bluuebunny/crossref_metadata_2025_split huggingface dataset:
Axes of Hope: Flights of Fancy in Recent Work on Urban Congo
Authors: Bouwer Karen 
Published: March 2023

Abstract
This article explores the question of hope in dystopian urban spaces as represented in recent work from the Democratic Republic of the Congo by developing the concept of ‘the hole’ used by Congolese people to comment upon the quality of their lives. The more literal reading of ‘le trou’ in Sinzo Aanza’s 2015 novel Généalogie d’une banalité, set in the mining community of Lubumbashi, is compared to the vertical aspiration of ‘la tour’ in The Tower, a 2016 film by Sammy Baloji and Filip De Boeck, set in Kinshasa. The two works, representing a unique landmark and the excesses of extractive economies, provide the opportunity to reflect on fanciful ventures that, despite the material conditions that thwart dreams of a better life, have not foreclosed all spaces of hope.
Effects ofWolbachiaon Transposable Element Expression Vary BetweenDrosophila melanogasterHost Genotypes
Authors: Eugénio Ana T , Marialva Marta S P , Beldade Patrícia 
Published: March 2023

AbstractTransposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia with changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying the expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels for our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 21.1% of the TE-genotype combinations tested, with up to 2.3 times differences in the median level of transcript. Our data show that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.
Conserved Molecular Players Involved in Human Nose Morphogenesis Underlie Evolution of the Exaggerated Snout Phenotype in Cichlids
Authors: Duenser Anna , Singh Pooja , Lecaudey Laurène Alicia , Sturmbauer Christian , Albertson R Craig , Gessl Wolfgang , Ahi Ehsan Pashay 
Published: March 2023

AbstractInstances of repeated evolution of novel phenotypes can shed light on the conserved molecular mechanisms underlying morphological diversity. A rare example of an exaggerated soft tissue phenotype is the formation of a snout flap in fishes. This tissue flap develops from the upper lip and has evolved in one cichlid genus from Lake Malawi and one genus from Lake Tanganyika. To investigate the molecular basis of snout flap convergence, we used mRNA sequencing to compare two species with snout flap to their close relatives without snout flaps from each lake. Our analysis identified 201 genes that were repeatedly differentially expressed between species with and without snout flap in both lakes, suggesting shared pathways, even though the flaps serve different functions. Shared expressed genes are involved in proline and hydroxyproline metabolism, which have been linked to human skin and facial deformities. Additionally, we found enrichment for transcription factor binding sites at upstream regulatory sequences of differentially expressed genes. Among the enriched transcription factors were members of the FOX transcription factor family, especially foxf1 and foxa2, which showed an increased expression in the flapped snout. Both of these factors are linked to nose morphogenesis in mammals. We also found ap4 (tfap4), a transcription factor showing reduced expression in the flapped snout with an unknown role in craniofacial soft tissue development. As genes involved in cichlid snout flap development are associated with human midline facial dysmorphologies, our findings hint at the conservation of genes involved in midline patterning across distant evolutionary lineages of vertebrates, although further functional studies are required to confirm this.
An Adagio for Viruses, Played Out on Ancient DNA
Authors: de-Dios Toni , Scheib Christiana L , Houldcroft Charlotte J 
Published: March 2023

AbstractStudies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses—and in particular those with single- or double-stranded DNA genomes—are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.
Development of the Thymus and Kidney and Effects of Resveratrol on Their Aging in a Short-Lived Fish
Authors: Hou Yanhan , Li Shasha , Zhu Hongyan , Qiao Mengxue , Sun Xiaowen , Li Guorong 
Published: March 2023

Abstract
Annual fishes of the genus Nothobranchius have been widely used in cognitive, behavioral, and genetic studies, and have become an excellent animal model for studying aging. However, the development and degeneration of immune organs in annual fishes and the antagonistic effects of resveratrol remain unclear. In the present study, the development of thymus and kidney was investigated systematically using Nothobranchius guentheri from larvae, juveniles, and young and old fish with hematoxylin and eosin staining. We found that thymus primordium was observed first in the larvae at 2 days after hatching (dah). After the lymphoid cells became evident at 5 dah, the thymus acquired an irregular shape at 7 dah. Then it formed a wedge shape at 15 dah. Thymus looked as homogeneous distribution of lymphocytes at 1 month old, and it differentiated into cortex and medulla approximately in 2-month-old fish. Combined with TUNEL and senescence-associated β-galactosidase (SA-β-gal) staining, it showed the degeneration of the thymus appeared in 4-month-old fish. Kidney primordium appeared on 1 dah, and the glomerulus was visible at 7 dah. The nephrogenic activity was most apparent in 1-month-old fish. A large hematopoietic tissue was arranged in the renal interstitium in 2- and 3-month-old fish. In 6-month-old fish, the kidney structure became less dense. By 12 months, the kidney exhibited the most pronounced histological characteristics of aging. Feeding resveratrol ameliorated renal fibrosis and SA-β-gal staining with age, increased SIRT1 and SIRT3 expression, and decreased the levels of NF-κB and inflammatory factors in thymus and kidney of the fish. We provided basic data for the development and degeneration of immune organs and resveratrol’s anti-aging effects in short-lived fish.
Diurnal characterization of the atmospheric urban heat island over urban hot agglomerations
Authors: Sayad Bouthaina , Menni Younes , Imam Ayman Amin , Fallatah Ahmad , Faisal Kamil Said , Abed Ahmed Mohammed , Alhubashi Haytham Hussain , Hegazy Ibrahim Rizk 
Published: March 2023

