bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of RFC4 as a potential biomarker for pan‐cancer involving prognosis, tumour immune microenvironment and drugs
Authors: Yu Lei , Li Jing , Zhang Mingyang , Li Yu , Bai Jing , Liu Pengxia , Yan Jia , Wang Changshan 
Published: June 2024

AbstractRFC4 is required for DNA polymerase δ and DNA polymerase ε to initiate DNA template expansion. Downregulated RFC4 inhibits tumour proliferation by causing S‐phase arrest and inhibiting mitosis, resulting in the reduction of tumour cells. RFC4 has been implicated that it plays an important role in the initiation and progression of cancers, but a comprehensive analysis of the role of RFC4 in cancer has not been performed. We comprehensively analysed the expression, prognosis, methylation level, splicing level, relationship of RFC4 and immune infiltration, and pan‐cancer immunotherapy response used various databases (including TCGA, GTEx, UALCAN, Oncosplicing, TIDE, TISCH, HPA and CAMOIP), and experimented its biological function in HCC. Through pan‐cancer analysis, we found that RFC4 is significantly upregulated in most tumours. The tumour patients with high expression of RFC4 have poor prognosis. The methylation level and variable splicing level of RFC4 were abnormal in most tumours compared with the adjacent tissues. Furthermore, RFC4 was closely associated with immune cell infiltration in various cancers. RFC4 was significantly co‐expressed with immune checkpoints and other immune‐related genes. The expression of RFC4 could indicate the immunotherapy efficacy of some tumours. The RFC4 expression was associated with sensitivity to specific small molecule drugs. Cell experiments have shown that downregulated RFC4 can inhibit cell cycle and tumour cell proliferation. We conducted a systematic pan‐cancer analysis of RFC4, and the results showed that RFC4 can serve as a biomarker for cancer diagnosis and prognosis. These findings open new perspectives for precision medicine.
A validation study of the accuracy of the atrial pace map assessed with intracardiac pattern matching: Potential utility of non‐pulmonary vein mapping
Authors: Wakamatsu Yuji , Nagashima Koichi , Hayashida Satoshi , Watanabe Ryuta , Hirata Shu , Hirata Moyuru , Sawada Masanaru , Kurokawa Sayaka , Okumura Yasuo 
Published: June 2024

AbstractBackgroundIdentification of infrequent nonpulmonary vein trigger premature atrial contractions (PACs) is challenging. We hypothesized that pace mapping (PM) assessed by correlation scores calculated by an intracardiac pattern matching (ICPM) module was useful for locating PAC origins, and conducted a validation study to assess the accuracy of ICPM‐guided PM.MethodsAnalyzed were 30 patients with atrial fibrillation. After pulmonary vein isolation, atrial pacing was performed at one or two of four sites on the anterior and posterior aspects of the left atrium (LA, n = 10/10), LA septum (n = 10), and lateral RA (n = 10), which was arbitrarily determined as PAC. The intracardiac activation obtained from each pacing was set as an ICPM reference consisting of six CS unipolar electrograms (CS group) or six CS unipolar electrograms and four RA electrograms (CS–RA group).ResultsThe PM was performed at 193 ± 107 sites for each reference pacing site. All reference pacing sites corresponded to sites where the maximal ICPM correlation score was obtained. Sites with a correlation score ≥98% were rarely obtained in the CS‐RA than CS group (33% vs. 55%, P = .04), but those ≥95% were similarly obtained between the two groups (93% vs. 88%, P = .71), and those ≥90% were obtained in all. The surface areas with correlation scores ≥98% (0[0,10] vs. 10[0,35] mm2, P = .02), ≥95% (10[10,30] vs. 50[10,180] mm2, P = .002) and ≥90% (60[30,100] vs. 170[100,560] mm2, P = .0002) were smaller in the CS‐RA than CS group.ConclusionsICPM‐guided PM was useful for identifying the reference pacing sites. Combined use of RA and CS electrograms may improve the mapping quality.
Transgenerational cross‐susceptibility to heat stress following cold and desiccation acclimation in the Angoumois grain moth
Authors: Mpofu Precious , Machekano Honest , Airs Paul M. , Nyamukondiwa Casper 
Published: June 2024

