bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptide barcode of multidrug-resistant strains of Neisseria gonorrhoeae isolated from patients in Thailand
Authors: Roytrakul Sittiruk , Sangprasert Pongsathorn , Jaresitthikunchai Janthima , Phaonakrop Narumon , Arpornsuwan Teerakul
Published: August 2023

The emergence of multidrug-resistant strains of Neisseria gonorrhoeae constitutes a serious threat to public health. The present study aimed to investigate peptidome-based biomarkers of multidrug-resistant N. gonorrhoeae, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography tandem mass spectrometry (LC-MS). The peptide barcode database of multidrug resistant N. gonorrhoeae was generated from the whole-cell peptides of 93 N. gonorrhoeae isolated from patients in Thailand. The dendrogram of 93 independent isolates of antibiotic-resistant N. gonorrhoeae revealed five distinct clusters including azithromycin resistance group (AZ), ciprofloxacin resistance group (C), ciprofloxacin and penicillin resistance group (CP), ciprofloxacin and tetracycline resistance group (CT), ciprofloxacin, penicillin and tetracycline resistance group (CPT). The peptidomes of all clusters were comparatively analyzed using a high-performance liquid chromatography-mass spectrometry method (LC-MS). Nine peptides derived from 9 proteins were highly expressed in AZ (p value < 0.05). These peptides also played a crucial role in numerous pathways and showed a strong relationship with the antibiotic resistances. In conclusion, this study showed a rapid screening of antibiotic-resistant N. gonorrhoeae using MALDI-TOF MS. Additionally, potential specific peptidome-based biomarker candidates for AZ, C, CP, CT and CPT-resistant N. gonorrhoeae were identified.
Evaluating the ability of an artificial-intelligence cloud-based platform designed to provide information prior to locoregional therapy for breast cancer in improving patient’s satisfaction with therapy: The CINDERELLA trial
Authors: Kaidar-Person Orit , Antunes Marilia , Cardoso Jaime S. , Ciani Oriana , Cruz Helena , Di Micco Rosa , Gentilini Oreste D. , Gonçalves Tiago , Gouveia Pedro , Heil Jörg , Kabata Pawel , Lopes Daniela , Martinho Marta , Martins Henrique , Mavioso Carlos , Mika Martin , Montenegro Helena , Oliveira Helder P. , Pfob André , Rotmensz Nicole , Schinköthe Timo , Silva Giovani , Tarricone Rosana , Cardoso Maria-Joao ,   on behalf of the CINDERELLA Consortium
Published: August 2023

Background

Breast cancer therapy improved significantly, allowing for different surgical approaches for the same disease stage, therefore offering patients different aesthetic outcomes with similar locoregional control. The purpose of the CINDERELLA trial is to evaluate an artificial-intelligence (AI) cloud-based platform (CINDERELLA platform) vs the standard approach for patient education prior to therapy.

Methods

A prospective randomized international multicentre trial comparing two methods for patient education prior to therapy. After institutional ethics approval and a written informed consent, patients planned for locoregional treatment will be randomized to the intervention (CINDERELLA platform) or controls. The patients in the intervention arm will use the newly designed web-application (CINDERELLA platform, CINDERELLA APProach) to access the information related to surgery and/or radiotherapy. Using an AI system, the platform will provide the patient with a picture of her own aesthetic outcome resulting from the surgical procedure she chooses, and an objective evaluation of this aesthetic outcome (e.g., good/fair). The control group will have access to the standard approach. The primary objectives of the trial will be i) to examine the differences between the treatment arms with regards to patients’ pre-treatment expectations and the final aesthetic outcomes and ii) in the experimental arm only, the agreement of the pre-treatment AI-evaluation (output) and patient’s post-therapy self-evaluation.

Discussion

The project aims to develop an easy-to-use cost-effective AI-powered tool that improves shared decision-making processes. We assume that the CINDERELLA APProach will lead to higher satisfaction, better psychosocial status, and wellbeing of breast cancer patients, and reduce the need for additional surgeries to improve aesthetic outcome.
System analysis identifies UBE2C as a novel oncogene target for adrenocortical carcinoma
Authors: Huang Renlun , Guo Lang , Chen Chiwei , Xiang Yuyang , Li Guohao , Zheng Jieyan , Wu Yanping , Yuan Xiu , Zhou Jianfu , Gao Wenxi , Xiang Songtao
Published: August 2023

Ubiquitin Conjugating Enzyme 2C (UBE2C) is an emerging target gene for tumor progression. However, the tumorigenic effect and mechanism of UBE2C in adrenocortical carcinoma (ACC) remains unclear. Systematic investigation of the tumorigenic effect of UBE2C may help in understanding its prognostic value in adrenocortical carcinoma. First, we exploited the intersection on DFS-related genes, OS-related genes, highly expressed genes in adrenocortical carcinoma as well as differentially expressed genes (DEGs) between tumor and normal, and then obtained 20 candidate genes. UBE2C was identified to be the most significant DEG between tumor and normal. It is confirmed that high expression of UBE2C was strongly associated with poor prognosis in patients with ACC by analyzing RNA-seq data of ACC obtained from the Cancer Genome Atlas (TCGA) database implemented by ACLBI Web-based Tools. UBE2C expression could also promote m6A modification and stemness in ACC. We found that UBE2C expression is positively associated with the expression of CDC20, CDK1, and CCNA2 using ACLBI Web-based Tools, indicated the hyperactive cell cycle progression present in ACC with high UBE2C expression. In addition, UBE2C knockdown could significantly inhibit the proliferation, migration, invasion, EMT of adrenocortical carcinoma cells as well as the cell cycle progression in vitro. Notably, pan-cancer analysis also identified UBE2C as an oncogene in various tumors. Taken together, UBE2C was strongly associated with poor prognosis of patients with ACC by promoting cell cycle progression and EMT. This study provides a new theoretical basis for the development of UBE2C as a molecular target for the treatment of ACC.
TGM2, HMGA2, FXYD3, and LGALS4 genes as biomarkers in acquired oxaliplatin resistance of human colorectal cancer: A systems biology approach
Authors: Cheraghi-shavi Tayebeh , Jalal Razieh , Minuchehr Zarrin
Published: August 2023

