bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction
Authors: Torrengo Giuliano
Published: June 2024

In this introductory chapter, the author lays the groundwork by presenting key terminology and fundamental concepts featured throughout the book. The chapter delineates the distinction between cogent and interpretational phenomenology, highlighting the difference between a detailed, attentive phenomenology and a more ambiguous, indeterminate one. The utilization of experience-based claims is introduced as a methodological tool for indirectly but purposefully describing experiences. Examples of such claims include ‘The fork fell from the table to the floor’, ‘the smell of burnt pizza is going away’, ‘I can see what is happening now in the garden’, and ‘the thunder followed the lightning flash’. Additionally, the chapter explores the principle of temporal transparency and its correlation with phenomenal objectivity. It also delves into the notion of certain aspects within our phenomenology being overarching, engaging indirectly with times different from their current occurrence. Finally, the chapter concludes with an overview of the core principles of the atomist dynamic model, offering readers a guide to navigate subsequent chapters.
Change and movement
Authors: Torrengo Giuliano
Published: June 2024

In this chapter, the author explores the characterization of our phenomenology through experience-based claims centred on change and movement. The chapter introduces a taxonomy illustrating various temporal elements presented within the pure-qualitative spectrum, ranging from ‘change’ at the qualitative end to ‘passage’ at the pure end. Critique is directed towards two opposing views: the snapshot views, positing non-temporally extended experiences or contents; and the specious present views, suggesting temporally extended experiential contents or experiences themselves. Ultimately, the author defends the atomist dynamic model—a framework associating the phenomenology of change and motion with detection systems presenting dynamically evolving properties. These properties encompass movement and change, encapsulated within temporally undivided experiences.
The outer flow and the inner flow
Authors: Torrengo Giuliano
Published: June 2024

In this chapter, the author investigates the structure of phenomenological time examining its dual nature as an outer flow, wherein the external world unfolds before us, and encapsulating personal sensations and thoughts. The author scrutinizes the phenomenology of having one experience after another and distinguishing it from other temporal phenomenal characters such as change, duration, and continuity. He then argues that even though the flow of experience is often described as smooth, we do not experience the temporal dimension as a continuous series of locations and gives reasons to believe that experience is not just discontinuous, but also constituted by disunified flows. Finally, the author discusses the roles that thoughts play in our inner life by introducing and articulating the idea of narrative cognition.
How Identity Works
Authors: Darby Derrick , Martinez Eduardo J
Published: June 2024

Breaking free from identities that are too tightly scripted, and avoiding the identity trouble associated with this phenomenon, requires a deeper understanding of how identities work. This chapter provides this understanding by drawing on a taxonomy from Kwame Anthony Appiah that describes three core practices around which identities take shape. This taxonomy is used to demonstrate that collective identities are dynamic and complex. Identity group members will be situated differently based on variation in labeling, identification, and treatment-as practices. The intragroup heterogeneity that results from this variation poses challenges for the collective pursuit of life-shaping projects. But it also provides opportunities for collective self-authorship which is vital for making identities safe for democratic accountability.
Holy Things
Authors: McGovern Nathan
Published: June 2024

Scholars of religion have increasingly rejected the model of religious syncretism, in which apparent deviations from normative practice are explained as the result of a mixture of religions. Nevertheless, there are aspects of Thai Buddhist practice that still stubbornly appear syncretistic, such as the worship of particular Buddha images for mundane boons in the same way as gods and spirits. Moreover, increasingly Thai Buddhists themselves are adopting the language of syncretism, referring to traditional Thai religion as a mixture of local, Hindu, and Buddhist practices. This raises the question: If syncretism is so wrong, then why does it seem so right? Holy Things answers this question through an in-depth study of the worship of spirits, gods, and Buddha images—all known as sing saksit, or “holy things”—in Thailand. It shows that what appears to be syncretism is actually an illusion created by an array of historically transforming and interacting discourses: Pali Buddhist, Sanskritic Hindu, and the modern discourse of religion. Holy Things thus explains not only why a stubborn case of apparent syncretism is actually not so, but also why syncretism seems so appealing in the first place.
The Genealogy of the Sacred
Authors: McGovern Nathan
Published: June 2024

