bluuebunny/crossref_metadata_2025_split huggingface dataset:
maGENEgerZ: An Efficient AI-Based Framework Can Extract More Expressed Genes and Biological Insights Underlying Breast Cancer Drug Response Mechanism
Authors: Turki Turki , Taguchi Y-h. 
Published: December 2023

AbstractUnderstanding breast cancer drug response mechanism can play a crucial role in improving the treatment outcomes and survival rates. Existing bioinformatics-based approaches are far from perfect and do not adopt computational methods based on advanced artificial intelligence concepts. Therefore, we introduce a novel computational framework based on an efficient support vector machines (esvm) working as follows. First, we downloaded and processed three gene expression datasets related to breast cancer responding and non-responding to the treatments from the gene expression omnibus (GEO) according to the following GEO accession numbers: GSE130787, GSE140494, and GSE196093. Our method esvm is formulated as a constrained optimization problem in the dual form as a function of λ. We recover the importance of each gene as a function of λ, y, and x. Then, we selectpgenes out ofn,provided as input to enrichment analysis tools, Enrichr and Metascape. Compared to existing baseline methods including deep learning, results demonstrate superiority and efficiency of esvm achieving high performance results and having more expressed genes in well-established breast cancer cell lines including MD-MB231, MCF7, and HS578T. Moreover, esvm is able to identify (1) various drugs including clinically approved ones (e.g., tamoxifen and erlotinib); (2) seventy-four unique genes (including tumor suppression genes such as TP53 and BRCA1); and (3) thirty-six unique TFs (including SP1 and RELA). These results have been reported to be linked to breast cancer drug response mechanism, progression, and metastasizing. Our method is available publicly in the maGENEgerZ web server athttps://aibio.shinyapps.io/maGENEgerZ/.
Pronounced early differentiation underlies zebra finch gonadal germ cell development
Authors: Biegler Matthew T. , Belay Kirubel , Wang Wei , Szi Christina , Collier Paul , Luo Ji-Dung , Haase Bettina , Gedman Gregory L. , Sidhu Asha V. , Harter Elijah , Rivera-López Carlos , Amoako-Boadu Kwame , Fedrigo Olivier , Tilgner Hagen U. , Carroll Thomas , Jarvis Erich D. , Keyte Anna L. 
Published: December 2023

AbstractThe diversity of germ cell developmental strategies has been well documented across many vertebrate clades. However, much of our understanding of avian primordial germ cell (PGC) specification and differentiation has derived from only one species, the chicken (Gallus gallus). Of the three major classes of birds, chickens belong to Galloanserae, representing less than 4% of species, while nearly 95% of extant bird species belong to Neoaves. This represents a significant gap in our knowledge of germ cell development across avian species, hampering efforts to adapt genome editing and reproductive technologies developed in chicken to other birds. We therefore applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis), a Neoaves songbird species and a common model of vocal learning. Analysis of early embryonic male and female gonads revealed the presence of two distinct early germ cell types in zebra finch and only one in chicken. Both germ cell types expressed zebra finch Germline Restricted Chromosome (GRC) genes, present only in songbirds among birds. One of the zebra finch germ cell types expressed the canonical PGC markers, as did chicken, but with expression differences in several signaling pathways and biological processes. The second zebra finch germ cell cluster was marked by proliferation and fate determination markers, indicating beginning of differentiation. Notably, these two zebra finch germ cell populations were present in both male and female zebra finch gonads as early as HH25. Using additional chicken developmental stages, similar germ cell heterogeneity was identified in the more developed gonads of females, but not males. Overall, our study demonstrates a substantial heterochrony in zebra finch germ cell development compared to chicken, indicating a richer diversity of avian germ cell developmental strategies than previously known.
The risks of chronic exposure to ultraviolet light in laboratory environment
Authors: Xavier Eric Almeida 
Published: December 2023

