bluuebunny/crossref_metadata_2025_split huggingface dataset:
BTR: A Bioinformatics Tool Recommendation System
Authors: Green Ryan , Qu Xufeng , Liu Jinze , Yu Tingting 
Published: October 2023

AbstractMotivationThe rapid expansion of Bioinformatics research has resulted in a vast array of computational tools utilized in the development of scientific analysis pipelines. However, constructing these pipelines is a laborious and intricate task, one which demands extensive domain knowledge and careful consideration at all stages. As the Bioinformatics landscape continues to evolve, researchers, both novice and expert, may find themselves overwhelmed when working in unfamiliar fields. Consequently, this may result in the selection of unsuitable or suboptimal tools during workflow development.ResultsIn this paper, we propose the Bioinformatics Tool Recommendation system (BTR), an innovative deep learning model designed to recommend the most suitable tools for a given workflow-in-progress. BTR utilizes recent advances in graph neural network technology and introduces a novel approach, representing the entire workflow as a graph to capture essential context and structural information. Additionally, natural language processing techniques are integrated to enhance the quality of tool recommendations by analyzing associated tool descriptions. Experiments demonstrate that BTR outperforms the existing Galaxy tool recommendation system, highlighting its potential to greatly facilitate scientific workflow construction.Availability and implementationThe Python source code is available athttps://github.com/ryangreenj/bioinformatics_tool_recommendation
Network analyses reveal D clade ethylene response factors as major regulators of jasmonic acid-mediated resistance to early blight disease complex in tomato
Authors: Tominello-Ramirez Christopher , Muñoz Hoyos Lina , Oubounyt Mhaned , Stam Remco 
Published: October 2023

AbstractResistance mechanisms to early blight disease complex (EBDC) in tomato remain obscure given its polygenic and quantitative nature. We investigated the early defense responses of Heinz 1706 tomato to EBDC using RNA-seq. We observed distinct transcriptional reprofiling upon exposure to two EBDC isolates and the PAMP chitin. Avirulent isolate CS046 (Alternaria alternata) elicited a vigorous defense response in the host, whilst the virulent isolate 1117-1 (Alternariasect.Porri) showed subdued gene expression, suggesting a suppression of defense responses during compatible pathogenesis. We emphasize the specific roles ofETHYLENE RESPONSE FACTORs(ERFs) in defense against EBDC, with a particular focus on the D cladeERFs. Co-expression network analysis revealed the principal genes in early defense responses to EBDC are secondary metabolite biosynthesis genes, transcription factors, and hormone response genes. We constructed a gene regulatory network and predicted novel hub genes as putative global regulators of the defense response, including the D cladeERFs, WRKY, andNACtranscription factors. Our work highlights the failure of virulent EBDC pathogenesis to elicit hormone responses that suppress cell death. Additionally, we found a selective induction for specific ERFs that strongly influence the topology of the EBDC defense transcriptional network.
The effects of the infarct volume on cytokines and immune status in patients with acute ischemic stroke
Authors: Su Xingqi , Zhao Lingmin , Ma Di , You Jiulin , Feng LiangShu , Wang Jing , Hao YuLei , Wang XinYu , Feng JiaChun 
Published: October 2023

AbstractObjectiveTo investigate and analyze the effects of the infarct volume on cytokines and immune status in patients with acute ischemic stroke.MethodsPatients with acute ischemic stroke that presented within 72 h of onset from October 2017 to October 2019 were enrolled. Patients with severe cerebral infarction (large-area cerebral infarction) (n=34) were enrolled and categorized as group A; Additionally, 33 patients with non-large-area cerebral infarction with matching baseline characteristics (sex and age) to group A were included in group B. We measured IL-2, IL-4, IL-6, IL-10, IL-17A, TNF-α, and IFN-γ levels in serum using a cytometric bead array.In addition,we compared the absolute value of lymphocytes (LYM#), lymphocyte percentage (LYM%), neutrophil/lymphocyte ratio (NLR), cytokine levels, and immune status indicators (IFN-γ IL-4 ratio, TNF-α/IL-4 ratio, and TNF-α/IL-10 ratio) between groups A and B, and evaluated the effect of infarct size on inflammatory factors and immune status.ResultsCompared with group B, the LYM# and LYM% in group A were significantly lower, and the NLR and cytokines (IL-2, IL-4, IL-6, IL-10, IL-17A, TNF-α, and IFN-γ) levels were significantly higher. TNF-α/IL-4 ratio was significantly lower, and the IFN-γ/IL-4 ratio (P=0.09) and TNF-α/IL-10 ratio (P=0.146) in group A demonstrated a decreasing trend although not significant.ConclusionsThe immune status of patients with acute cerebral infarction is related to the infarct volume; patients with large-area cerebral infarction are more likely to develop immunosuppression.
A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9
Authors: Dey Dhritiman , Chakravarti Rudra , Bhattacharjee Oindrila , Majumder Satyabrata , Chaudhuri Dwaipayan , Ahmed Kazi Tawsif , Bhattacharya Bireswar , Gautam Anupam , Singh Rajveer , Gupta Rahul , Ravichandiran Velayutham , Chattopadhyay Dhrubajyoti , Ghosh Abhrajyoti , Giri Kalyan , Roy Syamal , Ghosh Dipanjan 
Published: October 2023

