bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions
Authors: Chen Jiayang , Hu Zhihang , Sun Siqi , Tan Qingxiong , Wang Yixuan , Yu Qinze , Zong Licheng , Hong Liang , Xiao Jin , Shen Tao , King Irwin , Li Yu 
Published: August 2022

AbstractNon-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM’s effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.
Translation of dipeptide repeat proteins inC9ORF72-ALS/FTD through unique and redundant AUG initiation codons
Authors: Sonobe Yoshifumi , Lee Soojin , Krishnan Gopinath , Gu Yuanzheng , Kwon Deborah Y. , Gao Fen-Biao , Roos Raymond P. , Kratsios Paschalis 
Published: August 2022

ABSTRACTA hexanucleotide repeat expansion in the first intron ofC9ORF72is the most common monogenic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A hallmark of ALS/FTD pathology is the presence of dipeptide repeat (DPR) proteins, produced from both sense GGGGCC (poly-GA, poly-GP, poly-GR) and antisense CCCCGG (poly-PR, poly-PG, poly-PA) transcripts. Although initiation codons and regulatory factors have been identified for sense DPR translation, they remain mostly unknown for antisense DPRs. Here, we show that an AUG initiation codon is necessary for poly-PR synthesis, suggesting canonical AUG dependent translation. Remarkably, although an AUG located 194 base pairs (bp) upstream of the repeat is the main start codon for poly-PG synthesis, two other AUG codons (−212 bp, -113 bp) can also initiate translation, demonstrating a striking redundancy in start codon usage. eIF2D is required for CUG start codon-dependent poly-GA translation from the sense transcript in human motor neurons derived from induced pluripotent stem cells ofC9ORF72ALS/FTD patients, but AUG-dependent poly-PG or poly-PR synthesis does not require eIF2D, indicating that distinct translation initiation factors control DPR synthesis from sense and antisense transcripts. Our findings provide key molecular insights into DPR synthesis from theC9ORF72locus, which may be broadly applicable to many other nucleotide-repeat expansion disorders.
Macrophage differentiation is marked by increased abundance of the mRNA 3’ end processing machinery, altered poly(A) site usage, and sensitivity to the level of CstF64
Authors: Mukherjee Srimoyee , Graber Joel H. , Moore Claire L. 
Published: August 2022

AbstractRegulation of mRNA polyadenylation is important for response to external signals and differentiation in several cell types, and results in mRNA isoforms that vary in the amount of coding sequence or 3’ UTR regulatory elements. However, its role in differentiation of monocytes to macrophages has not been investigated. Macrophages are key effectors of the innate immune system that help control infection and promote tissue-repair. However, overactivity of macrophages contributes to pathogenesis of many diseases. In this study, we show that macrophage differentiation is characterized by shortening and lengthening of mRNAs in relevant cellular pathways. The cleavage/polyadenylation (C/P) proteins increase during differentiation, suggesting a possible mechanism for the observed changes in poly(A) site usage. This was surprising since higher C/P protein levels correlate with higher proliferation rates in other systems, but monocytes stop dividing after induction of differentiation. Depletion of CstF64, a C/P protein and known regulator of polyadenylation efficiency, delayed macrophage marker expression, cell cycle exit, attachment, and acquisition of structural complexity, and impeded shortening of mRNAs with functions relevant to macrophage biology. Conversely, CstF64 overexpression increased use of promoter-proximal poly(A) sites and caused the appearance of differentiated phenotypes in the absence of induction. Our findings indicate that regulation of polyadenylation plays an important role in macrophage differentiation.
Influence of relay intercropping of barley with chickpea on biochemical characteristics and yield under water stress
Authors: Assadi Negin Mohavieh , Bijanzadeh Ehsan 
Published: August 2022