AbstractThe use of ultraviolet (UV) sources in laboratories requires safety practices. For example, when the ultraviolet light of laminar flow is on, it is important that the researcher or team members do not remain in the environment. There are laminar flows that have glasses with an ultraviolet light filter, but many models do not have any protection against ultraviolet light. Thus, we measured the irradiance inside and outside two types of laminar flows without UV filter and with UV filter respectively. And calculated the radiation levels that a researcher could receive at one meter distance for one hour daily in a time interval of one year. Thus, we found that chronic exposure to UV radiation from laminar flow can cause health risks. And we concluded that all laboratories must adopt safety measures, for example does not allow the presence of people during the disinfection stage of laminar flow with UV light.
Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation
Authors: Cornejo Karen G. , Venegas Andie , Sono Morgan H. , Door Madeline , Gutierrez-Ruiz Brenda , Karabedian Lucy B. , Nandi Supratik G. , Dykhuizen Emily C , Saha Ramendra N 
Published: December 2023

SummarySignal-dependent RNA Polymerase II (Pol2) productive elongation is an integral component of gene transcription, including those of immediate early genes (IEGs) induced by neuronal activity. However, it remains unclear how productively elongating Pol2 overcome nucleosomal barriers. Using RNAi, three degraders, and several small molecule inhibitors, we show that the mammalian SWI/SNF complex of neurons (neuronal BAF, or nBAF) is required for activity-induced transcription of neuronal IEGs, includingArc. The nBAF complex facilitates promoter-proximal Pol2 pausing, signal-dependent Pol2 recruitment (loading), and importantly, mediates productive elongation in the gene body via interaction with the elongation complex and elongation-competent Pol2. Mechanistically, Pol2 elongation is mediated by activity-induced nBAF assembly (especially, ARID1A recruitment) and its ATPase activity. Together, our data demonstrate that the nBAF complex regulates several aspects of Pol2 transcription and reveal mechanisms underlying activity-induced Pol2 elongation. These findings may offer insights into human maladies etiologically associated with mutational interdiction of BAF functions.
Differential substrate specificity of ERK, JNK, and p38 MAP kinases toward Connexin 43
Authors: Latchford Lauren P. , Perez Liz S. , Conage-Pough Jason E. , Turk Reem , Cusimano Marissa A. , Vargas Victoria I. , Arora Sonal , Shienvold Sophia R. , Kulp Ryan R. , Belverio Hailey M. , White Forest M. , Thévenin Anastasia F. 
Published: December 2023

ABSTRACTPhosphorylation of connexin 43 (Cx43) is an important regulatory mechanism of gap junction (GJ) function. Cx43 is modified by several kinases on over 15 sites within its ∼140 amino acid-long C-terminus (CT). Phosphorylation of Cx43CT on S255, S262, S279, and S282 by ERK has been widely documented in several cell lines, by many investigators. Phosphorylation of these sites by JNK and p38, on the other hand, is not well-established. Indeed, ERK is a kinase activated by growth factors and is upregulated in diseases, such as cancer. JNK and p38, however, have a largely tumor-suppressive function due to their stress-activated and apoptotic role. We investigated substrate specificity of all three MAPKs toward Cx43CT, first by using purified proteins, and then in two cell lines (MDCK - non-cancerous, epithelial cells and porcine PAECs – pulmonary artery endothelial cells). Cx43 phosphorylation was monitored through gel-shift assays on an SDS-PAGE, immunodetection with phospho-Cx43 antibodies, and LC-MS/MS phosphoproteomic analyses. Our results demonstrate that p38 and JNK specificity differ from each other and from ERK. JNK has a strong preference for S255, S262, and S279, while p38 readily phosphorylates S262, S279, and S282. While we confirmed that ERK can phosphorylate all four serines (255, 262, 279, and 282), we also identified T290 as a novel ERK phosphorylation site. In addition, we assessed Cx43 GJ function upon activation or inhibition of each MAPK in PAECs. This work underscores the importance of delineating the effects of ERK, JNK, and p38 signaling on Cx43 and GJ function.
RepeatOBserver: tandem repeat visualization and centromere detection
Authors: Elphinstone Cassandra , Elphinstone Rob , Todesco Marco , Rieseberg Loren 
Published: December 2023