AbstractThe Angoumois grain moth, Sitotroga cerealella (Olivier), is a significant cosmopolitan primary pest of cereals worldwide and has thrived in divergent environments. However, the mechanisms underlying its survival in multiple contrasting environments are poorly understood. Here, we hypothesised that when facing diverse environmental stress, F1 generation exhibits transgenerational cross‐protection as a mechanism to persist under divergent stressful environments. Notably, F1 acclimation to cold or desiccation conditions could either enhance or lower heat tolerance in the F2 generation. Specifically, we tested whether typical diurnal fluctuations and/or winter rapid or chronic cold temperatures (18–22°C) as well as desiccation acclimation of F1 parental population yields transgenerational cross‐protection/susceptibility to heat stress on F2 offspring. F1 moths were exposed to cold hardening (2 h), chronic (72 h) and variable (fluctuating between 18 and 22°C for 72 h) temperature treatment groups. Desiccation treatment included incubation at 0%–1% relative humidity (24 h). F2 generation moths were then assessed for heat tolerance using critical thermal maxima (CTmax) at three different ramping rates (0.06, 0.25 and 0.5°C/min) as well as heat knockdown time (HKDT). Findings indicated that (i) desiccation, cold hardening and chronic low‐temperature acclimations in F1 reduced heat tolerance in F2 populations and (ii) ramping rate was crucial to decipher differences between treatment groups, with lower ramping rates associated with lower CTmax. Transgenerational cross‐susceptibility to heat stress indicates possible fitness costs of exposure to multiple contrasting stressors in the Angoumois grain moth and can be used in designing physical pest management strategies.
What does racial ascription have to do with perception of Swedishness?
Authors: Osanami Törngren Sayaka , Nyström Marcus 
Published: June 2024

AbstractHow do Swedes, who are not exposed to administrative routines of reporting race and ethnicity, perceive, and categorize faces with different phenotypical features? This study examines identity contestation that can occur and address how race affects the way you are perceived as Swedish. A sample of Swedish participants were asked to assign racial categories to images of faces with different phenotypes, identify the skin color of the faces and rate how ‘Swedish’ the faces are perceived. We also use eye‐tracking to explore whether participants look differently at the faces of different racial groups. The results show greater identity contestation among Latino and Black faces. Moreover, while Swedish respondents identify the skin color of faces self‐identified as Black as darker compared to other racial backgrounds, the differences in skin color reported between Asian, White and Latinos were very small. Despite these small differences in the perception of skin color among Asian, White, and Latino faces, faces self‐reported as White were rated as significantly more Swedish by the respondents compared Asian and Latino faces. All these results contribute to the understanding of not only how race matters in Sweden but also to the understanding of constructivist nature of race.
Applying whole genome sequencing to predict phenotypic drug resistance in
Mycobacterium tuberculosis
: leveraging 20 years of nationwide data from Denmark
Authors: Kurtzhals Mads Lindholm , Norman Anders , Svensson Erik , Lillebaek Troels , Folkvardsen Dorte Bek 
Published: June 2024

ABSTRACT

Infection with
Mycobacterium tuberculosis
remains one of the biggest causes of death from a single microorganism worldwide, and the continuous emergence of drug resistance aggravates our ability to cure the disease. New improved resistance detection methods are needed to provide adequate treatment, such as whole genome sequencing (WGS), which has been used increasingly to identify resistance-conferring mutations over the last decade. The steadily increasing knowledge of resistance-conferring mutations increases our ability to predict resistance based on genomic data alone. This study evaluates the performance of WGS to predict
M. tuberculosis
complex resistance. It compares WGS predictions with the phenotypic (culture-based) drug susceptibility results based on 20 years of nationwide Danish data. Analyzing 6,230 WGS-sequenced samples, the sensitivities for isoniazid, rifampicin, ethambutol, and pyrazinamide were 82.5% [78.0%–86.5%, 95% confidence interval (CI)], 97.3% (90.6%–99.7%, 95% CI), 58.0% (43.2%–71.8%, 95% CI), and 60.5% (49.0%–71.2%, 95% CI), respectively, and specificities were 99.8% (99.7%–99.9%, 95% CI), 99.8% (99.7%–99.9%, 95% CI), 99.4% (99.2%–99.6%, 95% CI), and 99.9% (99.7%–99.9%, 95% CI), respectively. A broader range of both sensitivities and specificities was observed for second-line drugs. The results conform with previously reported values and indicate that WGS is reliable for routine resistance detection in resource-rich tuberculosis low-incidence and low-resistance settings such as Denmark.
Synthetic lethality and the minimal genome size problem
Authors: Rahiminejad Sara , De Sanctis Bianca , Pevzner Pavel , Mushegian Arcady 
Published: June 2024