This chapter explores the discourse out of which the concept of saksit arises. It argues that the Thai word saksit meant something quite different prior to its modern use in translating the Western concept of “holy.” The chapter traces the genealogy of the word saksit in premodern Siamese literature. Prior to the modern colonial encounter, saksit was used to refer to the power possessed by supernatural beings that was also accessible to Brahmans through their specialized forms of knowledge (veda and āgama). As such, it was part of a broader discourse of saiyasāt, which referred to Brahmanism and was juxtaposed with phutthasāt, or Buddhism. While most of the vocabulary of saiyasāt was used in the nineteenth century to translate Western concepts associated with “magic,” saksit was idiosyncratically used to translate the concept of “holy,” thus placing it in the realm of religion.
The European Union’s Demoicratic Legislature
Authors: van den Brink Martijn
Published: June 2024

Assuming that the European Union (EU) legislative process lacks democratic legitimacy, legal scholars have argued that the EU should ideally exercise its authority through the judicial process. This chapter argues, instead, that the value of political legitimacy militates in favour of judicial deference to legislation. It explains why the justification of political authority is a normative and not a sociological or legal question and then argues that the proper content of this normative conception of legitimacy is input-oriented instead of output-oriented. More specifically, it elaborates a demoicratic conception of political legitimacy according to which the national peoples must have shared and equal control over the EU. It shows, finally, that the legislature has greater demoicratic legitimacy than the judiciary, thereby providing a strong justification for judicial deference to legislation.
An integrated database of experimentally validated major histocompatibility complex epitopes for antigen-specific cancer therapy
Authors: Kawakita Satoru , Shen Aidan , Chao Cheng-Chi , Wang Zhaohui , Cheng Siliangyu , Li Bingbing , Jiang Chongming
Published: June 2024

Cancer immunotherapy represents a paradigm shift in oncology, offering a superior anti-tumor efficacy and the potential for durable remission. The success of personalized vaccines and cell therapies hinges on the identification of immunogenic epitopes capable of eliciting an effective immune response. Current limitations in the availability of immunogenic epitopes restrict the broader application of such therapies. A critical criterion for serving as potential cancer antigens is their ability to stably bind to the major histocompatibility complex (MHC) for presentation on the surface of tumor cells. To address this, we have developed a comprehensive database of MHC epitopes, experimentally validated for their MHC binding and cell surface presentation. Our database catalogs 451 065 MHC peptide epitopes, each with experimental evidence for MHC binding, along with detailed information on human leukocyte antigen allele specificity, source peptides, and references to original studies. We also provide the grand average of hydropathy scores and predicted immunogenicity for the epitopes. The database (MHCepitopes) has been made available on the web and can be accessed at https://github.com/jcm1201/MHCepitopes.git. By consolidating empirical data from various sources coupled with calculated immunogenicity and hydropathy values, our database offers a robust resource for selecting actionable tumor antigens and advancing the design of antigen-specific cancer immunotherapies. It streamlines the process of identifying promising immunotherapeutic targets, potentially expediting the development of effective antigen-based cancer immunotherapies.
SARS-CoV-2 incidence, seroprevalence, and antibody dynamics in a rural, population-based cohort: March 2020 – July 2022
Authors: Petrie Joshua G , Pattinson David , King Jennifer P , Neumann Gabriele , Guan Lizheng , Jester Peter , Rolfes Melissa A , Meece Jennifer K , Kieke Burney A , Belongia Edward A , Kawaoka Yoshihiro , Nguyen Huong Q
Published: June 2024

Studies of SARS-CoV-2 incidence are important for response to continued transmission and future pandemics. We followed a rural community cohort with broad age representation with active surveillance for SARS-CoV-2 identification from November 2020 through July 2022. Participants provided serum specimens at regular intervals and following SARS-CoV-2 infection or vaccination. We estimated the incidence of SARS-CoV-2 infection identified by study RT-PCR, electronic health record documentation or self-report of a positive test, or serology. We also estimated the seroprevalence of SARS-CoV-2 spike and nucleocapsid antibodies measured by ELISA. Overall, 65% of the cohort had ≥1 SARS-CoV-2 infection by July 2022, and 19% of those with primary infection were reinfected. Infection and vaccination contributed to high seroprevalence, 98% (95% CI: 95%, 99%) of participants were spike or nucleocapsid seropositive at the end of follow-up. Among those seropositive, 82% were vaccinated. Participants were more likely to be seropositive to spike than nucleocapsid following infection. Infection among seropositive individuals could be identified by increases in nucleocapsid, but not spike, ELISA optical density values. Nucleocapsid antibodies waned more quickly after infection than spike antibodies. High levels of SARS-CoV-2 population immunity, as found in this study, are leading to changing epidemiology necessitating ongoing surveillance and policy evaluation.
The 2018-2019 FoodNet Population Survey: a tool to estimate risks and behaviors associated with enteric infections
Authors: Devine Carey J , Molinari Noelle-Angelique , Shah Hazel J , Blackstock Anna J , Geissler Aimee , Marder Ellyn P , Payne Daniel C
Published: June 2024