AbstractCRISPR-Cas9 is the newest technology available for targeted genome editing. It is very efficient and cheap compared to other genome editing techniques. However, its therapeutic application is limited due to its off-target activity. To have a better understanding of this off-target effect, we concentrated our efforts on its mismatch-prone PAM distal end. Current off-target prediction algorithms use RNA-DNA complementation derived energy as a major factor in predicting off-target effect. RNA-DNA complementation derived energy drives Cas9 conformational change, which in turn drives its functional activity. In the case of lower RNA-DNA complementarity, a partial conformational change occurs resulting in a slower reaction rate and partial activity. However, extensive mismatches are often tolerated despite lower complementation derived energy available from RNA: DNA duplex formation. Thus, the off-target activity of Cas9 depends directly on the nature of mismatches which in turn result in deviation of the active site of the enzyme due to structural instability in the duplex strand. In order to test the hypothesis, we have designed an array of mismatched target sites and performed in vitro and cell line-based experiments to assess the effects of PAM distal mismatches in Cas9 activity. For further mechanistic validation, Molecular dynamics simulation was performed and it revealed that certain mismatch mutations induced pronounced conformational instability within the RNA-DNA duplex, leading to elevated root mean square deviation (RMSD) values. We found that, target sites having mismatches in the 18th to 16th position upstream of the PAM showed no to little activity.
A new subspecies ofFicusL. (Moraceae) from North Andaman Island, India
Authors: Kusom Raja Kullayiswamy , Naidu SarojiniDevi 
Published: October 2023

AbstractFicus pellucidopunctatasubsp.obpyriformisis described and illustrated from the North Andaman Island of India. The new taxon resemblesFicus pellucidopunctatain punctale leaf, leaf shape and venation, but differs with the typical species by its longer and obpyriform fig, (verses ellipsoid); scaly minute (ca. 2 mm) basal bracts that do not cover the base of the fig (verses larger (ca. 6 mm) basal bracts that cover the base of the fig); fig orange to dark brown (verses green to yellow); branches terete (verses. angular).Ficus pellucidopunctatasubsp.obpyriformisseeds germinated and saplings were planted and are growing in the Dharmavana Nature Ark (DNA), Bhongir, Telangana as part of the DNA’sexsituconservation programme.
One-pot virus detection based on isothermal amplification coupled with temperature-activated argonaute
Authors: Ye Xingyu , Li Zhonglei , Fang Zhengwei , Shen Nan , Zhou Yuanjie , Sun Peng , Xu Heshan , Liu Qian , Feng Yan 
Published: October 2023

AbstractAdvances in programmable nucleases like CRISPR-associated protein (Cas) and Argonaute (Ago), combined with isothermal amplification, have made point-of-care testing (POCT) more accessible. However, the specific binding of the nuclease resulted in compatibility issues between the amplification and nuclease systems, substantially limiting the feasibility of a one-step workflow. Here, a temperature control solution based on immobilized thermotolerantPyrococcus furiosusAgo (PfAgo) has been proposed. The use of immobilizedPfAgo can effectively prevent interference with loop-mediated isothermal amplification (LAMP) at 65°C and accurately identifies amplicons when activated at 95°C. Following optimization, a sensitivity of 0.6 copies/μL was achieved within 45 minutes, and high specificity was verified with no cross-reactivity among 22 other viruses. Additionally, the multiplex detection was designed for herpes virus sensing, with agreements of 86.4% for positive and 100% for negative samples. Our research presents an effective method for combining amplification and cleavage through the use of controllable nucleases, significantly improving the clinical applicability of diagnostic techniques dependent on programmable nucleases.
The ArabidopsisSNAREcomplex genes regulate the early stages of pollen-stigma interactions
Authors: Macgregor Stuart R. , Beronilla Paula K.S. , Goring Daphne R. 
Published: October 2023