ABSTRACT

Gene knockout studies suggest that ~300 genes in a bacterial genome and ~1,100 genes in a yeast genome cannot be deleted without loss of viability. These single-gene knockout experiments do not account for negative genetic interactions, when two or more genes can each be deleted without effect, but their joint deletion is lethal. Thus, large-scale single-gene deletion studies underestimate the size of a minimal gene set compatible with cell survival. In yeast
Saccharomyces cerevisiae
, the viability of all possible deletions of gene pairs (2-tuples), and of some deletions of gene triplets (3-tuples), has been experimentally tested. To estimate the size of a yeast minimal genome from that data, we first established that finding the size of a minimal gene set is equivalent to finding the minimum vertex cover in the lethality (hyper)graph, where the vertices are genes and (hyper)edges connect
k
-tuples of genes whose joint deletion is lethal. Using the Lovász-Johnson-Chvatal greedy approximation algorithm, we computed the minimum vertex cover of the synthetic-lethal 2-tuples graph to be 1,723 genes. We next simulated the genetic interactions in 3-tuples, extrapolating from the existing triplet sample, and again estimated minimum vertex covers. The size of a minimal gene set in yeast rapidly approaches the size of the entire genome even when considering only synthetic lethalities in
k
-tuples with small
k
. In contrast, several studies reported successful experimental reductions of yeast and bacterial genomes by simultaneous deletions of hundreds of genes, without eliciting synthetic lethality. We discuss possible reasons for this apparent contradiction.

IMPORTANCE
How can we estimate the smallest number of genes sufficient for a unicellular organism to survive on a rich medium? One approach is to remove genes one at a time and count how many of such deletion strains are unable to grow. However, the single-gene knockout data are insufficient, because joint gene deletions may result in negative genetic interactions, also known as synthetic lethality. We used a technique from graph theory to estimate the size of minimal yeast genome from partial data on synthetic lethality. The number of potential synthetic lethal interactions grows very fast when multiple genes are deleted, revealing a paradoxical contrast with the experimental reductions of yeast genome by ~100 genes, and of bacterial genomes by several hundreds of genes.
Liposomal Fba and Met6 peptide vaccination protects mice from disseminated candidiasis
Authors: Huang Wei-Chiao , Eberle Karen , Colon Jonothan Rosario , Lovell Jonathan F. , Xin Hong 
Published: June 2024