Abstract
The urban heat island ($\mathrm{UHI}$) is a physical climatic phenomenon; its effects in built-up areas can be observed in terms of air temperatures above the atmosphere, as well as in terms of thermal comfort under the urban canopy. This study aims to carry out a diurnal characterization of the atmospheric UHI over the agglomeration of $\mathrm{Guelma}$, Algeria during summertime. The characterization is organized into three main steps. First, quantifying the $\mathrm{UHI}$ intensity. Second, highlighting the factors contributing to affect the thermal environment in downtown $\mathrm{Guelma}$ and finally, defining an appropriate scale to measure it over $\mathrm{Guelma}$’s agglomeration of Guelma. The $\mathrm{UHI}$ quantification was done by calculating the positive differences of urban temperatures in daytime based on in situ and static approach. The results indicate that the maximum daily difference reached $4.8$ to $5.1{}^{\circ}\mathrm{C}$ with a positive difference of $6.1{}^{\circ}\mathrm{C}$ at $10:00$ a.m. and $6.4{}^{\circ}\mathrm{C}$ at noon, which means that $\mathrm{Guelma}$’s agglomeration is affected by the atmospheric UHI phenomenon. Depending on the difference of urban temperatures, we have defined appropriate scale to quantify the intensity of UHI phenomenon over Guelma’s agglomeration as follows: ${UHI}_{intensity}=0.3688\times \boldsymbol{\Delta }{T}_{\boldsymbol{urb}}+3.3157.$
Reconciling Theory and Practice: Confronting Violent Histories in Poland and Israel–Palestine
Authors: Gutman Yifat 
Published: March 2023

AbstractThe role of violent histories and their legacies in reconciliation processes has been a central question in debates on reconciliation and nation building after conflict: whether, how, and when painful events should be remembered in post-conflict and post-transition societies. A dominant approach to this question since the 1980s has been the “reconciliation paradigm,” which views addressing violent histories as condition for reconciliation. A comparative study of the implementation in practice of this global paradigm by civil society–based memory activists in Poland and Israel–Palestine raises questions about its applicability. The findings point to two weaknesses: first, mistreatment of asymmetrical violence and power relations between the conflict sides and, second, the lack of systematic consideration of how reconciliation is perceived by local actors in practice. In light of these weaknesses, local memory activists developed alternative strategies to those of the reconciliation paradigm, while governments infused reconciliation with different meanings that impede reconciliation instead of advancing it. Cultivating a sociological approach to reconciliation theory, this article proposes new theoretical modifications that would expand the paradigm's applicability: reciprocity or mutual respect instead of mutual acknowledgments, a normative basis that transcends the liberal boundaries of reconciliation, and an agonistic memory instead of consensus about the past.
Activity of lipid-loaded lectin against co-infection ofCandida albicansandStaphylococcus aureususing the zebrafish model
Authors: Subramaniyan Siva Bala , Ameen Fuad , Zakham Fathiah A , Anbazhagan Veerappan 
Published: March 2023