Acquired resistance to oxaliplatin is considered as the primary reason for failure in colorectal cancer (CRC) therapy. Identifying the underlying resistance mechanisms may improve CRC treatment. The present study aims to identify the key genes involved in acquired oxaliplatin-resistant in CRC by confirming the oxaliplatin resistance index (OX-RI). To this aim, two public microarray datasets regarding oxaliplatin-resistant CRC cells with different OX-RI, GSE42387, and GSE76092 were downloaded from GEO database to identify differentially expressed genes (DEGs). The results indicated that the OX-RI affects the gene expression pattern significantly. Then, 54 common DEGs in both datasets including 18 up- and 36 down-regulated genes were identified. Protein-protein interaction (PPI) analysis revealed 13 up- (MAGEA6,TGM2,MAGEA4,SCHIP1,ECI2,CD33,AKAP12,MAGEA12,CALD1,WFDC2,VSNL1,HMGA2, andMAGEA2B) and 12 down-regulated (PDZK1IP1,FXYD3,ALDH2,CEACAM6,QPRT,GRB10,TM4SF4,LGALS4,ALDH3A1,USH1C,KCNE3, andCA12) hub genes. In the next step, two novel up-regulated hub genes includingECI2andSCHIP1were identified to be related to oxaliplatin resistance. Functional enrichment and pathway analysis indicated that metabolic pathways, proliferation, and epithelial-mesenchymal transition may play dominant roles in CRC progression and oxaliplatin resistance. In the next procedure, two in vitro oxaliplatin-resistant sub-lines including HCT116/OX-R4.3 and HCT116/OX-R10 cells with OX-IR 3.93 and 10.06 were established, respectively. The results indicated the up-regulation ofTGM2andHMGA2in HCT116/OX-R10 cells with high OX-RI and down-regulation ofFXYD3,LGALS4, andECI2in both cell types. Based on the results,TGM2,HMGA2,FXYD3, andLGALS4genes are related to oxaliplatin-resistant CRC and may serve as novel therapeutic targets.
From colorblind to systemic racism: Emergence of a rhetorical shift in higher education discourse in response to the murder of George Floyd
Authors: Toraif Noor , Gondal Neha , Paudel Pujan , Frisella Alison
Published: August 2023

We use topic modeling and exponential random graph models (ERGM) to analyze statements issued by Institutions of Higher Education (IHEs) (N = 356) in the United States in the aftermath of George Floyd’s murder in May 2020. Prior research investigating discourse on race in IHEs demonstrates the prevalence of two paradigms. First, the ideology of ‘colorblind racism’ treats systemic racism—a form of racism where social, political, and economic institutions are organized in a way that disadvantages people of color—as having largely existed in the past. Consistent with this, IHE responses to prior race-related incidents on campus have emphasized individual prejudice, avoiding discussion of systemic racism. Second, ‘diversity’ orthodoxy, which treats race as a cultural identity and emphasizes the instrumental benefits of racial heterogeneity on campus, is commonplace in IHEs. Topic modeling of statements issued in 2020 reveals the prevalence of several themes including the systemic and enduring nature of racism in the United States, diversity orthodoxy, humanist responses reflecting rhetoric consistent with colorblind racism, and COVID-19 response strategies. ERGM reveals fragmentation in the discourse based on IHE attributes. Religiously affiliated IHEs and those located in Republican-voting states attend more to diversity and humanist discourse, and less to systemic racism. Elite IHEs, those in Democrat-voting states, and IHEs with high percentages of Black students are more focused on systemic racism. Overall, as compared to colorblind racism and diversity orthodoxy established in prior work, our analysis reveals two striking rhetorical shifts on race discourse in IHEs in the aftermath of George Floyd’s murder: (1) from a colorblind ideology to discussing the systemic nature of racism in the United States, and (2) from acknowledging perpetrators but not the broader context of racism in on-campus incidents to acknowledging diffuse racism manifest in society but refraining from explicitly naming any wrongdoers.
Identification and validation of a m7G-related lncRNA signature for predicting the prognosis and therapy response in hepatocellular carcinoma
Authors: Peng Yue-Ling , Dong Ya-Fang , Guo Li-Li , Li Mu-Ye , Liao Hui , Li Rong-Shan
Published: August 2023

Background

N7-methylguanosine (m7G) is one of the most common RNA posttranscriptional modifications; however, its potential role in hepatocellular carcinoma (HCC) remains unknown. We developed a prediction signature based on m7G-related long noncoding RNAs (lncRNAs) to predict HCC prognosis and provide a reference for immunotherapy and chemotherapy.