The FoodNet Population Survey is a periodic survey of randomly selected residents at 10 US sites on exposures and behaviors that may be associated with acute diarrheal infections and the health care sought for those infections. This survey is used to estimate the true disease burden of enteric illness in the United States and to estimate rates of exposure to potential sources of illness. Unlike previous FoodNet Population Surveys, this cycle used multiple sampling frames and administration modes, including cell phone and web-based questionnaires, that allowed for additional question topics and a larger sample size. It also oversampled children to increase representation of this population. Analytic modeling adjusted for mode effects when estimating the prevalence estimates of exposures and behaviors. This report describes the design, methodology, challenges, and descriptive results from the 2018-2019 FoodNet Population Survey.
Impact of Hematoma on Capsular Contracture: A Comparative Study of Smooth and Textured Implants in a Miniature Pig Model
Authors: Zhang Xiaoyu , Lin Yan , Li Haoran , Mu Dali
Published: June 2024

Background

Capsular contracture is a significant complication following mammaplasty, with varying incidence rates and symptoms. The etiology of capsular contracture is multifactorial, with postoperative hematoma recognized as a potential contributing factor.

Objectives

In this study we aimed to investigate the impact of postoperative hematoma on capsular contracture following mammaplasty, utilizing pig models and modified biomechanical testing. We sought to compare the severity of capsular contracture between smooth and textured implants in the presence of hematoma, assess the biomechanical properties of the capsules, and explore the histological and molecular changes associated with the condition.

Methods

The study involved 5 female miniature pigs, implanted with both smooth and textured implants. Hematoma models were established, and various methods were employed to evaluate the impact of the prosthesis surface and hematoma on capsular contracture, including ultrasound assessment, biomechanical tests, scanning electron microscopy, histological analysis, and transcriptome sequencing.

Results

Capsules in hematoma groups were classified as Baker III/IV, with significantly unfavorable thickness, elastic modulus, and relaxation and creep amounts compared to nonhematoma groups. Smooth implants under hematoma conditions exhibited increased muscle content and biomechanical strength of the capsule. Transcriptomic analysis highlighted differential gene expression related to muscle development and contraction in smooth implants with hematomas.

Conclusions

Hematomas increase the risk of capsular contracture, with smooth implants exacerbating this effect by enhancing pathways related to muscle development and contraction. This underscores the importance of hematoma prevention and treatment strategies, particularly when placing smooth implants, to minimize the occurrence of capsular contracture. The study provides insights into the mechanisms underlying capsular contracture and offers evidence to guide surgical and postoperative management strategies.
Helpers show plasticity in their responses to breeder turnover
Authors: Ausband David E , Bassing Sarah B
Published: June 2024

Nonbreeding helpers can greatly improve the survival of young and the reproductive fitness of breeders in many cooperatively breeding species. Breeder turnover, in turn, can have profound effects on dispersal decisions made by helpers. Despite its importance in explaining group size and predicting the population demography of cooperative breeders, our current understanding of how individual traits influence animal behavior after disruptions to social structure is incomplete particularly for terrestrial mammals. We used 12 yr of genetic sampling and group pedigrees of gray wolves (Canis lupus) in Idaho, USA, to ask questions about how breeder turnover affected the apparent decisions by mature helpers (≥2-yr-old) to stay or leave a group over a 1-yr time interval. We found that helpers showed plasticity in their responses to breeder turnover. Most notably, helpers varied by sex and appeared to base dispersal decisions on the sex of the breeder that was lost as well. Male and female helpers stayed in a group slightly more often when there was breeder turnover of the same sex, although males that stayed were often recent adoptees in the group. Males, however, appeared to remain in a group less often when there was breeding female turnover likely because such vacancies were typically filled by related females from the males’ natal group (i.e. inbreeding avoidance). We show that helpers exploit instability in the breeding pair to secure future breeding opportunities for themselves. The confluence of breeder turnover, helper sex, and dispersal and breeding strategies merge to influence group composition in gray wolves.
Does sentinel presence improve foraging success? A study in a cooperative breeder
Authors: Ostreiher Roni , Mundry Roger , Heifetz Aviad
Published: June 2024