AbstractAimNosocomial infection caused by mixed species of methicillin-resistant Staphylococcus aureus (MRSA) and Candida albicans (CA) is difficult to manage with existing antimicrobials, particularly in the presence of mixed-species biofilm. This study evaluates the activity of cationic lipid, specifically functionalized with lectin, against mixed biofilms of MRSA and CA and their effectiveness in vivo using the zebrafish model.Methods and ResultsThe present study demonstrates for the first time the antimicrobial activity of 2-((N-[2-hydroxyethyl]palmitamido)methyl)-1-methylpyridin-1-ium iodide (cN16E) against MRSA and mixed species of MRSA + CA. The cN16E functionalized with Butea monosperma seed lectin (BMSL) showed a lower minimum inhibitory concentration (MIC) as compared with cN16E. BMSL-cN16E (BcN16E) exhibited strong membrane-damaging activity at a lower concentration than cN16E. Crystal violet assay showed that BcN16E inhibits mixed-species biofilm at the concentration of 15.63 µM, which is four-fold lower than the MIC. Especially, BcN16E was found to be effective in disturbing mature mixed biofilm at 31.25 µM, which is two-fold lower than the MIC, suggesting true antibiofilm activity without pressurizing the microorganisms. The treatment with BcN16E significantly reduced the exopolysaccharide synthesis (&gt; 78%), cell surface hydrophobicity (&gt; 70 %), hyphae formation, staphyloxanthin biosynthesis (&gt; 41 %), and antioxidant enzyme and hemolysin activity (&gt; 70 %). Notably, BcN16E was efficient in reducing the in vivo colonization of bacterial and fungal burden in the blood and muscle tissues of zebrafish.ConclusionAntimicrobial and antibiofilm efficacy of BcN16E against MRSA, and mixed species of MRSA + CA were demonstrated. Importantly, BcN16E treatment rescued Zebrafish coinfected with mixed species of MRSA + CA. Significance and Impact of the study: The results highlight that antimicrobial loaded on lectin provides an additional advantage to recognize microorganism surface glycans and maximize drug delivery to treat polymicrobial infections caused by MRSA and CA.
Artificial pollination of kiwifruit (Actinidia chinensis Planch. var. chinensis) (Ericales: Actinidiaceae) results in greater fruit set compared to flowers pollinated by managed bees (Apis mellifera L. (Hymenoptera: Apidae) and Bombus impatiens Cresson (Hymenoptera: Apidae))
Authors: Abbate Anthony P , Campbell Joshua W , Williams Geoffrey R 
Published: March 2023

Abstract
Due to a lack of knowledge on the pollination requirements of kiwifruit cultivars grown within the United States, farmers simultaneously implement multiple pollination methods, like the rental of managed bee species or artificial pollination to achieve high fruit yields. However, implementing multiple pollination methods is costly and possibly an inefficient use of resources. We assessed the contribution of two managed bees (Apis mellifera and Bombus impatiens) to the pollination of kiwifruit by i) determining the relative abundance of kiwifruit pollen collected by foragers of each bee species, and ii) comparing fruit set and fruit quality among insect and artificially pollinated flowers through an insect exclusion experiment. A significant difference was observed between the mean relative abundance of kiwifruit pollen carried in the corbicula of A. mellifera and B. impatiens, with B. impatiens carrying on average 46% more kiwifruit pollen than A. mellifera. Artificially pollinated kiwifruit flowers set significantly greater numbers of fruit per flower at four weeks post-bloom and at harvest compared to insect pollination, wind pollination, and pollen exclusion treatment. Artificial pollination produced fruits of greater weight, size, and seed number compared to insect-pollinated flowers, and few fruits were produced in the pollen exclusion and wind pollination treatments. Kiwifruit producers experiencing similar conditions to ours should focus on artificially pollinating their crops rather than relying on managed or wild insects for kiwifruit pollination. Future research should evaluate other methods of artificial pollination to determine their effectiveness, efficiency, and economics in the pollination of kiwifruit grown within the United States.
Carbon Taxation and Greenflation: Evidence from Europe and Canada
Authors: Konradt Maximilian , Weder di Mauro Beatrice 
Published: March 2023

Abstract
This paper studies the effects of carbon pricing on inflation dynamics. We construct a sample of carbon taxes implemented in Europe and Canada over three decades and estimate the response of inflation and price components to carbon pricing. Our empirical results suggest that carbon taxes did not significantly increase inflation, with dynamic effects estimated around zero in most specifications. Instead we find support for relative price changes, increasing the cost of energy but leaving the price of other goods and services unaffected. This is consistent with previous findings on the limited aggregate economic costs of carbon taxes. Based on the cross-section of taxes in Europe, we provide suggestive evidence that the response of inflation was especially muted in countries with revenue-neutral carbon taxes and autonomous central banks that can accommodate potential inflationary pressure associated with carbon pricing.
On the cyclotron absorption line and evidence of the spectral transition in SMC X-2 during 2022 giant outburst
Authors: Jaisawal G K , Vasilopoulos G , Naik S , Maitra C , Malacaria C , Chhotaray B , Gendreau K C , Guillot S , Ng M , Sanna A 
Published: March 2023