Methods

RNA-seq data from The Cancer Genome Atlas (TCGA) database and relevant clinical data were used. Univariate and multivariate Cox regression analyses were conducted to identify m7G-related lncRNAs with prognostic value to build a predictive signature. We evaluated the prognostic value and clinical relevance of this signature and explored the correlation between the predictive signature and the chemotherapy treatment response of HCC. Moreover, an in vitro study to validate the function of CASC19 was performed.

Results

Six m7G-related lncRNAs were identified to create a signature. This signature was considered an independent risk factor for the prognosis of patients with HCC. TIDE analyses showed that the high-risk group might be more sensitive to immunotherapy. ssGSEA indicated that the predictive signature was strongly related to the immune activities of HCC. HCC in high-risk patients was more sensitive to the common chemotherapy drugs bleomycin, doxorubicin, gemcitabine, and lenalidomide. In vitro knockdown of CASC19 inhibited the proliferation, migration and invasion of HCC cells.

Conclusion

We established a 6 m7G-related lncRNA signature that may assist in predicting the prognosis and response to chemotherapy and immunotherapy of HCC.
Trait anxiety and depressive rumination mediate the effect of perceived childhood rearing on adulthood presenteeism
Authors: Shimasaki Akifumi , Deguchi Ayaka , Ishii Yoshitaka , Seki Tomoteru , Iwata Yoshio , Tamada Yu , Honyashiki Mina , Fujimura Yota , Inoue Takeshi , Masuya Jiro
Published: August 2023

Aim

Productivity loss in the workplace due to physical or mental health problems, which is called presenteeism, leads to large financial losses. Personal and work environment factors, as well as physical and mental illnesses are associated with presenteeism, but the detailed underlying mechanism remains unclear. In this study, we analyzed the effects of perceived childhood rearing on the presenteeism of adult workers, and the mediating effects of trait anxiety and depressive rumination.

Methods

In 2017 and 2018, a cross-sectional paper-based survey was conducted, and written consent from 447 adult workers was obtained. Demographic information and results from the Parental Bonding Instrument, trait anxiety of State-Trait Anxiety Inventory Form Y, Ruminative Responses Scale, and Work Limitations Questionnaire were surveyed. Multiple regression analyses and structural equation modeling were conducted.

Results

The low perceived quality of rearing from parents in childhood, i.e., low care and high overprotection, indirectly worsened current presenteeism via trait anxiety and depressive rumination. Presenteeism was directly worsened by trait anxiety and depressive rumination, and the low perceived quality of rearing from parents directly affected trait anxiety and depressive rumination, and trait anxiety affected depressive rumination.

Conclusion

The results of this study clarified the long-term influences of the low perceived quality of rearing experienced in childhood on adulthood presenteeism via trait anxiety and depressive rumination. Therefore, assessing the quality of childhood rearing, trait anxiety, and depressive rumination of individuals may help to elucidate the causes of presenteeism in the workplace, and how to manage it effectively.
Spermidine enhances chilling tolerance of kale seeds by modulating ROS and phytohormone metabolism
Authors: Cao Dongdong , Huang Yutao , Mei Gaofu , Zhang Sheng , Wu Huaping , Zhao Tiyuan
Published: August 2023

Chilling stress is an important constraint for kale seed germination and seedlings establishment. It is vital to develop an effective approach to enhance kale seed germination ability under chilling stress. The present study reported that spermidine (Spd) could improve seed chilling tolerance in two kale cultivars ‘Nagoya’ (MGW) and ‘Pigeon’ (BB) during germination. The results showed that MGW was cold tolerant with a 90.67% germination percentage (GP) under chilling stress, while BB was cold sensitive with a 70.67% GP under chilling stress. Spd content in MGW and BB seeds during seed germination were up-regulated and down-regulated by chilling stress, respectively. Besides, chilling stress apparently decreased the gibberellin (GA) and ethylene (ET) contents, while increased the levels of abscisic acid (ABA) and reactive oxygen species (ROS) in MGW and BB seeds during germination. Exogenous Spd application increased GA, ET contents and decreased ABA content through regulating the gene expressions of metabolic-related enzymes, thus effectively alleviating the low temperature damage on kale seed germination. Besides, Spd significantly increased the activities of superoxide dismutase (SOD) and peroxidase (POD), and reduced the levels of hydrogen peroxide (H2O2) and superoxide anion (O2·-). The present study demonstrated that endogenous Spd metabolism plays an important role in kale seed germination under chilling stress. The effect of exogenous Spd on the metabolism of endogenous Spd, GA, ABA, ET and antioxidant enzymes might be the important reason for promoting the kale seed vigor at low temperature.
Acoustic signatures in Mexican cavefish populations inhabiting different caves
Authors: Hyacinthe Carole , Attia Joël , Schutz Elisa , Lego Lény , Casane Didier , Rétaux Sylvie
Published: August 2023