AbstractIn the Brassicaceae, the process of accepting compatible pollen is a key step in successful reproduction and highly regulated following interactions between the pollen and the stigma. Central to this, is the initiation of secretion in the stigma, which is proposed to provide resources to the pollen for hydration and germination and pollen tube growth. Previously, the eight exocyst subunit genes were shown to be required in the Arabidopsis stigma to support these pollen responses. One of the roles of the exocyst is to tether secretory vesicles at the plasma membrane for membrane fusion by the SNARE complex to enable vesicle cargo release. Here, we investigate the role of ArabidopsisSNAREgenes in the stigma for pollen responses. Using a combination of different knockout and knockdownSNAREmutant lines, we show thatVAMP721, VAMP722, SYP121, SYP122andSNAP33are involved in this process. Significant disruptions in pollen hydration were observed following pollination of wildtype pollen on the mutantSNAREstigmas. Overall, these results place the Arabidopsis SNARE complex as a contributor in the stigma for pollen responses and reaffirm the significance of secretion in the stigma to support the pollen-stigma interactions.Key MessageThe VAMP721, VAMP722, SYP121, SYP122 and SNAP33 SNAREs are required in the Arabidopsis stigma for pollen hydration, further supporting a role for vesicle trafficking in the stigma’s pollen responses.
Bidirectional feedforward regulatory loop of Dicer-like 4 and flavonoids causes floral bicolor patterning in petunia and dahlia
Authors: Kuriyama Kazunori , Ohno Sho , Yamazaki Niichi , Tabara Midori , Koiwa Hisashi , Moriyam Hiromitsu , Fukuhara Toshiyuki 
Published: October 2023

AbstractFloral bicolor pigmentation is caused by naturally occurring RNA interference (RNAi) in some cultivars of petunia and dahlia. In both plants, the chalcone synthase gene is highly expressed only in the pigmented region of bicolor petals. However, it remains unknown why RNAi is induced only in the unpigmented region. To elucidate the mechanism of this clear bicolor pattern formation, we examined the dicing activity of Dicer-like 4 (DCL4), which produces small interfering RNAs essential for the induction of RNAi. We showed that the crude extract in the pigmented petal region inhibits dicing activity of DCL4, but not when flavonoids were depleted from the extract. Moreover, we showed the inhibitory activity was associated with flavonoid aglycons. Thein vivodicing activities were detected in the intact protoplasts prepared from the unpigmented region but not from the pigmented region. These results suggest that in the unpigmented region, flavonoids that inhibit DCL4 are not synthesized, and RNAi is maintained, whereas in the pigmented region, DCL4 is inhibited by flavonoids, RNAi is not induced, and anthocyanin biosynthesis is maintained, which ensures RNAi inhibition. Therefore, a clear bicolor pattern is generated by the bidirectional feedforward mechanism of antagonizing DCL4 and flavonoids.
The PDIM paradox ofMycobacterium tuberculosis: new solutions to a persistent problem
Authors: Mulholland Claire V. , Wiggins Thomas J. , Cui Jinhua , Vilchèze Catherine , Rajagopalan Saranathan , Shultis Michael W. , Reyes-Fernández Esmeralda Z. , Jacobs William R. , Berney Michael 
Published: October 2023

AbstractPhthiocerol dimycocerosate (PDIM) is an essential virulence lipid ofMycobacterium tuberculosis.In vitroculturing rapidly selects for spontaneous mutations that cause PDIM loss leading to virulence attenuation and increased cell wall permeability. We discovered that PDIM loss is due to a metabolic deficiency of methylmalonyl-CoA that impedes the growth of PDIM-producing bacilli. This can be remedied by supplementation with odd-chain fatty acids, cholesterol, or vitamin B12. We developed a much-needed facile and scalable routine assay for PDIM production and show that propionate supplementation enhances the growth of PDIM-producing bacilli and selects against PDIM-negative mutants, analogous toin vivoconditions. Our results solve a major issue in tuberculosis research and exemplify how discrepancies between the host andin vitronutrient environments can attenuate bacterial pathogenicity.
Arabidopsis LRR-MAL Receptor-like Kinasesregulate intraspecific and interspecific pollen-stigma interactions
Authors: Lee Hyun Kyung , Sanchez Laura E. Canales , Bordeleau Stephen J. , Goring Daphne R. 
Published: October 2023

