bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital data storage on DNA tape using CRISPR base editors
Authors: Sadremomtaz Afsaneh , Glass Robert F. , Guerrero Jorge Eduardo , LaJeunesse Dennis R. , Josephs Eric A. , Zadegan Reza 
Published: February 2023

AbstractWhile the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA’s enormous potential as a digital storage medium with superior information durability, capacity, and energy consumption. However, the majority of the proposed systems require on-demandde-novoDNA synthesis techniques that produce a large amount of toxic waste and therefore are not industrially scalable and environmentally friendly. Inspired by the architecture of semiconductor memory devices and recent developments in gene editing, we created a molecular digital data storage system called “DNA Mutational Overwriting Storage” (DMOS) that stores information by leveraging combinatorial, addressable, orthogonal, and independentin vitroCRISPR base-editing reactions to write data on a blank pool of greenly synthesized DNA tapes. As a proof of concept, we wrote both a bitmap representation of our school’s logo and the title of this study on the DNA tapes, and accurately recovered the stored data.
Neuronal properties of pyramidal cells in lateral prefrontal cortex of the aging rhesus monkey brain are associated with performance deficits on spatial working memory but not executive function
Authors: Moore Tara L. , Medalla Maria , Ibañez Sara , Wimmer Klaus , Mojica Chromewell A. , Killiany Ronald J. , Moss Mark B. , Luebke Jennifer I. , Rosene Douglas L. 
Published: February 2023

AbstractAge-related declines in cognitive abilities occur as early as middle-age in humans and rhesus monkeys. Specifically, performance by aged individuals on tasks of executive function (EF) and working memory (WM) is characterized by greater frequency of errors, shorter memory spans, increased frequency of perseverative responses, impaired use of feedback and reduced speed of processing. However, how aging precisely differentially impacts specific aspects of these cognitive functions and the distinct brain areas mediating cognition are not well understood. The prefrontal cortex (PFC) is known to mediate EF and WM and is an area that shows a vulnerability to age-related alterations in neuronal morphology. In the current study, we show that performance on EF and WM tasks exhibited significant changes with age and these impairments correlate with changes in biophysical properties of L3 pyramidal neurons in lateral LPFC (LPFC). Specifically, there was a significant age-related increase in excitability of Layer 3 LPFC pyramidal neurons, consistent with previous studies. Further, this age-related hyperexcitability of LPFC neurons was significantly correlated with age-related decline on a task of WM, but not an EF task. The current study characterizes age-related performance on tasks of WM and EF and provides insight into the neural substrates that may underlie changes in both WM and EF with age.
Cardiomyocyte-fibroblast interaction regulates ferroptosis and fibrosis after myocardial injury
Authors: Mohr Mary E. , Li Shuang , Trouten Allison M. , Stairley Rebecca A. , Roddy Patrick L. , Liu Chun , Zhang Min , Sucov Henry M. , Tao Ge 
Published: February 2023

SUMMARYNeonatal mouse hearts have transient renewal capacity which is lost in juvenile and adult hearts. After myocardial infarction (MI) in neonatal hearts, an initial loss of cardiomyocytes occurs but it is unclear through which type of regulated cell death (RCD). In the current studies, we induced MI in neonatal and juvenile mouse hearts, and show that ischemic cardiomyocytes primarily undergo ferroptosis, a non-apoptotic and iron-dependent form of RCD. We demonstrate that cardiac fibroblasts (CFs) protect cardiomyocytes from ferroptosis through paracrine factors and direct cell-cell interaction. CFs show strong resistance to ferroptosis due to high ferritin expression. Meanwhile, the fibrogenic role of CFs, typically considered detrimental to heart function, is negatively regulated by paired-like homeodomain 2 (Pitx2) signaling from cardiomyocytes. In addition, Pitx2 prevents ferroptosis in cardiomyocytes by regulating ferroptotic genes. Understanding the regulatory mechanisms of cardiomyocyte survival and death can identify potentially translatable therapeutic strategies for MI.
A PARP inhibitor, rucaparib, improves cardiac dysfunction inADP-ribose-acceptor hydrolase 3(Arh3) deficiency
Authors: Yamashita Sachiko , Bu Xiangning , Ishiwata-Endo Hiroko , Kato Jiro , Springer Danielle , Noguchi Audrey , Peiravi Morteza , Liu Chengyu , Zhang Fan , Yu Zu-Xi , Clevenger Randy , Keeran Karen , San Hong , Lizak Martin J. , Moss Joel 
Published: February 2023