Complex patterns of acoustic communication exist throughout the animal kingdom, including underwater. The river-dwelling and the Pachón cave-adapted morphotypes of the fish Astyanax mexicanus are soniferous and share a repertoire of sounds. Their function and significance is mostly unknown. Here, we explored whether and how sounds produced by blind cavefishes inhabiting different Mexican caves may vary. We compared “Clicks” and “Serial Clicks” produced by cavefish in six different caves distributed in three mountain ranges in Mexico. We also sampled laboratory-bred cavefish lines originating from four of these caves. Sounds were extracted and analyzed using both a manual method and a machine learning-based automation tool developed in-house. Multi-parametric analyses suggest wild cave-specific acoustic signatures, or “accents”. An acoustic code also existed in laboratory cavefish lines, suggesting a genetic basis for the evolution of this trait. The variations in acoustic parameters between caves of origin did not seem related to fish phenotypes, phylogeography or ecological conditions. We propose that the evolution of such acoustic signatures would progressively lead to the differentiation of local accents that may prevent interbreeding and thus contribute to speciation.
Defeating a superbug: A breakthrough in vaccine design against multidrug-resistant Pseudomonas aeruginosa using reverse vaccinology
Authors: Fereshteh Sepideh , Haririzadeh Jouriani Fatemeh , Noori Goodarzi Narjes , Torkamaneh Mahdi , Khasheii Behnoush , Badmasti Farzad
Published: August 2023

Background

Multidrug-resistant Pseudomonas aeruginosa has become a major cause of severe infections. Due to the lack of approved vaccines, this study has presented putative vaccine candidates against it.

Methods

P. aeruginosa 24Pae112 as a reference strain was retrieved from GenBank database. The surface-exposed, antigenic, non-allergenic, and non-homologous human proteins were selected. The conserved domains of selected proteins were evaluated, and the prevalence of proteins was assessed among 395 genomes. Next, linear and conformational B-cell epitopes, and human MHC II binding sites were determined. Finally, five conserved and highly antigenic B-cell epitopes from OMPs were implanted on the three platforms as multi-epitope vaccines, including FliC, the bacteriophage T7 tail, and the cell wall-associated transporter proteins. The immunoreactivity was investigated using molecular docking and immune simulation. Furthermore, molecular dynamics simulation was done to refine the chimeric cell-wall-associated transporter-TLR4 complex as the best interaction.

Results

Among 6494 total proteins of P. aeruginosa 24Pae112, 16 proteins (seven OMPs and nine secreted) were ideal according to the defined criteria. These proteins had a molecular weight of 110 kDa and were prevalent in ≥ 75% of P. aeruginosa genomes. Among the presented multi-epitope vaccines, the chimeric cell-wall-associated transporter had the strongest interaction with TLR4. Moreover, the immune simulation response revealed that the bacteriophage T7 tail chimeric protein had the strongest ability to stimulate the immune system. In addition, molecular docking and molecular dynamic simulation indicated the proper and stable interactions between the chimeric cell-wall-associated transporter and TLR4.

Conclusion

This study proposed 16 shortlisted proteins as promising immunogenic targets. Two novel platforms (e.g. cell-wall-associated transporter and bacteriophage T7 tail proteins) for designing of multi-epitope vaccines (MEVs), showed the better performance compared to FliC. In our future studies, these two MEVs will receive more scrutiny to evaluate their immunoreactivity.
Environmental temperature influences ophidiomycosis progression and survival in experimentally challenged prairie rattlesnakes (Crotalus viridis)
Authors: Kendall Michelle Waligora , Wright Allison D. , Adamovicz Laura A. , Durante Kennymac , Andersson Kirsten E. , Frederickson Kelcie , Vivirito Katie , Ospina Emilie A. , Delaney Martha A. , Allender Matthew C.
Published: August 2023

Ophidiomycosis is a prevalent and intermittently pervasive disease of snakes globally caused by the opportunistic fungal pathogen, Ophidiomyces ophidiicola. Host response has yet to be fully explored, including the role of temperature in disease progression and hematologic changes. This study enrolled twelve adult prairie rattlesnakes (Crotalus viridis) in an experimental challenge with O. ophidiicola at two temperatures, 26°C (n = 6) and 20°C (n = 6). Each temperature cohort included four inoculated and two control snakes. Assessments involving physical exams, lesion swabbing, and hematology were performed weekly. Differences were observed between inoculated and control snakes in survival, behavior, clinical signs, ultraviolet (UV) fluorescence, hematologic response, and histologic lesions. All inoculated snakes held at 20°C were euthanized prior to study end date due to severity of clinical signs while only one inoculated animal in the 26°C trial met this outcome. In both groups, qPCR positive detection preceded clinical signs with regards to days post inoculation (dpi). However, the earliest appearance of gross lesions occurred later in the 20°C snakes (20 dpi) than the 26°C snakes (13 dpi). Relative leukocytosis was observed in all inoculated snakes and driven by heterophilia in the 20°C snakes, and azurophilia in the 26°C group. Histologically, 20°C snakes had more severe lesions, a lack of appropriate inflammatory response, and unencumbered fungal proliferation and invasion. In contrast, 26°C snakes had marked granulomatous inflammation with encapsulation of fungi and less invasion and dissemination. The results of this study identified that O. ophidiicola-infected rattlesnakes exposed to lower temperatures have decreased survival and more robust hematologic change, though minimal and ineffective inflammatory response at site of infection. Ophidiomycosis is a complex disease with host, pathogen, and environmental factors influencing disease presentation, progression, and ultimately, survival. This study highlighted the importance of temperature as an element impacting the host response to O. ophidiicola.
Behavioral interplay between mosquito and mycolactone produced by Mycobacterium ulcerans and bacterial gene expression induced by mosquito proximity
Authors: Kim Dongmin , Crippen Tawni L. , Dhungel Laxmi , Delclos Pablo J. , Tomberlin Jeffery K. , Jordan Heather R.
Published: August 2023