ABSTRACT

Epitopes from the
Candida
cell surface proteins Fba and Met6 are putative vaccine targets for invasive candidiasis. Here, we describe a
Candida
vaccine approach in which short peptides derived from Fba and Met6 are used in spontaneous nanoliposome antigen particle (SNAP) format. SNAP was enabled by the interaction of cobalt porphyrin phospholipid in liposomes with three histidine residues on the N-terminus of synthetic short peptide immunogens from Fba (F-SNAP), Met6 (M-SNAP), or bivalent Fba and Met6 (FM-SNAP). Liposomes were adjuvanted with synthetic monophosphoryl lipid and QS-21. In mice, immunization with F-SNAP, M-SNAP, or FM-SNAP induced antigen-specific IgG responses and mixed Th1/Th2 immunity. The duplex FM-SNAP vaccine elicited stronger antibody responses against each peptide, even at order-of-magnitude lower peptide dosing than a comparable adjuvanted, conjugate vaccine. Enzyme-linked immunosorbent spot analysis revealed the induction of antigen-specific, cytokine-producing T cells. Compared to F-SNAP or M-SNAP, higher production of TNFα, IL-2, and IFNγ was observed with re-stimulation of splenocytes from bivalent FM-SNAP-immunized mice. When vaccinated BALB/c mice were challenged with
Candida auris
, analysis of the fungal burden in the kidneys showed that SNAP vaccination protected from disseminated candidiasis. In a lethal fungal exposure model in A/J mice, F-SNAP, M-SNAP, and FM-SNAP vaccination protected mice from candidiasis challenge. Together, these results show that further investigation into the SNAP adjuvant platform is warranted using Fba and Met6 epitopes for a pan-
Candida
peptide vaccine that provides multifaceted protective immune responses.

IMPORTANCE

This study introduces a promising vaccine strategy against invasive candidiasis, a severe fungal infection, by targeting specific peptides on the surface of
Candida
. Using a novel approach called spontaneous nanoliposome antigen particle (SNAP), we combined peptides from two key
Candida
proteins, Fba and Met6, into a vaccine. This vaccine induced robust immune responses in mice, including the production of protective antibodies and the activation of immune cells. Importantly, mice vaccinated with SNAP were shielded from disseminated candidiasis in experiments. These findings highlight a potential avenue for developing a broad-spectrum vaccine against
Candida
infections, which could significantly improve outcomes for patients at risk of these often deadly fungal diseases.
Genomic insights into the evolution of secondary metabolism of
Escovopsis
and its allies, specialized fungal symbionts of fungus-farming ants
Authors: Berasategui Aileen , Salem Hassan , Moller Abraham G. , Christopher Yuliana , Vidaurre Montoya Quimi , Conn Caitlin , Read Timothy D. , Rodrigues Andre , Ziemert Nadine , Gerardo Nicole 
Published: June 2024

ABSTRACT

The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of
Escovopsis
and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative
Escovopsis
strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated
Sordariomycetes
, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in
Escovopsis
and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.

IMPORTANCE

Microbial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of
Escovopsis
species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts’ potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.
Distribution and reference values of peripheral perfusion index in neonates from population-wide screening
Authors: Sasikumar Navaneetha , Madhavankutty Nair Sreehari , Gutjahr Georg , Bendapudi Perraju , Moosa Abdulrazak , Prasenan Krishna , Rajan Vishnu Raj , Sudhakar Abish , Kumar Raman Krishna 
Published: June 2024

BackgroundPeripheral perfusion index (PPI) is useful in a variety of neonatal settings. Currently, available reference values are from small numbers and highly variable.MethodsWe sought to generate reference values of PPI by analysing previously collected data from newborns who underwent mandated universal pulse oximetry and PPI screening from 2018 to 2021 using uniform protocol and equipment. Q-Q plots and boxplots were used to visualise distributions. Kernel density estimation for heaped and rounded data was used to estimate percentiles of the distributions.ResultsData from 388 205 newborns who underwent universal pulse oximetry screening in the first week of life were used for this analysis. Pre and postductal values showed a non-normal distribution and skewed to the left, the former had a thicker tail with more extreme values. Minor, but statistically significant differences were seen in the PPI values from day 1 to 7. Median preductal PPI (2.77, IQR:1.83–3.93) was significantly higher than postductal (2.38 IQR: 1.41–3.55) (p<0.01). PPI values increased with weight and boys had higher PPI. Kernel estimates of the percentiles in the overall sample and subgroups for gender and weight have been provided for preductal and post-ductal values.ConclusionThis study, based on the largest available dataset, provides reference values for PPI in newborns. A significant influence of gender and birth weight on PPI values in newborns has been identified. Future research on understanding the influence of age, sex, birth weight, gestational age, ambient temperature and genetic factors on PPI is recommended.
Inhibition of receptor interacting protein kinase-1 (RIPK1) in the treatment of murine lupus
Authors: Peng Lin , Wang Pengcheng , Xu Xiaodong , Chen Dacheng , Xu Feng , Yang Fan , Yang Shuying , Xia Hongguang , Liu Zhi-Hong , Qin Weisong 
Published: June 2024