AbstractRelay intercropping of legumes with cereals is a useful technique for yield improvement. Intercropping may be affected the photosynthetic pigments, enzymes activity and yield of barley and chickpea under water stress. To investigate the effect of relay intercropping of barley with chickpea on pigments content, enzymes activity and yield under water stress, a field experiment as split plot based on a randomized complete block design was conducted during 2017 and 2018. The treatments included irrigation regimes (normal irrigation and cutting off irrigation at milk development stage) as main plot. Also, cropping systems consisted of sole cropping of barley in December (b1) and January (b2), sole cropping of chickpea in December (c1) and January (c2), barley + chickpea in December (b1c1), barley in December + chickpea in January (b1c2), barley in January + chickpea in December (b2c1) and barley + chickpea in January (b2c2) as sub plot. Chlorophyllacontent of barley increased in b1c2,by consuming less water compared to sole cropping. In barley, sowing of barley in December intercropped with chickpea in December and January (b1c1and b1c2) created a suitable canopy in pigment contents improvement. Late sowing of chickpea enhanced the carotenoid content of chickpea, catalase and peroxidase activities. Barley-chickpea intercropping reacted to water deficit through enzymes activity, water use efficiency and land equivalent enhancement compared to sole cropping. Under water stress, in b1c2, by increasing total chlorophyll and water use efficiency, grain yield of barley enhanced compared to b1. It seems that in b1c2, barley and chickpea response to water stress be increasing total chlorophyll and enzymes activity, respectively. In this relay intercropping treatment, each crop occupied and used the growth resources from different ecological niches at different times which is recommended in semi-arid areas.
Intermediate filament network perturbation in the C. elegans intestine causes systemic toxicity
Authors: Geisler Florian , Remmelzwaal Sanne , Boxem Mike , Leube Rudolf E. 
Published: August 2022

AbstractIntermediate filaments (IFs) are major components of the metazoan cytoskeleton. A long-standing debate concerns the question whether IF network organization only reflects or also determines cell and tissue function. Using C. elegans, we have recently described mutants of the MAPK SMA-5, which perturb the organization of the intestinal IF cytoskeleton resulting in luminal widening and cytoplasmic invaginations. Besides these structural phenotypes, systemic dysfunctions were also observed. We now identify the IF polypeptide IFB-2 as a highly efficient suppressor of both the structural and functional deficiencies by removing the aberrant IF network. Mechanistically, IF network morphogenesis is linked to the phosphorylated IFB-2 aminoterminus. The rescuing capability is IF isotype-specific and not restricted to SMA-5 mutants but extends to other regulators of IF network morphogenesis, i.e. the cytoskeletal linker IFO-1 and the IF-associated protein BBLN1. The findings provide strong evidence for a gain-of-toxic function of the deranged IF networks with implications for diseases that are characterized by altered IF network organization.
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
Authors: Nip Ka Ming , Hafezqorani Saber , Gagalova Kristina K. , Chiu Readman , Yang Chen , Warren René L. , Birol Inanc 
Published: August 2022

ABSTRACTLong-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. Using simulated datasets and spike-in control data, we show that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods. Furthermore, RNA-Bloom2 requires 27.0 to 80.6% of the peak memory and 3.6 to 10.8% of the total wall-clock runtime of a competing reference-free method. Finally, we showcase RNA-Bloom2 in assembling a transcriptome sample of Picea sitchensis (Sitka spruce). Since our method does not rely on a reference, it sets up the groundwork for large-scale comparative transcriptomics where high-quality draft genome assemblies are not readily available.
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75
Authors: Saito Akatsuki , Tamura Tomokazu , Zahradnik Jiri , Deguchi Sayaka , Tabata Koshiro , Kimura Izumi , Ito Jumpei , Nasser Hesham , Toyoda Mako , Nagata Kayoko , Uriu Keiya , Kosugi Yusuke , Fujita Shigeru , Yamasoba Daichi , Shofa Maya , Begum MST Monira , Oda Yoshitaka , Suzuki Rigel , Ito Hayato , Nao Naganori , Wang Lei , Tsuda Masumi , Yoshimatsu Kumiko , Yamamoto Yuki , Nagamoto Tetsuharu , Asakura Hiroyuki , Nagashima Mami , Sadamasu Kenji , Yoshimura Kazuhisa , Ueno Takamasa , Schreiber Gideon , Takaori-Kondo Akifumi ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Shirakawa Kotaro , Sawa Hirofumi , Irie Takashi , Takayama Kazuo , Matsuno Keita , Tanaka Shinya , Ikeda Terumasa , Fukuhara Takasuke , Sato Kei 
Published: August 2022

AbstractSARS-CoV-2 Omicron BA.2.75 emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically different from BA.5, the currently predominant BA.2 descendant. Here, we showed that the effective reproduction number of BA.2.75 is greater than that of BA.5. While the sensitivity of BA.2.75 to vaccination- and BA.1/2 breakthrough infection-induced humoral immunity was comparable to that of BA.2, the immunogenicity of BA.2.75 was different from that of BA.2 and BA.5. Three clinically-available antiviral drugs were effective against BA.2.75. BA.2.75 spike exhibited a profound higher affinity to human ACE2 than BA.2 and BA.5 spikes. The fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were comparable to those of BA.5 but were greater than those of BA.2. Our multiscale investigations suggest that BA.2.75 acquired virological properties independently of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.
Inositol pyrophosphate-controlled kinetochore architecture and mitotic entry in S. pombe
Authors: Kuenzel Natascha Andrea , Alcázar-Román Abel R. , Saiardi Adolfo , Bartsch Simon M. , Daunaraviciute Sarune , Fiedler Dorothea , Fleig Ursula 
Published: August 2022