In various cooperative breeding species, a group member often sentinels from a prominent position that enables early detection of approaching predators, and then utters alarm calls to which the other group members react immediately. We tested in the cooperatively breeding Arabian babbler (Argya squamiceps), whether in the presence of a sentinel the other group members forage for longer or more effectively. In natural observations, in different distances from shelter and in different group sizes, we found no effect of sentinel presence on foraging time. Likewise, in a giving-up density (GUD) experiment with artificial food patches containing mealworms in each of 3 different distances from shelter, fewer mealworms were consumed further from shelter, but irrespective of whether a sentinel was present or not during foraging. While foragers react to a sentinel’s alarm calls when a predator approaches, our findings indicate that Arabian babbler foragers do not improve their foraging efficiency due to the sentinel’s presence. Combined with previous studies on the Arabian babbler, these findings reinforce the conclusion that in this species the sentinel is “selfish” and benefits from early detection of predators. These results contrast with those from other cooperative breeders in which sentinels utter calming calls and foraging efficiency increases when sentinels are present. We, therefore, suggest that similar sentinel behavior may serve different sentinel systems and functions in different cooperative breeders.
Long-read RNA sequencing can probe organelle genome pervasive transcription
Authors: Sanita Lima Matheus , Silva Domingues Douglas , Rossi Paschoal Alexandre , Smith David Roy
Published: June 2024

40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate – organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.
Change in left atrial function and volume predicts incident heart failure with preserved and reduced ejection fraction: Multi-Ethnic Study of Atherosclerosis
Authors: Lim Daniel J , Varadarajan Vinithra , Quinaglia Thiago , Pezel Theo , Wu Colin , Noda Chikara , Heckbert Susan R , Bluemke David , Ambale-Venkatesh Bharath , Lima Joao A C
Published: June 2024

Aims

The role of change in left atrial (LA) parameters prior to the onset of heart failure (HF) remains unclear. We used cardiac magnetic resonance (CMR) imaging to investigate the relationship between longitudinal change in LA function and incident HF in a multi-ethnic population with subclinical cardiovascular disease (CVD).

Methods and results

In this prospective multi-ethnic cohort study, 2470 participants (60 ± 9 years, 47% males), free at baseline of clinical CVD, had LA volume and function assessed via multimodality tissue tracking on CMR imaging at baseline (2000–02) and a second study 9.4 ± 0.6 years later. Free of HF, 73 participants developed incident HF [HF with preserved ejection fraction (HFpEF), n = 39; reduced ejection fraction (HFrEF), n = 34] 7.1 ± 2.1 years after the second study. An annual decrease of 1 SD unit in peak LA strain (ΔLASmax) was most strongly associated with the risk of HFpEF [subdistribution hazard ratios (HR) = 2.56, 95% confidence interval (CI) (1.34–4.90), P = 0.004] and improved model reclassification and discrimination in predicting HFpEF [C-statistic = 0.84, 95% CI (0.79–0.90); net reclassification index (NRI) = 0.34, P = 0.01; and integrated discrimination index (IDI) = 0.02, P = 0.02], whilst an annual decrease of 1 mL/m2 of pre-atrial indexed LA volumes (ΔLAVipreA) was most strongly associated with the risk of HFrEF [subdistribution HR = 1.88, 95% CI (1.44–2.45), P < 0.001] and improved model reclassification and discrimination in predicting HFrEF [C-statistic = 0.81, 95% CI (0.72–0.90); NRI = 0.31, P = 0.03; and IDI = 0.01, P = 0.50] after adjusting for event-specific risk factors and baseline LA measures.

Conclusion

ΔLASmax and ΔLAVipreA were associated with and incrementally predictive of HFpEF and HFrEF, after adjusting for risk factors and baseline LA measures in this population of subclinical CVD.
A robust genome assembly with transcriptomic data from the striped bark scorpion, Centruroides vittatus
Authors: Yamashita Tsunemi , Rhoads Douglas D , Pummill Jeff
Published: June 2024