AbstractAimsPatients withADP-ribose-acceptor hydrolase 3(ARH3) deficiency exhibit stress-induced childhood-onset neurodegeneration with ataxia and seizures (CONDSIAS). ARH3 degrades protein-linked poly(ADP- ribose) (PAR) synthesized by poly(ADP-ribose)polymerase (PARP)-1 during oxidative stress, leading to cleavage of the ADP-ribose linked to protein.ARH3deficiency leads to excess accumulation of PAR, resulting in PAR-dependent cell death or parthanatos. Approximately one-third of patients with homozygous mutantARH3die from cardiac arrest, which has been described as neurogenic, suggesting that ARH3 may play an important role in maintaining myocardial function. To address this question, cardiac function was monitored inArh3-knockout (KO) and - heterozygous (HT) mice.Methods and resultsArh3-KO male mice displayed cardiac hypertrophy by histopathology and decreased cardiac contractility assessed by MRI. In addition, both genders ofArh3-KO and -HT mice showed decreased cardiac contractility by dobutamine stress test assessed by echocardiography. A direct role of ARH3 on myocardial function was seen with a Langendorff-perfused isolated heart model. Arh3-KO male mouse hearts showed decreased post-ischemic rate pressure products, increased size of ischemia-reperfusion (IR) infarcts, and elevated PAR levels. Consistently,in vivoIR injury showed enhanced infarct size inArh3-KO mice in both genders. In addition,Arh3-HT male mice showed increased size ofin vivoIR infarcts. Treatment with an FDA-approved PARP inhibitor, rucaparib, improved cardiac contractility during dobutamine-induced stress and exhibited reduced size ofin vivoIR infarcts. To understand better the role of ARH3, CRISPR-Cas9 was used to generate differentArh3genotypes of myoblasts and myotubes. Incubation with H2O2 decreased viability ofArh3-KO and -HT myoblasts and myotubes, resulting in PAR-dependent cell death that was reduced by PARP inhibitors or by transfection with theArh3gene.ConclusionARH3 regulates PAR homeostasis in myocardium to preserve function and protect against oxidative stress; PARP inhibitors reduce the myocardial dysfunction seen withArh3mutations.Graphical Abstract
Experience with mating receptivity cues affects sexual behaviour of male guppies, but not their strength of preference towards receptive females
Authors: Goberdhan Versara , Darolti Iulia , van der Bijl Wouter , Mank Judith E. , Corral-Lopez Alberto 
Published: February 2023

AbstractFemales are traditionally presented as the choosier sex, selecting males based on the quality of their traits. Yet, there is increasing evidence that male mate choice is also important, even in species without male parental care. Social environment and learning are key factors in determining mate preference, and animals are able to use the information they gather from previous experience to potentially increase their odds of obtaining a high-quality mate. We examined how the social environment affects male mate choice in the guppy (Poecilia reticulata). We evaluated whether male guppies with previous social experience of female receptivity cues learn to prefer and adapt their behavioural repertoire towards females with higher receptiveness levels, as this represents an optimal use of time and energy and is more likely to result in insemination. For this, we measured sexual preference and behaviour for receptive females in no-choice and dichotomous choice tests using guppy males experienced or naïve to female receptivity cues. Experience with receptivity cues did not change the strength of preference towards receptive females. However, male guppies that had previous experience with female receptivity cues adapted their mating tactic compared to naïve males. The change in mating tactics but lack of preference towards receptive females shows that the influence of social learning is present but might be weaker than predicted in this species. Furthermore, these results provide further support to studies of female mate choice suggesting mating status is not a key factor driving the strength of sexual preferences in natural populations.
Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen
Authors: Hall Brantley , Levy Sophia , Dufault-Thompson Keith , Ndjite Glory Minabou , Weiss Ashley , Braccia Domenick , Jenkins Conor , Yang Yiyan , Arp Gabi , Abeysinghe Stephenie , Jermain Madison , Wu Chih Hao , Jiang Xiaofang 
Published: February 2023