AbstractFlowering plants contain tightly controlled pollen-pistil interactions required for promoting intraspecies fertilization and preventing interspecies hybridizations. InArabidopsis, several receptor kinases (RKs) are known to regulate the later stages of intraspecies pollen tube growth and ovular reception in the pistil, but less is known about RK regulation of the earlier stages. TheArabidopsis RKF1cluster ofLeucine-Rich Repeat Malectin(LRR-MAL) RKswas previously found to function in the stigma to promote intraspecies pollen hydration. Here, we tested additional combinations of up to sevenArabidopsis LRR-MAL RKknockout mutants for theRKF1cluster,LIK1,RIR1andNILR2. TheseLRR-MAL RKswere discovered to function in the female stigma to support intraspeciesArabidopsispollen tube growth and to establish a pre-zygotic interspecies barrier againstCapsella rubellapollen. Thus this study uncovered new biological functions for these poorly understood group ofRKsin regulating the early stages ofArabidopsissexual reproduction.
Genetic and transcriptomic dissection of nitrate-independent function of Arabidopsis NRT1.1/NPF6.3/CHL1 under high ammonium condition
Authors: Hachiya Takushi , Makita Nobue , Bach Liên , Gojon Alain , Nakagawa Tsuyoshi , Sakakibara Hitoshi 
Published: October 2023

AbstractThe Arabidopsis nitrate transceptor NRT1.1/NPF6.3/CHL1 regulates physiological responses to nitrate. Several studies have reported that Arabidopsis plants lacking NRT1.1 show enhanced shoot growth under toxic levels of ammonium without nitrate, suggesting a nitrate-independent function for NRT1.1. To further investigate this nitrate-independent function and its impact on ammonium tolerance, we conducted genetic analysis, tissue-specific expression analysis, and transcriptome analysis using various NRT1.1-related lines. Transgenic plants expressing either nonphosphomimic or phosphomimic mutants of NRT1.1 exhibited similar ammonium tolerance to the wild-type. Thechl1-9mutant, in which NRT1.1 with the P492L substitution is localized intracellularly rather than at the plasma membrane and fails to transport nitrate, showed significantly improved ammonium tolerance. Confocal imaging revealed that the NRT1.1-GFP signal was detected in the plasma membrane of various tissues, including cotyledon pavement cells, hypocotyl epidermal cells, mesophyll cells, root cap cells, and epidermal cells near root tips. In early seedlings, the absence of functional NRT1.1 altered the expression of genes associated with aliphatic glucosinolate biosynthesis, ethylene signaling, and low pH stress. Genes predicted to encode products localized to the extracellular space were enriched among those differentially expressed due toNRT1.1deficiency. Our data suggest that in the absence of nitrate, plasma membrane-targeted NRT1.1 reduces ammonium tolerance irrespective of its phosphorylation state with alterations of gene expression associated with stress and senescence.
E-procurement adoption in Nigeria: perceptions from the public sector employees
Authors: Musa Usman , Jaafar Mastura , Raslim Faraziera Mohd 
Published: October 2023

PurposeThis study attempts to examine the factors that influence user intention to adopt e-procurement in the Nigerian public sector.Design/methodology/approachA well-structured questionnaire was used to collect primary data from 278 procurement and information technology (IT) departments’ officials of key federal government ministries and agencies. The technology acceptance model (TAM) model was adopted and extended with security-related factors, namely perceived trust and perceived security. A partial least squares-structural equation modelling (PLS-SEM) approach was used to test and validate the model.FindingsThe results indicated that perceived usefulness is the best predictor of users’ intention to adopt e-procurement, followed by perceived security and perceived trust. In contrast, however, perceived ease of use was found to have a significant negative effect on the intention to adopt e-procurement.Originality/valueThis study is among the first in the Nigerian public sector context to evaluate users’ perceptions on e-procurement adoption with the use of a distinctive research model (TAM). The study's findings contribute to a better understanding of the factors influencing the adoption of e-procurement in the Nigerian public sector.
A systematic approach to analyzing the enablers of post-pandemic supply chain resilience in an emerging economy: a fuzzy AHP approach
Authors: Shaikh Abdul Rehman 
Published: October 2023