AbstractTandem repeats can play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination, and the regulation of gene activity. There is a growing need for bioinformatics tools that can visualize and explore chromosome-scale repeats. Here we present RepeatOBserver, a new tool for visualizing tandem repeats and clustered transposable elements and for identifying potential natural centromere locations, using a Fourier transform of DNA walks:https://github.com/celphin/RepeatOBserverV1. RepeatOBserver can identify a broad range of repeats (3-20, 000bp long) in genome assemblies without anya prioriknowledge of repeat sequences or the need for optimizing parameters. RepeatOBserver allows for easy visualization of the positions of both perfect and imperfect repeating sequences across each chromosome. We use RepeatOBserver to compare DNA walks, repeat patterns and centromere positions across genome assemblies in a wide range of well-studied species (e.g., human, mouse-ear cress), crops, and non-model organisms (e.g., fern, yew). Analyzing 107 chromosomes with known centromere positions, we find that centromeres consistently occur in regions that have the least diversity in repeat types (i.e. one or a few repeated sequences are present in very high numbers). Taking advantage of this information, we use a genomic Shannon diversity index to predict centromere locations in several other chromosome-scale genome assemblies. The Fourier spectra produced by RepeatOBserver can help visualize historic centromere positions, potential neocentromeres, retrotransposon clusters and gene copy variation. Identification of patterns of split and inverted tandem repeats at inversion boundaries suggests that at least some chromosomal inversions or misassemblies can be predicted with RepeatOBserver. RepeatOBserver is therefore a flexible tool for comprehensive characterization of tandem repeat patterns that can be used to visualize and identify a variety of regions of interest in genome assemblies.
Genomic Underground: Unraveling NUMTs in Mole Voles
Authors: Prokopov Dmitry , Saluev Tigran , Romanenko Svetlana , Bakloushinskaya Irina , Graphodatsky Alexander 
Published: December 2023

AbstractNuclear mitochondrial DNA segments (NUMTs) are pervasive elements of eukaryotic genomes. This study focuses onEllobius talpinusandEllobius lutescens, for which we assembled full mitochondrial DNA sequences. Our study identified NUMTs encompassing approximately 0.0052% and 0.0086% of genome assembly length inE. talpinusandE. lutescens, respectively. These NUMTs collectively spanned a total length of 122,294 bp inE. talpinusand 194,875 bp inE. lutescens. Notably, the majority of NUMTs in both species were short, with lengths of less than 500 bp. InE. talpinus, the data indicated the presence of comparatively recent NUMT insertions. More than half of the NUMTs in each species are organized into clusters, primarily situated in intergenic regions or within introns. RNA genes are the most frequently occurring fragments within these NUMTs. Furthermore, our analysis identified LINE, SINE, and LTR retrotransposons within and flanking NUMT clusters. Our results demonstrate the intricate dynamics of NUMT integration and distribution inEllobiusspecies and provide insights into their genomic architecture and evolutionary history. This study contributes to the broader understanding of mitochondrial DNA contributions to nuclear genomes and underscores the complexity of distinguishing between mtDNA and nuclear DNA in genomic studies.
Sex- and strain-dependent effects of ageing on sleep and activity patterns inDrosophila
Authors: Woodling Nathan 
Published: December 2023

