bluuebunny/crossref_metadata_2025_split huggingface dataset:
LabEmbryoCam: An opensource phenotyping system for developing aquatic animals
Authors: Ibbini Ziad , Bruning Maria , Allili Sakina , Holmes Luke A , Tully Ellen , McCoy Jamie , Spicer John I. , Tills Oliver 
Published: April 2023

AbstractPhenomics is the acquisition of high-dimensional data on an individual-wide scale and is proving transformational in areas of biological research related to human health including medicine and the crop sciences. However, more broadly, a lack of available transferrable technologies and research approaches is significantly hindering the uptake of phenomics, in contrast to molecular-omics for which transferrable technologies have been a significant enabler. Aquatic embryos are natural models for phenomics, due to their small size, taxonomic diversity, ecological relevance, and high levels of temporal, spatial and functional change. Here, we present LabEmbryoCam, an autonomous phenotyping platform for timelapse imaging of developing aquatic embryos cultured in a multiwell plate format. The LabEmbryoCam capitalises on 3D printing, single board computers, consumer electronics and stepper motor enabled motion. These provide autonomous X, Y and Z motion, a web application streamlined for rapid setup of experiments, user email notifications and a humidification chamber to reduce evaporation over prolonged acquisitions. Downstream analyses are provided, enabling automated embryo segmentation, heartbeat detection, motion tracking, and energy proxy trait (EPT) measurement. LabEmbryoCam is a scalable, and flexible laboratory instrument, that leverages embryos and early life stages to tackle key global challenges including biological sensitivity assessment, toxicological screening and broader engagement with the earliest stages of life.Specifications table
Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning
Authors: de Moura Ferreira Maurício Alexander , Wendering Philipp , Arend Marius , da Silveira Wendel Batista , Nikoloski Zoran 
Published: April 2023

AbstractQuantification of how different environmental cues affect protein allocation can provide important insights for understanding cell physiology. While absolute quantification of proteins can be obtained by resource-intensive mass-spectrometry-based technologies, prediction of protein abundances offers another way to obtain insights into protein allocation. Here we present CAMEL, a framework that couples constraint-based modelling with machine learning to predict protein abundance for any environmental condition. This is achieved by building machine learning models that leverage static features, derived from protein sequences, and condition-dependent features predicted from protein-constrained metabolic models. Our findings demonstrate that CAMEL results in excellent prediction of protein allocation inE. coli(average Pearson correlation of at least 0.9), and moderate performance inS. cerevisiae(average Pearson correlation of at least 0.5). Therefore, CAMEL outperformed contending approaches without using molecular read-outs from unseen conditions and provides a valuable tool for using protein allocation in biotechnological applications.
Human pluripotent stem cells-derived inner ear organoids recapitulate otic developmentin vitro
Authors: Doda Daniela , Jimenez Sara Alonso , Rehrauer Hubert , Carreño Jose F. , Valsamides Victoria , Santo Stefano Di , Widmer Hans Ruedi , Edge Albert , Locher Heiko , van der Valk Wouter , Zhang Jingyuan , Koehler Karl R. , Roccio Marta 
Published: April 2023

AbstractOur molecular understanding of the early stages of human inner ear development has been limited by the difficulty in accessing fetal samples at early gestational stages. As an alternative, previous studies have shown that inner ear morphogenesis can be partially recapitulated using induced pluripotent stem cells (iPSCs) directed to differentiate into Inner Ear Organoids (IEOs). Once validated and benchmarked, these systems could represent unique tools to complement and refine our understanding of human otic differentiation and model developmental defects. Here, we provide the first direct comparisons of the early human embryonic otocyst and human iPSC-derived IEOs. We use multiplexed immunostaining, and single-cell RNA sequencing to characterize IEOs at three key developmental steps, providing a new and unique signature ofin vitroderived otic -placode, -epithelium, -neuroblasts, and -sensory epithelia. In parallel, we evaluate the expression and localization of critical markers at these equivalent stages in human embryos. We show that the placode derivedin vitro(days 8-12) has similar marker expression to the developing otic placode of Carnegie Stage (CS) 11 embryos and subsequently (days 20-40) this gives rise to otic epithelia and neuroblasts comparable to the CS13 embryonic stage. Differentiation of sensory epithelia, including supporting cells and hair cells startsin vitroat days 50-60 of culture. The maturity of these cells is equivalent to vestibular sensory epithelia at week 10 or cochlear tissue at week 12 of development, before functional onset. Together, our data indicate that the current state-of-the-art protocol enables the specification ofbona fideotic tissue, supporting the further application of IEOs to inform inner ear biology and disease.
The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery
Authors: Liu Liang , Yu Angela M , Wang Xiuye , Soles Lindsey V. , Chen Yiling , Yoon Yoseop , Sarkan Kristianna S.K. , Valdez Marielle Cárdenas , Linder Johannes , Marazzi Ivan , Yu Zhaoxia , Qiao Feng , Li Wei , Seelig Georg , Shi Yongsheng 
Published: April 2023

AbstractJTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3′ processing. Although CPSF73 is universally required for mRNA 3′ end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3′ processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3′ processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3′ processing machinery.
BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair
Authors: Lim Pei Xin , Zaman Mahdia , Jasin Maria 
Published: April 2023

HighlightsGap suppression requires BRCA2 C-terminal RAD51 binding in mouse and human cellsBrca2heterozygosity in mice results in fork protection and gap suppression defectsGap suppression mitigates sensitivity to hmdU, but only when HDR is unperturbedHDR deficiency is the primary driver of chemotherapeutic sensitivityeTOC blurbLimet al. report that gap suppression as well as fork protection require BRCA2 stabilization of RAD51 filaments in human and mouse cells but have minimal impact on genome integrity, oncogenesis, and drug resistance. BRCA2 suppression of PRIMPOL-mediated replication gaps confers resistance to the nucleotide hmdU, incorporation of which leads to cytotoxic abasic sites.This effect is diminished when HDR is abrogated.SummaryTumor suppressor BRCA2 functions in homology-directed repair (HDR), protection of stalled replication forks, and suppression of replicative gaps. The relative contributions of these pathways to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for both fork protection and gap suppression, but not HDR. Loss of fork protection and gap suppression do not compromise genome instability or shorten tumor latency in mice or cause replication stress in human mammary cells. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection and gap suppression defects are also observed inBrca2heterozygous mouse cells, likely due to reduced RAD51 stabilization at stalled forks and gaps. Gaps arise from PRIMPOL activity, which is associated with sensitivity to 5-hydroxymethyl-2’-deoxyuridine due to the formation of abasic sites by SMUG1 glycosylase and is exacerbated by poly(ADP-ribose) polymerase inhibition. However, HDR deficiency ultimately modulates sensitivity to chemotherapeutics, including PARP inhibitors.
Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history
Authors: Johri Parul , Pfeifer Susanne P. , Jensen Jeffrey D. 
Published: April 2023

ABSTRACTBuilding evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics – including quantifying the relative contributions of adaptive vs. non-adaptive processes – but it is also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g.,positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, while strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.
Arl3 regulates ODA16-mediated intraflagellar transport in motile cilia biogenesis
Authors: Huang Yameng , Dong Xiaoduo , Sun Stella Y. , Lim Teck-Kwang , Lin Qingsong , He Cynthia Y. 
Published: April 2023

ABSTRACTArl13b and Arl3 are ciliary GTPases implicated in human Joubert Syndrome, affecting ciliary membrane and axoneme organization. Although the mechanism of Arl13b as a guanine nucleotide exchange factor (GEF) of Arl3 and the function of Arl13b and Arl3 in ciliary membrane protein transport are well established, their role in axoneme biogenesis is unclear. InTrypanosoma brucei, TbArl13 acts as a GEF for two distinct TbArl3 proteins, TbArl3A and TbArl3C. Here, we identified theT. bruceihomolog of ODA16, a cargo adapter facilitating intraflagellar transport (IFT) of motile ciliary components, as an effector of both TbArl3A and TbArl3C. Depletion of TbArl3 GTPases stabilized TbODA16 interaction with IFT, while active TbArl3 variants displaced TbODA16 from IFT, demonstrating a mechanism of TbArl3 in motile ciliary cargo transport.One-sentence summaryArl3 acts as a displacement factor and releases ODA16 from IFT
Comparison of commercially available differentiation media on morphology, function, and virus-host interaction in conditionally reprogrammed human bronchial epithelial cells
Authors: Awatade Nikhil T , Reid Andrew T , Nichol Kristy S , Budden Kurtis F , Veerati Punnam C , Pathinayake Prabuddha S , Grainge Christopher L , Hansbro Philip M , Wark Peter AB 
Published: April 2023

