pricing strategies in tourism. It also provides innovative recommendations for tourism managers on how to use pricing strategies after the COVID-19 pandemic. The findings offer new insights that extend beyond previous research.
Learning to co-teach: understanding the co- in a mentored co-teaching activity
Authors: Chang Sharon , Goodwin A. Lin 
Published: October 2023

PurposeCo-teaching is a foundational mentoring model used in teacher residency programs in urban classrooms throughout the United States of America. Beyond the basic understanding of co-teaching in categorizing classroom models, the purpose of this qualitative case study is to investigate the dialectical tensions manifested in mentored co-teaching activities through the lens of cultural-historical activity theory (CHAT).Design/methodology/approachDesigned as a qualitative case study of 17 pairs of teaching-residents and mentor-teachers, the authors used thematic analysis to scrutinize archival interview data in an urban teacher residency program located in the largest megalopolis of the USA Northeast. The authors used CHAT-based concept coding to analyze the interview narratives from participants across different secondary school placements as they reflected on their co-teaching philosophy and the relationships they built.FindingsThe authors found that for teaching-residents and mentor-teachers to co-develop as co-teachers, they jointly must learn to resolve the dialectical tensions of unbalanced classroom ownership vs added co-working responsibilities, breaking from routine so that a partnership can grow. Furthermore, the findings suggest that the prefix co- should be understood as (1) shifts in thinking that transcend the status quo and (2) the orchestration of human capital to change norms.Originality/valueThis new understanding of the prefix co- allows teacher education programs to better mediate the dialectical tensions experienced by co-teachers in a mentored co-teaching activity, from individual teacher learning (e.g. a pair/dyad comprising one teaching-resident and one mentor-teacher) to collective co-learning across activity systems (e.g. partnership-based teacher education).