ObjectiveSystemic lupus erythematosus (SLE) is a type of autoimmune disease that involves multiple organs involved as well as cytokine dysregulation. The treatment of SLE is still challenging due to the side effects of the different drugs used. Receptor-interacting protein kinase 1 (RIPK1) is a kinase involved in T cell homeostasis and autoinflammation. Although clinical trials have shown that RIPK1 inhibition exhibits significant efficacy in different autoimmune diseases, its role in SLE remains unclear.MethodsMRL/lpr lupus-prone mice received RIPK1 inhibitor ZJU37 or vehicle intraperitoneally for 10 weeks. A BM12-induced chronic graft-versus-host-disease (cGVHD) lupus-like model was introduced in RIPK1 D138N mice or C57BL/6 mice. Nephritis, serum autoantibody levels, dysregulation of adaptive immune response and cytokines were compared in treated and untreated mice.ResultsZJU37 alleviated the clinical features of the MRL/lpr mice including nephritis and anti-dsDNA antibody production. In addition, ZJU37 treatment reduced the proportion of double-negative T cells in the spleen and the cytokines of TNFα, IFN-γ, IL-6, IL-17 and IL-1β in the serum. Moreover, RIPK1 D138N mice were able to prevent the cGVHD lupus-like model from SLE attack, manifesting as anti-dsDNA antibody production, the proliferation of germinal centre B cells, plasma cells, and T follicular helper cells as well as IgG and C3 deposits in kidneys.ConclusionRIPK1 inhibition has a protective effect in the mouse model of SLE and can potentially become a new therapeutic target for SLE in humans.
“Real Time Story Telling”: A Performance-Art Festival in the Context of International Networks during the Transitional Period in Poland before and after 1989
Authors: Kaźmierczak Małgorzata 
Published: June 2024

Abstract
The article explains the situation of performance artists in Poland during the transition period before and after 1989. Then it focuses on the first large performance art festival in Poland after 1989, Real Time Story Telling. It was organized in Sopot and Gdańsk in 1991 by Galeria Działań and curated by the outstanding artist and art theorist Jan Świdziński. The article explains the idea of the festival and briefly describes the curatorial activity of the invited international performance artists. The article also outlines the international network of connections between performance art festivals, which depended on the personal relationships between artists who organized them. Finally, it shows how the festival influenced the introduction of Polish performance artists to the international circuit and how it influenced the development of the festival network in Poland.
Developmental Dilemmas
Authors: Noor Tausif 
Published: June 2024

Abstract
Three recent volumes on the economic, infrastructural, and international networks of modernism reveal the extent to which notions of development have shaped the trajectory of modernist art practice outside the Western world, and Sarah-Neel Smith's Metrics of Modernity: Art and Development in Postwar Turkey (2022) considers how efforts by the Turkish state to join the new global political economy in the 1950s prompted artists and art administrators to synthesize the language of economic development into artistic discourse and institutional infrastructure. Devika Singh's International Departures: Art in India After Independence (2024) situates modernist artistic practice in India in the Nehruvian decades, wherein the state's developmental aspirations led to major upheavals and connections across international networks. Karin Zitzewitz's Infrastructure and Form: The Global Networks of Indian Contemporary Art, 1991–2008 (2022) examines an efflorescence of Indian contemporary art between economic liberalization in 1991 through the 2008 global financial crisis, marking shifts in the production, circulation, and discourse of art through a wide-ranging array of examples. Each of these texts move away from art history's fixation with self-contained nationalist histories toward a more critical apprehension of how relations between the state and international non-state actors within international political economy shaped the trajectory of visual art. The review considers how the authors combine sociopolitical discourse and economic changes with formal examinations of specific artworks in their local, national, and international contexts and addresses the importance of institution-building and the processes of legitimization for these authors' arguments.