AbstractIntroductionPrimary air liquid interface (ALI) cultures of bronchial epithelial cells are used extensively to model airway responses. A recent advance is the development of conditional reprogramming that enhances proliferative capability. Several different media and protocols are utilized, yet even subtle differences may influence cellular responses. We compared the morphology and functional responses, including innate immune responses to rhinovirus infection in conditionally reprogrammed primary bronchial epithelial cells (pBECs) differentiated using two commonly used culture media.MethodspBECs from healthy participants (n = 5) were CR using γ-irradiated 3T3 fibroblasts and Rho Kinase inhibitor. CRpBECs were differentiated at ALI in either PneumaCult™ (PN-ALI) or Bronchial Epithelial Growth Medium (BEGM)-based differentiation media (BEBM:DMEM, 50:50, Lonza™) - (AB-ALI) for 28 days. Transepithelial electrical resistance (TEER), immunofluorescence, histology, cilia activity, ion channel function, and expression of cell markers were analyzed. Viral load was assessed by RT-qPCR and anti-viral factors quantified by Legendplex following Rhinovirus-A1b (RVA1b) infection.ResultsCRpBECs differentiated in PneumaCult™ were smaller and had a lower TEER and cilia beat frequency (CBF) compared to BEGM media. PneumaCult™ media cultures exhibited significantly increasedFOXJ1expression, more ciliated cells with a larger active area, increased intracellular mucins, and increased calcium-activated chloride channel current. However, there were no significant changes in viral RNA or host antiviral responses.ConclusionThere are distinct structural and functional differences in CRpBECs cultured in the two commonly used ALI differentiation media. Such factors need to be taken into consideration when designing and comparing CRpBECs ALI experiments.
Elliptical one-side composite bonded repair analysis through a differential evolution algorithm
Authors: Chamorro-Cruz Isaías , López-Santiago Rebeca , Vázquez-Castillo Valentin , Hernández-Moreno Hilario , Beltrán-Zúñiga Manuel Alejandro , González-Velázquez Jorge Luis , Rivas-López Diego Israel 
Published: April 2023

Purpose
The purpose of this study is to determine the optimal shape of a one-sided elliptical composite material patch of an adhesively bonded repair of cracked metal plates under biaxial stress.

Design/methodology/approach
The approach consists on determining the patch topology and adhesive thickness that minimize the stress intensity factor and the bending moment caused by the asymmetry of the repair by applying a differential evolution algorithm with a selection phase using the Deb’s rules.

Findings
The results demonstrate that an elliptical patch of major axis length equal to the plate width, and minor axis length equal to the crack length, with a thin adhesive thickness, provides the highest stress intensity factor and bending moment reduction, maximizing the fatigue life of the repair.

Research limitations/implications
The results are limited to linear elastic behavior of the cracked plate and a fully rigid bond between the cracked plate and the patch. The effectiveness of the repair was verified by theoretical calculation of the fatigue life, thus experimental validation is still needed.

Practical implications
The results of this work can be applied to experimental validations of the effectiveness of the elliptical one-side composite bonded repairs, avoiding and extensive number of experiments, and also, encourage maintainers to explore on this technique that is more economical and easier to apply, in comparison to other repair techniques. By following the patch geometry recommendations proposed herein, it is analytically predicted that the fatigue life may increase by as much as 27 times that of the unpatched plate.

Originality/value
Currently, there are no detailed studies that assess one-side patch repair procedures, which require consideration of the bending moment and biaxial stress state, and therefore, the optimal patch geometry and adhesive thickness are unknown.
Between obedience and resistance: transforming the role of pupil councils and pupil organisations in Sweden (1928–1989)
Authors: Landahl Joakim 
Published: April 2023