AbstractThe degradation of heme and the interplay of its catabolic derivative, bilirubin, between humans and their gut microbiota is an essential facet of human health. However, the hypothesized bacterial enzyme that reduces bilirubin to urobilinogen, a key step that produces the excretable waste products of this pathway, has remained unidentified. In this study, we used a combination of biochemical analyses and comparative genomics to identify a novel enzyme, BilR, that can reduce bilirubin to urobilinogen. We delineated the BilR sequences from other members of the Old Yellow Enzyme family through the identification of key residues in the active site that are critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes in the gut microbiome. Our analysis of human gut metagenomes showed that BilR is a common feature of a healthy adult human microbiome but has a decreased prevalence in neonates and IBD patients. This discovery sheds new light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.
SorCS2 binds progranulin and regulates motor axon outgrowth
Authors: Thomasen PB , Salašová A , Login H , Beel S , Tranberg-Jensen J , Qvist P , Ovesen PL , Nolte S , Nejsum LN , Chao MV , Dasen J , Van Damme P , Kjaer-Sorensen K , Oxvig C , Nykjaer A 
Published: February 2023

AbstractMotor neuron development requires an orchestrated action of trophic factors and guidance cues for axons to reach their targets. Here, we identify SorCS2 as a novel receptor for progranulin (PGRN) that is required for motor axon outgrowth in zebrafish and mice. In both species motor neurons express SorCS2, and PGRN is produced in cells juxta-positioned the projecting axon, but in mice the neurons also co-express PGRN. In zebrafish,sorcs2knockdown produces stunted and aberrantly branched motor axons, and inSorcs2-/-mice, forelimb innervation and motor neuron regeneration are substantially perturbed; phenotypes also observed in fish and mice lacking PGRN. SorCS2 binds PGRN and while motor neuron cultures from wildtype mice respond to exogenous PGRN by axon outgrowth, knockout neurons are unresponsive. Remarkably, when co-expressed in the same cells, SorCS2 controls secretion of PGRN. We conclude that SorCS2 navigates motor neuron development and enables axon regeneration through binding of PGRN.
Dissecting cell state transitions by causal inference
Authors: Xu Longchen , Cong TingTing , Xu Hengyi , Yang Naixue , Tian Chen , Yang Sijie , Zhu Ming , Sinha Rahul , Yamamoto Ryo , Zhang Wei , Wang Jianwei , Lan Xun 
Published: February 2023

AbstractTrajectory inference methods are frequently used for cell fate analysis, however, most of them are similarity-based and lack an understanding of the causality underlying differentiation processes. Here, we present CIBER, aCausalInference–Based framework for theEvaluation of feature effects and theReconstruction of cellular differentiation networks. CIBER provides a novel paradigm for dissecting cell state transitions other than trajectory inference and differential analysis. It is a versatile framework that can be applied to various types of data, including transcriptomic, epigenomic and microarray data. It can identify both known and potential cell-lineage structures with minimal prior knowledge. By integrating the CIBER-learned network with structural causal model and applyingin silicoperturbation as inventions, we generated an effect matrix that quantifies the impact of different features on each differentiation branch. Using this effect matrix, CIBER can identify crucial features involved in haematopoiesis, even if these features show no significant difference in expression between lineages. Moreover, CIBER can predict novel regulation associations and provide insight into the potential mechanism underlying the influence of transcription factors on biological processes. To validate CIBER’s capabilities, we conductedin vivoexperiments onBcl11b, a non-differentially expressed transcription factor identified by CIBER. Our results demonstrate that dysfunction ofBcl11bleads to a bias towards myeloid lineage differentiation at the expense of lymphoid lineage, which is consistent with our predictions.
Evaluation ofCrenobia alpinaandCrenobia montenigrinafrom Parâng Mountains (Carpathians, Romania) according to the morphological and biological concepts of species
Authors: Felicia Babalean Anda 
Published: February 2023