AbstractThe fruit flyDrosophilais a major discovery platform in the biology of ageing due to its balance of relatively short lifespan and relatively complex physiology and behaviour. Previous studies have suggested that some important phenotypes of ageing, for instance increasingly fragmented sleep, are shared from humans toDrosophilaand can be useful measures of behavioural change with age: these phenotypes therefore hold potential as readouts of healthy ageing for genetic or pharmacological interventions aimed at the underpinning biology of ageing. However, some age-related phenotypes inDrosophilashow differing results among studies, leading to questions regarding the source of discrepancies among experiments. In this study, I have tested females and males from three common laboratory strains ofDrosophilato determine the extent to which sex and background strain influence age-related behavioural changes in sleep and activity patterns. Surprisingly, I find that some phenotypes – including age-related changes in total activity, total sleep, and sleep fragmentation – depend strongly on sex and strain, to the extent that some phenotypes show opposing age-related changes in different sexes or strains. Conversely, I identify other phenotypes, including age-related decreases in morning and evening anticipation, that are more uniform across sexes and strains. These results reinforce the importance of controlling for background strain in both behavioural and ageing experiments, and they imply that caution should be used when drawing conclusions from studies on a single sex or strain ofDrosophila. At the same time, these findings also offer suggestions for behavioural measures that merit further investigation as potentially more consistent phenotypes of ageing.
Do agency costs and business risk affect the corporate sustainability–financial performance relationship?
Authors: Kalash Ismail 
Published: December 2023

PurposeThe aim of this research is to examine the effect of corporate sustainability performance on financial performance and the role of agency costs and business risk in determining this effect.Design/methodology/approachThis study uses the data of 83 non-financial Turkish firms listed on Istanbul Stock Exchange during the period 2014–2021. Two-step system GMM models are applied to examine the study’s hypotheses.FindingsThe results indicate a positive effect of corporate sustainability performance on financial performance, and that this effect is significant only for firms that are more likely to suffer agency costs of equity, firms with R&D expenditures and firms with lower business risk.Practical implicationsThe results of this study confirm the importance of regulations introduced by regulators to support the sustainability initiatives for firms that have less ability to access funds required for their investments. In addition, the findings provide important insight into the role of the persistence of corporate sustainability performance in enhancing financial performance through mitigating managers' opportunistic behavior.Originality/valueTo the author’s knowledge, this research is one of few that examine the effect of agency costs and business risk on the corporate sustainability–financial performance relationship in emerging markets.
Outbound open innovation effectiveness measurement between big organizations and startups using Fuzzy MCDM
Authors: Quaiser Raunaque Mujeeb , Srivastava Praveen Ranjan 
Published: December 2023

PurposeThis research aims to identify the key factors affecting Outbound Open Innovation between Startups and Big organizations using the multiple criteria decision-making analysis (MCDM) approach. The MCDM technique ranks the four key factors identified from the literature study that can help to improve collaboration opportunities with Startups.Design/methodology/approachIdentification of key factors affecting Outbound Open Innovation between Startups and big organizations based on extant literature. A questionnaire is prepared based on these four identified key factors to gather views of the startup's employees, from the designer level to the startup's founder. MCDM techniques are used to evaluate the questionnaire. The ensemble technique is used to rank the key factors coming from three different MCDM methods.FindingsThe findings from the MCDM approach and Ensemble techniques give insight to the big organizations to facilitate outbound Open Innovation effectively. It also provides insight into the requirements of the startups and the kind of support they seek from the big organizations. The ranking can help the big organization close the gaps and make an informed decision to increase the effectiveness of the collaborations and boost innovation.Originality/valueThis is a unique research work where the MCDM approach is used to identify the ranking of key factors affecting outbound open innovation between startups and big organizations. The MCDM technique is followed by the ensemble method to rationalize the findings. Technology Relevance ranks highest, followed by Innovation Ecosystem, Organization commitment and Knowledge Sharing.
Asymmetric effect of environmental tax on CO2 emissions embodied in domestic final demand in South Africa: A NARDL approach
Authors: Ibe Godwin Imo , Ezeaku Hillary Chijindu , Okpara Itiri Idam , Eze Eze Festus , Igwemeka Ebele , Ubani Obinna 
Published: December 2023