Mycolactone is a cytotoxic lipid metabolite produced by Mycobacterium ulcerans, the environmental pathogen responsible for Buruli ulcer, a neglected tropical disease. Mycobacterium ulcerans is prevalent in West Africa, particularly found in lentic environments, where mosquitoes also occur. Researchers hypothesize mosquitoes could serve as a transmission mechanism resulting in infection by M. ulcerans when mosquitoes pierce skin contaminated with M. ulcerans. The interplay between the pathogen, mycolactone, and mosquito is only just beginning to be explored. A triple-choice assay was conducted to determine the host-seeking preference of Aedes aegypti between M. ulcerans wildtype (MU, mycolactone active) and mutant (MUlac-, mycolactone inactive). Both qualitative and quantitative differences in volatile organic compounds’ (VOCs) profiles of MU and MUlac- were determined by GC-MS. Additionally, we evaluated the interplay between Ae. aegypti proximity and M. ulcerans mRNA expression. The results showed that mosquito attraction was significantly greater (126.0%) to an artificial host treated with MU than MUlac-. We found that MU and MUlac produced differential profiles of VOCs associated with a wide range of biological importance from quorum sensing (QS) to human odor components. RT-qPCR assays showed that mycolactone upregulation was 24-fold greater for MU exposed to Ae. aegypti in direct proximity. Transcriptome data indicated significant induction of ten chromosomal genes of MU involved in stress responses and membrane protein, compared to MUlac- when directly having access to or in near mosquito proximity. Our study provides evidence of possible interkingdom interactions between unicellular and multicellular species that MU present on human skin is capable of interreacting with unrelated species (i.e., mosquitoes), altering its gene expression when mosquitoes are in direct contact or proximity, potentially impacting the production of its VOCs, and consequently leading to the stronger attraction of mosquitoes toward human hosts. This study elucidates interkingdom interactions between viable M. ulcerans bacteria and Ae. aegypti mosquitoes, which rarely have been explored in the past. Our finding opens new doors for future research in terms of disease ecology, prevalence, and pathogen dispersal outside of the M. ulcerans system.
Epigenetic regulation of nuclear processes in fungal plant pathogens
Authors: Kramer H. Martin , Cook David E. , Seidl Michael F. , Thomma Bart P.H.J.
Published: August 2023

Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
Phages on filaments: A genetic screen elucidates the complex interactions between Salmonella enterica flagellin and bacteriophage Chi
Authors: Esteves Nathaniel C. , Bigham Danielle N. , Scharf Birgit E.
Published: August 2023

The bacterial flagellum is a rotary motor organelle and important virulence factor that propels motile pathogenic bacteria, such as Salmonella enterica, through their surroundings. Bacteriophages, or phages, are viruses that solely infect bacteria. As such, phages have myriad applications in the healthcare field, including phage therapy against antibiotic-resistant bacterial pathogens. Bacteriophage χ (Chi) is a flagellum-dependent (flagellotropic) bacteriophage, which begins its infection cycle by attaching its long tail fiber to the S. enterica flagellar filament as its primary receptor. The interactions between phage and flagellum are poorly understood, as are the reasons that χ only kills certain Salmonella serotypes while others entirely evade phage infection. In this study, we used molecular cloning, targeted mutagenesis, heterologous flagellin expression, and phage-host interaction assays to determine which domains within the flagellar filament protein flagellin mediate this complex interaction. We identified the antigenic N- and C-terminal D2 domains as essential for phage χ binding, with the hypervariable central D3 domain playing a less crucial role. Here, we report that the primary structure of the Salmonella flagellin D2 domains is the major determinant of χ adhesion. The phage susceptibility of a strain is directly tied to these domains. We additionally uncovered important information about flagellar function. The central and most variable domain, D3, is not required for motility in S. Typhimurium 14028s, as it can be deleted or its sequence composition can be significantly altered with minimal impacts on motility. Further knowledge about the complex interactions between flagellotropic phage χ and its primary bacterial receptor may allow genetic engineering of its host range for use as targeted antimicrobial therapy against motile pathogens of the χ-host genera Salmonella, Escherichia, or Serratia.
Superheroes and Nazis: Re-examining the legacy of the Second World War in Eric Kripke’s The Boys
Authors: Whittall Abigail
Published: August 2023

The television adaptation of The Boys, originally a comic book series written by Garth Ennis, has garnered attention for its graphic violence and satirical treatment of the superhero genre. The Boys engages with a number of critiques of the superhero genre and its tropes, one of which is the recurring presence of a Nazi supervillain. This article links The Boys to previous examples of comic books and screen adaptations which feature Nazis or similar fascist organizations, such as Captain America, Superman and X-Men. In particular, it argues that The Boys’s status as a subversive superhero narrative impacts the portrayal of Nazism in new ways, further troubling the distinction between superhero and supervillain and providing insight into contemporary cultural concerns. Through its representation of the superhero origin story and the Nazi character Stormfront, The Boys draws upon the memories of the Second World War in order to condemn the rise of fascism in the twenty-first century. Despite this ostensibly worthy goal, it is also important to consider criticisms of this type of representation of the historically specific atrocities of the Second World War, the role of exploitation and its resulting reception by viewers.
Storying species extinction in Avengers: Infinity War and Avengers: Endgame
Authors: Dungan Sophie
Published: August 2023