PurposeThis study aims to identify the enablers of supply chain resilience (SCR) through a literature review and expert panel input in the context of Pakistan and the post-pandemic era. This study also aims to categorize and rank the identified enablers using expert panel input.Design/methodology/approachA review of the extant literature was conducted to investigate and identify the factors that contribute to SCR. The relative ranking of the enablers was carried out by a group of industry and academic experts. The expert panel was convened to compare the main categories and each enabler in pairs and to score the enablers using triangular fuzzy numbers.FindingsThis study identified 16 critical SCR enablers. Using the fuzzy analytic hierarchy process (AHP), these enablers were divided into three groups and analyzed. The results show that financial enablers, technology enablers and then social enablers are prioritized when it comes to SCR in emerging markets. The robustness of the ranking of enablers is tested through sensitivity analysis.Practical implicationsThe results shall be helpful for policymakers and managers to understand the important enablers and also help allocate resources to important enablers. Managers will be able to formulate strategies to achieve SCR in an uncertain environment.Originality/valueThis is one of the first attempts to identify and rank the enablers of SCR in an emerging economy context.
Filling in the gaps: examining the prevalence of Black homelessness in Canada
Authors: Wilkinson Ashley , Muhajir Khater , Bailey-Brown Patricia , Jones Alana , Schiff Rebecca 
Published: October 2023

Purpose
Due to ongoing inequities in the social determinants of health and systemic barriers, homelessness continues to be a significant concern that disproportionately impacts racialized communities. Despite constituting a small proportion of the population, Black individuals are over-represented among people experiencing homelessness in many Canadian cities. However, although Black homelessness in Canada is a pressing issue, it has received limited attention in the academic literature. The purpose of this paper is to examine the reported prevalence of Black homelessness across Canada.

Design/methodology/approach
By consulting enumerations from 61 designated communities that participated in the 2018 Nationally Coordinated Point-in-Time Count and two regional repositories – one for homeless counts supported by the government of British Columbia and another from the Rural Development Network – this paper reports on the scale and scope of Black homelessness across Canada.

Findings
Significantly, these reports demonstrate that Black people are over-represented among those experiencing homelessness compared to local and national populations. These enumerations also demonstrate significant gaps in the reporting of Black homelessness and inadequate nuance in data collection methods, which limit the ability of respondents to describe their identity beyond “Black.”

Originality/value
This research provides an unprecedented examination of Black homelessness across Canada and concludes with recommendations to expand knowledge on this important and under-researched issue, provide suggestions for future iterations of homeless enumerations and facilitate the development of inclusive housing policy.
Supply chain coordination: the application of consignment and zero wholesale price contracts under customized cap-and-trade and consumers' environmental awareness
Authors: Tat Roya , Heydari Jafar , Mlinar Tanja 
Published: October 2023

PurposeWithin a framework of supply chain (SC) coordination, this paper analyzes a green SC consisting of a retailer and a manufacturer, under government incentives and legislations and the consumer environmental awareness. To mitigate carbon emissions and promote the sustainability of the SC, a customized carbon emission trading mechanism is developed.Design/methodology/approachA game-theoretical decision model formulated determines the optimal sustainability level and the optimal quota of carbon credit from the ceiling capacity set by the government. In order to coordinate the SC and optimize environmental decisions, a novel combination of consignment and zero wholesale price contracts is proposed.FindingsAnalytical and numerical analyses conducted highlight that the proposed contract generates a Pareto improvement for both channel members, boosts the profit of the green SC, enhances the sustainability level of the channel and contributes to a reduction in the requested carbon emission credit by the manufacturer.Social implicationsWith the proposed mechanism, governments can protect their industries and, more importantly, comply with European Union (EU) rules on annually reducing emission ceilings allocated to industries.Originality/valueDifferent from previous studies on cap-and-trade strategies, the proposed mechanism enables companies to select lower emission quota/allowances than the maximum amount set by the government, and in return, companies can benefit from several incentive strategies of the government.