AbstractInositol pyrophosphates (IPPs) comprise a specific class of signaling molecules that regulate central biological processes in eukaryotes. The conserved Vip1/PPIP5K family controls intracellular IP8 levels, the highest phosphorylated form of IPPs present in yeasts, as it has both inositol kinase and pyrophosphatase activities. Previous studies have shown that the fission yeast S. pombe Vip1/PPIP5K family member Asp1 impacts chromosome transmission fidelity via modulation of spindle function. We now demonstrate that an IP8 analogue is targeted by endogenous Asp1 and that cellular IP8 is subject to cell cycle control. Mitotic entry requires Asp1 kinase function and IP8 levels are increased at the G2/M transition. In addition, the kinetochore, the conductor of chromosome segregation assembled on chromosomes is modulated by IP8. Members of the yeast CCAN kinetochore-subcomplex such as Mal2/CENP-O localize to the kinetochore depending on the intracellular IP8-level: higher than wild-type IP8 levels reduces Mal2 kinetochore targeting, while a reduction in IP8 has the opposite effect. As our perturbations of the inositol polyphosphate and IPP pathways demonstrate that kinetochore architecture depends solely on IP8 and not on other IPPs, we conclude that chromosome transmission fidelity is controlled by IP8 via an interplay between entry into mitosis, kinetochore architecture and spindle dynamics.
To wine or not to wine? A scientometric approach to 65+ years of wine preference and selection studies
Authors: Carollo Alessandro , Fong Seraphina , Gabrieli Giulio , Mulatti Claudio , Esposito Gianluca 
Published: August 2022

PurposeAmong the growing interest towards market segmentation and targeted marketing, the current study adopted a scientometric approach to examine the literature on wine selection and preferences. The current review specifically attempts to shed light on the research that explores the determinants of wine preferences at multiple levels of analysis.Design/methodology/approachCiteSpace was used to compute a Document Co-Citation Analysis (DCA) on a sample of 114,048 eligible references obtained from 2,846 publications downloaded from Scopus on 24 May 2021.FindingsAn optimized network of 1,505 nodes and 4,616 links was generated. Within the network, impactful publications on the topic and thematic domains of research were identified. Specifically, two thematic macro-areas were identified through a qualitative analysis of papers included in the 7 major clusters. The first one - “Methods of Wine Making” - included clusters #0, #3, #5, #6 and #18. The second one - “Consumers' Attitudes and Preferences Towards Wine” - included clusters #1 and #2. The first thematic macro-area included more technical aspects referring to the process of wine making, while the second thematic macro-area focused more on the factors influencing individuals' preferences and attitudes towards wine. To reflect the aims of the current paper, publications giving light to the “Consumers' Attitudes and Preferences Towards Wine” macro-area were analyzed in detail.Originality/valueThe resulting insights may help wine makers and wine sellers optimize their work in relation to market segments and to the factors influencing individuals' purchasing behaviors.
Evolution of entrepreneurship research in the food sector: a bibliometric review
Authors: Martín-Navarro Alicia , Lechuga Sancho María Paula , Martínez-Fierro Salustiano 
Published: August 2022

PurposeThis paper aims to analyse through a bibliometric study the academic literature that relates entrepreneurship to foods.Design/methodology/approachA database of 1,300 papers published in the ISI Web of Science was generated. The bibliometric techniques allowed us to describe scientific literature evolution, most productive authors, institutions and countries, most relevant sources and documents, trend topics and social structure.FindingsThe results illustrate an upward trend, more accentuated in the last four years, in publishing papers relating entrepreneurship to the food industry.Originality/valueThis research is novel because although numerous articles relate the food industry to entrepreneurship, no bibliometric articles that analyse the scientific production that relates both terms have been found in the literature.
Dual carbon goals and the impact on future agricultural development in China: a general equilibrium analysis
Authors: Wei Wei , Cui Qi , Sheng Yu 
Published: August 2022