This article places two Marvel Cinematic Universe (MCU) films, Avengers: Infinity War () and Avengers: Endgame (), in dialogue with the Marvel comic books on which they are based. As this article demonstrates, in their depiction of Thanos and the partial species extinction event, the films deviate substantially from their source material to reflect a contemporary cultural interest and growing anxiety over the real-world threat of species extinction. However, as this article argues, Avengers: Infinity War’s and Avengers: Endgame’s ecocritical potential are limited, owing partly to the villain’s role in superhero films and comic books more broadly. Limits also owe to the anthropocentric viewpoint that underwrites much of superhero fiction. Superheroes may serve a conservative function as an upholder of the social order, but, as this article shows, in Avengers: Infinity War and Avengers: Endgame, as well as films and television series in the MCU set thereafter, this function often comes at the detriment of the conservation of nature and species-other-than-human.
Paternalism, performative masculinity and the post-9/11 cowboy in Christopher Nolan’s Dark Knight trilogy
Authors: Avery Cathrine
Published: August 2023

The superhero as a masculine ideal has been extensively scrutinized; he is perceived as a man of physical strength, selflessness and conformity but also one capable of aggression, toxic violence, vigilantism and emotional detachment. Nolan’s superhero, Batman, is situated within this discourse of contradictory masculinity. Recent scholarly discussion has considered how superheroes, including Batman, portray a masculinity designed to fulfil the desires of a post-9/11 audience. This article will extend this examination of contradictory masculinity to consider the father figures who teach Batman to be a superhero and what their instruction identifies as desirable heroic traits in the decade following the 9/11 tragedy. This form of heroic masculinity is not new and exhibits an uncanny resemblance to the cowboy who, like the superhero, is a stylized, uniquely American character. This article will argue that this is a masculinity that is learned and then performed: it reveals the imitative nature of gender, such that Nolan’s trilogy acts as a series of lessons in the problematic, fictive and performative expressions of masculinity in a post-9/11 world.
The phenotypic and genotypic antimicrobial resistance patterns of Salmonella isolated from chickens and meat at poultry slaughterhouses in Japan and Thailand
Authors: Noenchat Pattarakitti , Direksin Kochakorn , Sornplang Pairat
Published: August 2023

Background and Aim: Poultry meat is a popular food consumed globally. However, poultry farming is a source of Salmonella contamination which causes human salmonellosis. This study aimed to estimate the prevalence and antimicrobial resistance (AMR) of Salmonella among chickens and meat at poultry slaughterhouses in province study areas in Thailand and Japan.

Materials and Methods: Chicken meat and feces samples were collected in Thailand and Japan. In Nakhon Ratchasima Province, Thailand, 558 samples were obtained from slaughterhouses from January 2021 to March 2022. In Gifu Prefecture, Japan, 140 samples (70 each of intestinal contents and meat) were purchased from slaughterhouses from June to October 2022. For Salmonella detection, the samples were cultivated according to the International Organization for Standardization 6579:2002/AMD 1:2007 method and confirmed using polymerase chain reaction (PCR) and agglutination tests for serotyping. Isolated Salmonella were tested for AMR to nine antibiotics using the disk diffusion method. Selected phenotypic multidrug-resistant (MDR) isolates were evaluated for AMR genes (AMRGs) using PCR.

Results: Salmonella prevalence from chickens and meat at slaughterhouses in Thailand and Japan was 41.2% and 40.7%, respectively. All the Salmonella isolates in Japan were serotyped as Schwarzengrund, and no Salmonella isolates were resistant to the nine antibiotics tested. In contrast, most of the Thai Salmonella isolates from chicken cloacal swabs and meat were resistant to doxycycline (78.3%) and colistin (63.5%). The prevalence of MDR Salmonella (MDRS) in chickens and meat from Thailand and Japan was 29.1% (67/230) and 0% (0/57), respectively. However, the most frequent AMRGs found in MDRS in Thailand were extended-spectrum beta-lactamase-Temoneira (ESBL-TEM) (45.1%). All isolated Salmonella from Japan revealed a class 1 integron gene (Int-1).

Conclusion: Phenotypic MDRS isolates from Thailand showed the greatest correlation to AMRG and ESBL-TEM. Although there were no phenotypic AMR Salmonella isolates found in Japan, they can be found associated with Int-1, which may carry other AMRGs within the gene cassettes.

Keywords: antimicrobial resistance, broiler chickens, meat, Salmonella, slaughterhouse.
Expression of toll-like receptor 4 and its associated cytokines from peripheral blood mononuclear cells in Leghorn chickens
Authors: Jeenkeawpieam Juthatip , Tantikositruj Chananphat , Kitpipit Warangkana , Thiptara Anyarat , Kayan Autchara , Unjit Kittichai , Sintupachee Siriluk , Boonkaewwan Chaiwat
Published: August 2023

Background and Aim: Immune cells require toll-like receptor 4 (TLR4) to respond to lipopolysaccharides (LPS) by releasing pro-inflammatory cytokines. Peripheral blood mononuclear cells (PBMCs) are used to assess changes in cytokines released in response to diseases or pathogens. This study aimed to assess TLR4 gene expression in PBMCs from Leghorn chicken and the release of related cytokines.