AbstractMotivated by the pressing need to address environmental concerns, this study explores the relationship between environmental taxes and CO2 emissions embodied in domestic final demand in South Africa. The study uses a non‐linear autoregressive distributed lag (NARDL) model to analyse the asymmetric impact of environmental taxes. Results indicate that environmental taxes have an asymmetric impact on CO2 emissions embodied in domestic final demand in both the short and long runs. Specifically, both positive and negative shifts in environmental taxes are linked with a respective 0.06% decrease and a more pronounced 0.22% decrease in CO2 emissions embodied in domestic final demand. Moreover, positive shocks in the GDP growth rate are associated with an approximately 0.002% uptick in CO2 emissions, while negative shocks lead to a 0.012% decrease. Additionally, both positive and negative shocks in population growth exhibit a significant positive correlation with the response variable. The baseline estimates demonstrate that the joint effect of environmental taxes and the GDP growth rate is correlated with reductions in CO2 emissions embodied in domestic final demand. Similarly, the joint influence of environmental taxes and population growth rate is linked to declines in CO2 emissions. The study highlights the practical policy implications of these findings.
Therapy for the Dead: Working Clinically with Jung's Black Books and The Red Book
Authors: Hill Ginny 
Published: December 2023

AbstractWith the 2020 publication of the facsimile edition of The Black Books, we have an opportunity to study the layers of C. G. Jung's creative writing process for the first time. In this paper, I explore Jung's practice of active imagination in relation to his fantasy dialogues with the dead during two specific episodes in 1914 and 1916. I discuss Jung's concept of the collective unconscious corresponding to the “mythic land of the dead” and I show how this idea develops in The Black Books and The Red Book, or Liber Novus, culminating in Septem Sermones ad Mortuos. I describe my work with a patient, who, in an early session, said she felt like the "living dead". I recount how the patient's experience of her own internal world began to change as we were able to wonder about the inner world of the patient's late mother and, together, to imagine her mother's lament. I consider the use of imagination when working with the concept of "therapy for the dead" (Hillman & Shamdasani, 2013, p. 164) in the context of intergenerational trauma.
Fraud Power Laws
Authors: CHEYNEL EDWIGE , CIANCIARUSO DAVIDE , ZHOU FRANK S. 
Published: December 2023

ABSTRACTUsing misstatement data, we find that the distribution of detected fraud features a heavy tail. We propose a theoretical mechanism that explains such a relatively high frequency of extreme frauds. In our dynamic model, a manager manipulates earnings for personal gain. A monitor of uncertain quality can detect fraud and punish the manager. As the monitor fails to detect fraud, the manager's posterior belief about the monitor's effectiveness decreases. Over time, the manager's learning leads to a slippery slope, in which the size of frauds grows steeply, and to a power law for detected fraud. Empirical analyses corroborate the slippery slope and the learning channel. As a policy implication, we establish that a higher detection intensity can increase fraud by enabling the manager to identify an ineffective monitor more quickly. Further, nondetection of frauds below a materiality threshold, paired with a sufficiently steep punishment scheme, can prevent large frauds.
Difficulty differentiating primary mediastinal classical Hodgkin lymphoma from inflammatory myofibroblastic tumor: A case report
Authors: Akata Kentaro , Yamasaki Kei , Chiba Yosuke , Kawaguchi Takako , Dosaka Hiroki , Morimoto Toshiki , Higashi Yasuyuki , Nishida Chinatsu , Shimajiri Shohei , Yatera Kazuhiro 
Published: December 2023

AbstractA 20‐year‐old Japanese man visited our hospital because an enlarged mediastinal shadow had been detected on chest x‐ray. Chest computed tomography revealed a large mediastinal mass with multiple lymph node enlargement, pericardial effusion, and bilateral pleural effusion. He was diagnosed with inflammatory myofibroblastic tumor (IMT) based on a thoracoscopic tumor biopsy. Initial corticosteroid and celecoxib treatment was only partially effective; therefore, additional tumor rebiopsy and left axillary lymph node biopsy were performed. Based on the findings, the patient was rediagnosed with classical Hodgkin lymphoma (CHL). To date, there has only been one report of a case initially diagnosed as IMT and rediagnosed as CHL, as in our case, and only three reports of malignant lymphoma mimicking IMT. When IMT is suspected based on pathological findings and subsequently with treatment failure, possible CHL and performing rebiopsy should be considered.