PurposeThis paper aims to explore the future path of agricultural development in China toward 2060 under the dual carbon goals, so as to inform better policy choices for facilitating agricultural and rural transformation toward the goal of maintaining food security, sustainable income growth and low carbon emission.Design/methodology/approachThis study employs a single-country, multi-sectoral computable general equilibrium model, CHINAGEM model and develops eight illustrative scenarios to simulate the impacts of attaining dual carbon goals on agricultural development in China. Additional two scenarios have also been designed to inform better policy making with the aim to offset the negative impact of the decarbonization schemes through facilitating agricultural technology progress.FindingsDual carbon goals are projected to impose substantial negative impact on agricultural productions and consumptions in China in the coming four decades. Under the assumption of business as usual, agricultural production will reduce by 0.49–8.94% along with the attainment of carbon neutrality goal by 2060, with the production of cereals and high-value being more severely damaged. To mitigate the adverse impact of the decarbonization schemes, it is believed that fastening technology progress in agriculture is one of the most efficient ways for maintaining domestic food security without harming the dual carbon goals. In particular, if agricultural productivity (particularly, for cereals and high-value products) can be increased by another 1% per year, the production losses caused by carbon emission mitigation will be fully offset. This implies that promoting technology progress is still the best way to facilitate agricultural development and rural transformation in future China.Originality/valueThe paper contributes to the literature in better informing the impact of dual carbon goals on China's agriculture and the effectiveness of technology progress in agriculture on buffering the adverse impact of the decarbonization schemes and promoting agricultural development.
Far from “Fauda”: creators with disabilities in an established-outsider figuration in the Israeli film and television industries
Authors: Kuna Shani 
Published: August 2022

PurposeAmple literature has demonstrated that workers in the creative industries are excluded in terms of gender, race and class. Fewer studies, however, have examined the career advancement challenges faced by creators with disabilities. Drawing on insights from the established-outsider theory, this study aims to fill this lacuna.Design/methodology/approachThe participants were 24 creators in the Israeli film and television industries (FTIs) contending with severe forms of mental or physical and sensory impairment. In-depth semi-structured interviews were conducted to explore practitioners’ conceptions of the challenges they face in making careers in the FTI, as well as how they contend with these challenges.FindingsIntergroup dynamics yield an established-outsider figuration that situates creators with disabilities in a marginal occupational position in the FTI. Creators with disabilities' lack of access to networks of prominent creators place them in a disadvantageous position in the ongoing struggles over scarce resources in the FTI. The structural features of the FTI, which are intertwined with the social mechanisms of stigmatization and exclusion, make it difficult to breach any figuration once established. In defiance of their occupational figuration, creators with disabilities utilize two tactics aimed at professional advancement: hyper-meritocracy and advocacy. These tactics yield only partial success.Research limitations/implicationsThis study does not represent the voices of decision-makers in the film and television industries in Israel.Practical implicationsImplications are suggested regarding the role of culture funds as well as policymakers in advancing workforce diversity and opportunity in the film and television industries.Originality/valueThis study addresses covert and unspoken barriers to equality in the creative workforce. The findings also shed light on the impact of the COVID-19 pandemic on workforce diversity and opportunity in the FTI.
Outcomes of job insecurity among hotel employees during COVID-19
Authors: Karatepe Osman M. , Okumus Fevzi , Saydam Mehmet Bahri 
Published: August 2022

PurposeThis paper investigates the consequences of job insecurity among hotel employees during the COVID-19 pandemic.Design/methodology/approachData were obtained from the employees of two five-star chain hotels in Turkey. The study hypotheses were tested via structural equation modeling.FindingsThe research findings demonstrate that job insecurity exacerbates job tension. Job tension erodes employees’ trust in organization and aggravates their propensity to leave work early and be late for work. As hypothesized, job tension mediates the effect of job insecurity on organizational trust and the abovementioned outcomes.Originality/valueThis study adds to the hospitality literature by assessing the interrelationships of job insecurity, job tension, organizational trust and nonattendance intentions.
Being ethically resilient during COVID-19: a cross-sectional study of Indian supply chain companies
Authors: Verma Shivangi , Garg Naval , Arumugam Thangaraja 
Published: August 2022

PurposeThe present study aims to examine the relationship between techno-ethical orientation and ethical decision-making (EDM) in Indian supply chain companies during the COVID-19 pandemic. It also aims to explore the moderating role of technological frames (TF) in the relationship between techno-ethical orientation and EDM.Design/methodology/approachThe relationship between techno-ethical orientation and EDM is examined using correlation and regression analysis. The moderating effect of five dimensions of TFs (personal attitude, application value, organisational influence, supervisor influence and industry influence) is analysed using structural equation modelling.FindingsThe correlation coefficient between techno-ethical orientation and EDM is 0.513. Also, the regression coefficient (β = 0.213) is significant at 0.05, establishing a positive linkage between the two. R-square values showed a 45.2% variation in EDM is explained by techno-ethical orientation. Similarly, all variables of TFs have a positive and significant moderating effect on the relationship between techno-ethical orientation and EDM.Originality/valueThis is one of the pioneer studies exploring techno-ethical orientation’s impact on EDM in supply chain companies.