Materials and Methods: Peripheral blood mononuclear cells were isolated from blood samples obtained from Leghorn chicks. The PBMC cultures were stimulated with various concentrations of LPS (0.01-1 µg/ml). Polymerase chain reaction was used to detect TLR4 expression. The production of tumor necrosis factor-alpha (TNF-α) and interleukins (IL-1β and IL-6) was quantified using an enzyme-linked immunosorbent assay.

Results: We found that TLR4 was expressed in both non-stimulated and stimulated Leghorn chicken PBMCs. In addition, the release of TNF-α, IL-1β, and IL-6 levels in Leghorn chicken PBMCs increased significantly with an increase in LPS concentration (0.01–1 µg/mL) (p < 0.05).

Conclusion: Although TLR4 was expressed in both non-stimulated and stimulated Leghorn chicken PBMCs, its expression was significantly higher in LPS-stimulated PBMCs Therefore, the chicken’s endotoxin response can be assessed by evaluating the pro-inflammatory cytokine production from PBMCs.

Keywords: Leghorn chicken, peripheral blood mononuclear cell, pro-inflammatory cytokine, Toll-like receptor 4.
Molecular detection of Bartonella and Borrelia in pet dogs in Metro Manila and Laguna, Philippines
Authors: Lee Chae Eun , Ikeda Jeong Hee , Manongdo Mikaella Andrea M. , Romerosa Dan Rica T. , Sandalo-De Ramos Kristina Andrea C. , Tanaka Tetsuya , Galay Remil L.
Published: August 2023

Background and Aim: Bartonella and Borrelia are zoonotic vector-borne pathogens that can infect dogs and humans. Data on Bartonella and Borrelia in dogs in the Philippines are lacking. This study was conducted to validate previous reports and further investigate the occurrence of Bartonella and Borrelia spp. in cities of Metro Manila.

Materials and Methods: A total of 182 canine blood samples were acquired with DNA using a commercial extraction kit from selected veterinary clinics in the cities of Metro Manila and Laguna, Philippines. The mammalian actin was amplified through polymerase chain reaction (PCR), followed by PCR assays targeting Bartonella gltA and Borrelia flaB. Further PCR assays targeting 16S of Borrelia and ospA and ospC of Borrelia burgdorferi were performed for those that showed flaB bands.

Results: A positive band for gltA of Bartonella was observed in 9 (4.95%) samples, whereas a positive band for flaB of Borrelia was observed in 15 (8.24%) samples. Subsequent PCR assays for other genes of Borrelia were negative.

Conclusion: These results confirmed the presence of Bartonella and warranted further investigation for the possible presence of other Borrelia species.

Keywords: Bartonella, Borrelia, dogs, polymerase chain reaction, tick-borne pathogens.
It’s Time to Stop Talking About Cellular Therapy Disparities and Take Action
Authors:   Center for International Blood and Marrow Transplant Research (CIBMTR), Auletta Jeffery J. , Davies Stella M. ,   Cincinnati Children’s Hospital Medical Center
Published: August 2023

The cellular therapy community has long recognized inequality in access to treatment and disparities in treatment outcomes based on patient race, ethnicity, and socioeconomic status. It is no longer enough to recognize the problem exists. As the late John Lewis stated, “If you see something that is not right, not fair, not just, you have a moral obligation to do something about it.” The cellular therapy community, which includes hematopoietic cell transplantation (HCT), must advance efforts to end these inequities.
Data Integrity in GxP Relevant Areas: A Hot Topic in the Pharmaceutical Sector
Authors:   PharmaLex, Chervonenko Olena
Published: August 2023

The world around us provides us with an abundance of data at every moment of every day and we constantly analyze this data to make decisions. In this process, the attributability, accuracy, legibility, permanence, contemporaneousness, and originality of the data we receive are of utmost importance. So, what does “data” mean? Data is a formalized representation of information suitable for communication, interpretation, or processing, according to ISO/IEC 2382:2015. Data integrity (DI) is the property of data where accuracy and consistency are preserved regardless of changes made, according to the same ISO/IEC standard.
Fieldwork during violent conflict: The Philippine National Red Cross Experience during the Zamboanga Siege
Authors: Legarde Lean Monique
Published: August 2023

This academic research examines the experiences of the Philippine National Red Cross (PNRC) during the Zamboanga Siege, focusing on the challenges and lessons learned from conducting fieldwork in the midst of violent conflicts. Drawing upon primary data collected through interviews with PNRC staff and volunteers, as well as documentary analysis, the study sheds light on the practical realities faced by humanitarian organizations operating in volatile environments. The findings reveal that the PNRC encountered numerous obstacles during the Zamboanga Siege, including restricted access to affected areas, heightened security risks, and limited resources. However, the organization demonstrated resilience and adaptability in overcoming these challenges, employing innovative strategies to provide life-saving assistance and support to affected communities. Notably, the PNRC emphasized the importance of establishing strong partnerships with local stakeholders, coordinating closely with government agencies, and leveraging technological tools for efficient and effective response. This study contributes to the existing literature on humanitarian fieldwork by providing empirical evidence of the specific challenges faced by organizations operating in conflict settings. The insights gained from this study inform best practices for humanitarian actors, policymakers, and practitioners involved in emergency response and preparedness. The findings underscore the critical role of flexibility, collaboration, and resourcefulness in navigating complex and dangerous operational environments.
Waste management practices for food and agricultural by-products: Case studies of public markets in Zamboanga City
Authors: Tendero Emerissa Jane
Published: August 2023