AbstractThis paper assesses the taxonomic status - species or subspecies of the monopharyngeal and polypharyngealCrenobiain Parâng Mt. Romania. From the morphological point of view, the two forms belong toCrenobia alpina, respectively toCrenobia montenigrina. The analysis of the copulatory apparatus indicates a seasonal reproductive isolation (restriction from reproduction) of the two forms: the monopharyngealalpinabecome able to mate during the warm season while the polypharyngealmontenigrinabecome able to mate during the cold season. Data on the reproductive biology and peculiar morphological data are also given. The study concludes that the monopharyngeal and the polypharyngeal Crenobia from Parâng Mt. are good species according to both morphological and biological concepts.
An Unexpected Role of Neutrophils in Clearing Apoptotic HepatocytesIn Vivo
Authors: Cao Luyang , Ma Lixiang , Zhao Juan , Wang Xiangyu , Fan Xinzou , Li Wei , Qi Yawen , Tang Yingkui , Liu Jieya , Peng Shengxian , Yang Li , Zhou Liangxue , Li Li , Hu Xiaobo , Ji Yuan , Hou Yingyong , Zhao Yi , Zhang Xianming , Zhao Youyang , Zhao Yong , Wei Yuquan , Malik Asrar B. , Saiyin Hexige , Xu Jingsong 
Published: February 2023

AbstractBillions of apoptotic cells are removed daily in a human adult by professional phagocytes (e.g. macrophages) and neighboring nonprofessional phagocytes (e.g. stromal cells). Despite being a type of professional phagocyte, neutrophils are thought to be excluded from apoptotic sites to avoid tissue inflammation. Here we report a fundamental and unexpected role of neutrophils as the predominant phagocyte responsible for the clearance of apoptotic hepatic cells in the steady state. In contrast to the engulfment of dead cells by macrophages, neutrophils burrowed directly into apoptotic hepatocytes, a process we termperforocytosis, and ingested the effete cells from the inside. The depletion of neutrophils caused defective removal of apoptotic bodies, induced tissue injury in the mouse liver and led to the generation of autoantibodies. Human autoimmune liver disease showed similar defects in the neutrophil-mediated clearance of apoptotic hepatic cells. Hence, neutrophils possess a specialized immunologically silent mechanism for the clearance of apoptotic hepatocytes through perforocytosis, and defects in this key housekeeping function of neutrophils contribute to the genesis of autoimmune liver disease.
Spanish validation of the Glasgow depression scale for people with intellectual disabilities (GDS-LD) and of the Glasgow depression care supplement scale (GDS-CS)
Authors: Nuñez-Polo Mercedes Hernandez , Lorenzo-Llamas Elena-María , Alonso-Rodriguez Maria-Concepcion , Ayuso-Mateos Jose-Luis , Martorell Almudena 
Published: February 2023

Purpose
This study aims to validate a Spanish version of the Glasgow Depression Scale for Learning Disability (GDS-LD) and of the Glasgow Depression Care Supplement Scale (GDS-CS).

Design/methodology/approach
The GDS-LD was administered to 120 adults with mild and moderate intellectual disabilities and the GDS-CS to the staff from their occupational workshops (n = 120) to detect symptoms of depression. Internal consistency, inter-rater reliability, test-retest reliability, criterion validity, construct validity and the feasibility and applicability of both scales were analysed.

Findings
Both scales showed an adequate internal consistency (GDS-LD, a = 0.86) (GDS-CS, a = 0.88). Exploratory factor analysis revealed four well-defined factors in GDS-LD and three in GDS-CS. Pearson correlation analysis data has also been carried out with both tools for test-retest and inter-rater, showing good correlations.

Research limitations/implications
In terms, of limitations, the participants were recruited from the same centre, so this could be a problem in terms of generalisation. In addition, the GDS-LD and GDS-CS scales were developed for people with mild and moderate ID; it would be worth it to develop a version for people with severe and profound disabilities.

Practical implications
From its clinical perspective, it will be possible to have a specific tool that assesses the symptoms of depression in the Spanish population with ID. Furthermore, as it is a user-friendly scale; it can be administrated by both mental health and other professionals working in the field of disability.