ABSTRACT
We report comprehensive spectral and temporal properties of the Be/X-ray binary pulsar SMC X-2 using X-ray observations during the 2015 and 2022 outbursts. The pulse profile of the pulsar is unique and strongly luminosity dependent. It evolves from a broad-humped into a double-peaked profile above luminosity 3 × 1038 erg s−1. The pulse fraction of the pulsar is found to be a linear function of luminosity as well as energy. We also studied the spectral evolution of the source during the latest 2022 outburst with NICER. The observed photon index shows a negative and positive correlation below and above the critical luminosity, respectively, suggesting evidence of spectral transition from the sub-critical to supercritical regime. The broad-band spectroscopy of four sets of NuSTAR and XRT/NICER data from both outbursts can be described using a cut-off power-law model with a blackbody component. In addition to the 6.4 keV iron fluorescence line, an absorption-like feature is clearly detected in the spectra. The cyclotron line energy observed during the 2015 outburst is below 29.5 keV, however latest estimates in the 2022 outburst suggest a value of 31.5 keV. Moreover, an increase of 3.4 keV is detected in the cyclotron line energy at equal levels of luminosity observed in 2022 with respect to 2015. The observed cyclotron line energy variation is explored in terms of accretion induced screening mechanism or geometrical variation in line forming region.
The core degenerate scenario for the type Ia supernova SN 2020eyj
Authors: Soker Noam , Bear Ealeal 
Published: March 2023

ABSTRACTWe argue that the core-degenerate (CD) scenario of type Ia supernovae (SNe Ia) can explain the compact helium-rich circumstellar material (CSM) of SN 2020eyj. In the new channel of the CD scenario, we propose that there are two major common envelope evolution (CEE) phases. After the white dwarf (WD) companion removes the hydrogen-rich envelope of the asymptotic giant branch star, its spiralling-in halts at few solar radii from the core rather than continuing to the carbon oxygen (CO) core as in the hydrogen-rich SNe Ia-CSM CD scenario. Only hundreds to tens of thousands of years later, after the helium-rich core expands, does the WD enters a CEE with the helium-rich layer. By that time, the hydrogen-rich envelope is at a large distance from the centre. The WD merges with the CO core during the second CEE phase, and only after a merger to explosion delay (MED) time of weeks to tens of years, the merger remnant explodes. The SN Ia ejecta collides with a helium-rich CSM at tens to hundreds of AU. We follow the evolution of two stellar models with initial masses of 5M⊙ and 7M⊙ to their asymptotic giant branch phase when they are supposed to engulf the WD companion. We find that there is a sufficiently massive CO core to merge with the WD in the frame of the CD scenario as well as a massive helium-rich layer, ≃ 0.3–1M⊙, to account for the helium-rich CSM of SN 2020eyj.
Precise homology-directed installation of large genomic edits in human cells with cleaving and nicking high-specificity Cas9 variants
Authors: Wang Qian , Liu Jin , Janssen Josephine M , Gonçalves Manuel A F V 
Published: March 2023

Abstract
Homology-directed recombination (HDR) between donor constructs and acceptor genomic sequences cleaved by programmable nucleases, permits installing large genomic edits in mammalian cells in a precise fashion. Yet, next to precise gene knock-ins, programmable nucleases yield unintended genomic modifications resulting from non-homologous end-joining processes. Alternatively, in trans paired nicking (ITPN) involving tandem single-strand DNA breaks at target loci and exogenous donor constructs by CRISPR-Cas9 nickases, fosters seamless and scarless genome editing. In the present study, we identified high-specificity CRISPR-Cas9 nucleases capable of outperforming parental CRISPR-Cas9 nucleases in directing genome editing through homologous recombination (HR) and homology-mediated end joining (HMEJ) with donor constructs having regular and ‘double-cut’ designs, respectively. Additionally, we explored the ITPN principle by demonstrating its compatibility with orthogonal and high-specificity CRISPR-Cas9 nickases and, importantly, report that in human induced pluripotent stem cells (iPSCs), in contrast to high-specificity CRISPR-Cas9 nucleases, neither regular nor high-specificity CRISPR-Cas9 nickases activate P53 signaling, a DNA damage-sensing response linked to the emergence of gene-edited cells with tumor-associated mutations. Finally, experiments in human iPSCs revealed that differently from HR and HMEJ genome editing based on high-specificity CRISPR-Cas9 nucleases, ITPN involving high-specificity CRISPR-Cas9 nickases permits editing allelic sequences associated with essentiality and recurrence in the genome.
The spatial landscape of gene expression isoforms in tissue sections
Authors: Lebrigand Kevin , Bergenstråhle Joseph , Thrane Kim , Mollbrink Annelie , Meletis Konstantinos , Barbry Pascal , Waldmann Rainer , Lundeberg Joakim 
Published: March 2023

Abstract
In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.