This research examines waste management practices pertaining to food and agricultural by-products in public markets within Zamboanga City, Philippines. The study adopts a comprehensive approach to assess current strategies employed by local authorities and market vendors to manage waste generated from these sectors. Through the collection of primary data via interviews and on-site observations, this research investigates the effectiveness of waste management systems in addressing the environmental and health concerns associated with food and agricultural by-product waste. The findings reveal that waste management practices in public markets in Zamboanga City are characterized by a mix of strengths and shortcomings. While the study identifies commendable efforts in waste segregation and recycling, significant gaps persist in terms of collection, disposal, and overall waste reduction strategies. Despite the existence of regulations and policies, the lack of awareness, limited infrastructure, and inadequate coordination among stakeholders hinder the proper implementation of waste management practices. The research highlights the pressing need for improved institutional support, enhanced education and awareness programs, and investment in infrastructure for efficient waste management systems. Addressing these challenges will contribute to the reduction of environmental pollution, minimize health risks, and foster sustainable development in Zamboanga City's public market ecosystem. This study provides valuable insights for policymakers, local authorities, and market vendors, offering recommendations to enhance waste management practices and promote a healthier and cleaner environment.
Primality test and repeating decimal digits
Authors: Blackburn Simon-Pierre
Published: August 2023

This paper addresses the topic of prime numbers, in particular the challenge to determine whether a number is prime or composite. For that matter, we propose a new type of deterministic primality test inspired by Fermat’s little theorem and based on the properties of repeating decimal digits.
Potencial petrolífero remanescente do Brasil - Estado da arte 2023
Authors: Zalán Pedto Victor
Published: August 2023

O petróleo ainda será a principal fonte de energia da humanidade por, no mínimo, 50 anos. O Brasil já é e certamente será um provedor ainda mais importante desta matéria prima durante décadas. Há muitas bacias com grande potencial ainda intactas e muitas áreas ainda não exploradas e outras que já possuem reservas e produção. O objetivo deste trabalho é fazer previsões sobre o potencial petrolífero remanescente das bacias sedimentares do Brasil. As previsões são feitas com base no enorme acervo de dados acumulado nos 83 anos de história da exploração petrolífera brasileira, com base nos conceitos mais atualizados da ciência da geologia do petróleo, e, principalmente, com base em minha experiência de 45 anos de atividade no ramo. Nossa previsão final, para o potencial remanescente de petróleo (potencial de recursos prospectivos, identificados ou não, mas ainda não descobertos) de todas as bacias brasileiras fica na faixa de 50-100 bilhões de barris de óleo equivalente recuperável (boer). As bacias que mais deverão contribuir para a realização deste potencial serão Santos/Campos, Pará-Maranhão/Foz do Amazonas/Barreirinhas, Pelotas e Paraná. Em menor escala, mas ainda importantes, Sergipe-Alagoas, Espírito Santo, Camamu-Almada, Solimões e Parnaíba. Temos plena consciência de que a Geologia é uma ciência complexa e surpreendente. Dados novos, tecnologias inovadoras e conceitos criativos nunca dantes imaginados poderão facilmente destruir (para melhor ou para pior) tais previsões.
Exploring Pre-Service Elementary and Middle School Earth Science Teachers' Perceptions of Earth Science Learning Via Drawing
Authors:   Center For Educational Research, Choi Yoon-Sung
Published: August 2023

Purpose: The purpose of this study was to investigate the perceptions of elementary pre-serviceteachers and secondary pre-service teachers regarding Earth Science learning.
Methods: A total of 134 pre-service teachers participated in this research survey, including 92elementary pre-service teachers from A Education University, 42 secondary pre-service teachers fromB University. and C University majoring in Earth Science education. Among the participants, 12pre-service teachers, including three elementary pre-service teachers and nine secondary pre-serviceteachers, agreed to additional interviews, which were conducted through online meetings.
Results: The survey results revealed a tendency among both elementary and secondary pre-serviceteachers to emphasize the aspect of knowledge acquisition when defining earth science learning. Theperception of “good” and “bad” classes could be interpreted as being influenced by the presence orabsence of interaction between teachers and students. Regarding past experiences with Earth Science,elementary pre-service teachers reported the highest frequency of experiences related to knowledgeacquisition in classroom settings, while secondary pre-service teachers reported the highest frequencyof experiences related to astronomical observations. In terms of envisioning future Earth Scienceinstruction, both elementary and secondary pre-service teachers demonstrated implicit understandingof subject matter knowledge (including knowledge of the curriculum, content knowledge, andknowledge of online learning environments).
Conclusion: The findings of this study are expected to provide an indicator of the perceptions heldby elementary and secondary pre-service teachers regarding Earth Science learning, serving asfundamental data with academic value that can be utilized in future international comparative researchon Earth Scien ce education.