PurposeThe overall aim of this article is to discuss the conditions and character of collective protest in schools. When do pupils as a collective gain the ability to express critical views on the policies of schools, and what is that criticism about? Using Sweden as an example, I discuss this question by studying the collective organisation of pupils from the 1920s to the 1980s.Design/methodology/approachThe article discusses and compares two phases of pupils' collective organisation in Sweden: one dominated by pupil councils, one by national organisations. The article discusses how pupil councils at individual schools arose in the wake of the 1928 grammar school charter, and illustrates its influence using a case study of a grammar school in Stockholm. Furthermore, the article investigates how national organisations, first formed in 1952, expressed their concerns about national school policies.FindingsThe first phase (ca. 1928–1951) was dominated by the idea of discipline, and the main task of pupil councils was to help teachers in maintaining discipline. The second phase (ca. 1952–1989) was instead characterised by a heightened focus on protests and democracy. From then on, the main idea was that pupil councils and national pupil organisations should change the school, making it more suited to the needs of the pupils.Originality/valueThere is much research on university students and student uprisings. However, much of the previous research on the student voice is related to the upheavals of the long 1968. By concentrating its efforts on a limited time period when protest was more obvious, previous research has arguably not been able to discuss transformations over time.
The importance of entrepreneurial leadership in fostering bank performance
Authors: Djalil Muslim Abdul , Amin Muslim , Herjanto Halimin , Nourallah Mustafa , Öhman Peter 
Published: April 2023

PurposeThis study investigates how entrepreneurial leadership fosters market orientation, bank innovativeness and bank performance; it also investigates how market orientation contributes to brand orientation, bank innovativeness and bank performance.Design/methodology/approachIn total, 1500 questionnaires were distributed to 100 bank branches in Indonesia (500 to managers and 1000 to employees); 300 responses (20% response rate) were used for further statistical analysis.FindingsThe results confirmed the existence of relationships among entrepreneurial leadership, market orientation, bank innovativeness, brand orientation and bank performance. The role of entrepreneurial leadership in fostering market orientation, bank innovativeness, brand orientation and bank performance demonstrates that leaders can motivate employees to complete their tasks.Practical implicationsThe findings suggest that entrepreneurial leadership, new ideas and innovative products and services can foster bank performance.Originality/valueThe emerging banking industry in Indonesia has witnessed changing market conditions. Banks will benefit from being more market-driven and diverse in their customer relationships to generate value.
Income and price elasticity of residential electricity demand in Latin America and the Caribbean: a meta-analysis and meta-regression analysis
Authors: Marques Maria Laura Victória , Uhr Daniel de Abreu Pereira , Uhr Julia Ziero 
Published: April 2023

Purpose
This paper aims to identify the income and price elasticities of demand for residential electricity in Latin America and the Caribbean (LAC) and to verify their main determinants.

Design/methodology/approach
Meta-analysis and meta-regression methods were applied. After collecting and filtering journal articles, the authors obtained a sample composed of 76 studies covering 1979–2020.

Findings
The results show that the LAC's income elasticity is approximately 0.20 and 0.92 for the short and long term, respectively. The LAC's price elasticity is approximately −0.37 and −0.46 for the short and long term, respectively. Furthermore, the estimates are affected by the data structure, the estimation method used and the sampling period.

Originality/value
The authors close a gap in the literature by analyzing the price and income elasticities of demand through meta-analysis and meta-regression.
Efficiency decomposition in three-stage network with fuzzy desirable and undesirable output and fuzzy input in data envelopment analysis
Authors: Saeedi Aval Noughabia Fatima , Malekmohammadi Najmeh , Hosseinzadeh Lotfi Farhad , Razavyan Shabnam 
Published: April 2023

PurposeThe purpose of this paper is to improve the recent models for the evaluation of the efficiency of decision making units (DMUs) comprising a network structure with undesirable intermediate measures and fuzzy data.Design/methodology/approachIn this paper a three-stage network structure model with desirable and undesirable data is presented and is solved as linear triangular fuzzy planning problems.FindingsA new three stage network data envelopment analysis (DEA) model is established to evaluate the efficiency of industries with undesirable and desirable indicators in fuzzy environment.Practical implicationsThe implication of this study is to evaluate the furniture services and the chipboard industries of wood lumber as a three-stage process.Originality/valueIn some cases, DMUs include two or multi-stage process (series or parallel) operating with a structure called a network DEA. Also, in the real world problems, the data are often presented imprecisely. Additionally, the intermediate measures under the real-world conditions include desirable and undesirable data. These mentioned indexes show the value of the proposed model.