Originality/value
The Spanish version of the GDS-LD and GDS-CS showed adequate rates of feasibility and reliability to assess symptoms depression among Spanish speaking adults with mild and moderate ID.
The 5G C-band auctions across Europe: an assessment
Authors: Curwen Peter , Whalley Jason 
Published: February 2023

Purpose
This study aims to investigate how the licensing of 3.6 GHz (C-band) spectrum has progressed throughout Europe.

Design/methodology/approach
Original databases have been created by the authors covering every aspect of the C-band auctions in Europe, and these have been subjected to analysis to draw out the key themes.

Findings
Although there have been delays in licensing the C-band, the process is now largely complete and the first launches have taken place. However, there has been considerable diversity in the rules underpinning the licenses and considerable differences in the amounts raised measured in $/MHz/pop.

Research limitations/implications
It is difficult to make comparisons across a substantial sample of disparate countries because of the need to compare on a like-for-like basis – an issue that is generally glossed over in the literature. This has been addressed in this paper but some issues inevitably remain unresolved.

Practical implications
The development of 5G is highly contingent on the use of the C-band not just in Europe but elsewhere in the world where less-developed countries can learn from the European experience.

Originality/value
While the subject matter has received attention elsewhere, this represents the most up-to-date version with the largest sample of European countries.
How privacy concerns impact Swedish citizens’ willingness to report crimes: a quantitative mobile phone survey
Authors: Lindqvist Gunnar , Kävrestad Joakim 
Published: February 2023

Purpose
The purpose of this paper is to identify whether there is a lower willingness to report a crime if a victim must hand in their mobile phone as evidence. If that is the case, the research seeks to examine whether privacy concerns and lower willingness correlate with one another and thereby investigate whether privacy concerns could lead to fewer crimes being reported and resolved.

Design/methodology/approach
A mobile phone survey was distributed to 400 Swedish adults to identify their hypothetical willingness to report certain crimes with and without handing in their mobile phones as evidence. The results were then analysed using inferential statistics.

Findings
The result suggests that there is no meaningful correlation between privacy attitudes and willingness to report crime when the handover of a mobile phone is necessary. The results of this study however show a significant lower willingness to report crimes when the mobile phone must be handed in.

Research limitations/implications
Because the chosen target group were Swedish adults, the research results may lack generalisability for other demographics. Therefore, researchers are encouraged to test other demographics.

Originality/value
This paper’s contribution is the novel exploration of attitudes and behaviours regarding the combination of privacy, digital forensics, mobile phones and crime reportage. This research effort examined the problematic situation that can arise for victims of crime, the invasion of privacy when providing evidence by handing in a mobile phone to the police’s forensic unit for examination.
The moderating role of financial managers’ honesty-humility on aggressive financial reporting: evidence from Iran
Authors: Taki Abdollah , Soroushyar Afsaneh 
Published: February 2023

Purpose
The purpose of this study is to investigate the moderating role of honesty-humility of financial managers on aggressive financial reporting behavior.

Design/methodology/approach
To test the research hypotheses, a scenario-based questionnaire taken from Brink et al. (2018) was used. Using a cross-sectional survey design, the authors collected primary data of 160 financial managers of firms in Iran using structured questionnaires. The research sample selected was based on Cohen et al.’s (2000) table. To test the research hypotheses, analysis of variance was used.

Findings
The results showed that increasing honesty-humility of financial managers decreases the impact of social pressure and risk appetite interaction on aggressive financial reporting. In addition, the results of further analysis showed that reducing the honesty-humility of financial managers increases the impact of risk appetite on aggressive financial reporting. Moreover, the results indicate that reducing the honesty-humility of financial managers increases the impact of social pressure on aggressive financial reporting.

Research limitations/implications
This finding provides significant evidence for auditor, managers and policymakers in Iran. Policymakers, auditor and company managers can emphasize compliance with the code of ethics, internal control and corporate governance to increase ethics and reduce negative economic consequences.

Originality/value
To the best of the authors’ knowledge, this is the first case in an emerging economy to survey the moderating role of honesty-humility of financial managers on aggressive financial reporting behavior. Also, this study contributes to understanding how factors at the individual, social and organizational level combine to influence financial managers’ aggressive financial reporting behavior.