Scorpions, a seemingly primitive, stinging arthropod taxa, are known to exhibit marked diversity in their venom components. These venoms are known for their human pathology, but they are also important as models for therapeutic and drug development applications. In this study, we report a high-quality genome assembly and annotation of the striped bark scorpion, Centruroides vittatus, created with several shotgun libraries. The final assembly is 760 Mb in size, with a BUSCO score of 97.8%, a 30.85% GC, and an N50 of 2.35 Mb. We estimated 36,189 proteins with 37.32% assigned to Gene Ontology (GO) terms in our GO annotation analysis. We mapped venom toxin genes to 18 contigs and 2 scaffolds. We were also able to identify expression differences between venom gland (telson) and body tissue (carapace) with 19 sodium toxin and 14 potassium toxin genes to 18 contigs and 2 scaffolds. This assembly, along with our transcriptomic data, provides further data to investigate scorpion venom genomics.
Analysis on the development of modern rural power grids with low carbon serving rural revitalization from the perspective of scientific and technological innovation
Authors: Cao Yi , Xiao Tianying , Liang Yu
Published: June 2024

Our country is a large agricultural nation where the development of rural areas holds paramount importance. To achieve rural revitalization, the development of electric power infrastructure is crucial. However, to ensure sustainable growth, attention must be directed towards low-carbon initiatives. With the continuous advancement of science and technology, rural power grids are steadily transitioning towards intelligent development, marking a significant stride in our nation’s power grid evolution. The establishment of smart grids can effectively address energy consumption issues in rural areas, simultaneously aiding in the reduction of energy usage and carbon emissions. Information technology, interactivity and automation are pivotal technical features characterizing the intelligence of rural power grids, leveraging technological advancements to drive the reform of modern rural power systems. This article intends to focus on optimizing low-carbon development within the ambit of intelligent rural power grid construction, alongside a comprehensive analysis of related developments. Such efforts aim to seamlessly integrate rural power development with a low-carbon economy, offering crucial insights and guidance for the sustainable growth of rural power grids. This endeavor contributes to the overarching objectives of rural revitalization and fostering a low-carbon economy.
Clinical Presentation of Early Syphilis and Genomic Sequences of Treponema pallidum Strains in Patient Specimens and Isolates Obtained by Rabbit Inoculation
Authors: Yang Ligang , Zhang Xiaohui , Chen Wentao , Seña Arlene C , Zheng Heping , Jiang Yinbo , Zhao Peizhen , Chen Rongyi , Wang Liuyuan , Ke Wujian , Salazar Juan C , Parr Jonathan B , Tucker Joseph D , Hawley Kelly L , Caimano Melissa J , Hennelly Christopher M , Aghakanian Farhang , Bettin Everton B , Zhang Feifei , Chen Jane S , Moody M Anthony , Radolf Justin D , Yang Bin
Published: June 2024

Background

The global resurgence of syphilis necessitates vaccine development.

Methods

We collected ulcer exudates and blood from 17 participants with primary syphilis (PS) and skin biopsies and blood from 51 patients with secondary syphilis (SS) in Guangzhou, China, for Treponema pallidum subsp pallidum (TPA) quantitative polymerase chain reaction, whole genome sequencing (WGS), and isolation of TPA in rabbits.

Results

TPA DNA was detected in 15 of 17 ulcer exudates and 3 of 17 blood PS specimens. TPA DNA was detected in 50 of 51 SS skin biopsies and 27 of 51 blood specimens. TPA was isolated from 47 rabbits with success rates of 71% (12/17) and 69% (35/51), respectively, from ulcer exudates and SS bloods. We obtained paired genomic sequences from 24 clinical samples and corresponding rabbit isolates. Six SS14- and 2 Nichols-clade genome pairs contained rare discordances. Forty-one of the 51 unique TPA genomes clustered within SS14 subgroups largely from East Asia, while 10 fell into Nichols C and E subgroups.

Conclusions

Our TPA detection rate was high from PS ulcer exudates and SS skin biopsies and over 50% from SS blood, with TPA isolation in more than two-thirds of samples. Our results support the use of WGS from rabbit isolates to inform vaccine development.
Knowledge and utilization of iodized salt among expectant mothers in Harar City's public health facilities: a multicenter study in Eastern Ethiopia
Authors: Mohammed Hanan , Abebe Dawit , Yetwale Fisseha , Mekuannint Worku , Mesfin Sinetibeb
Published: June 2024

Background

Insufficient iodine intake during pregnancy can result in abortion, stillbirths, neonatal mortality, cretinism and permanent cognitive impairment. Even although iodized salt is widely accessible in Ethiopia, pregnant women still experience persistent problems related to iodine deficiency disorders.

Methods

A facility-based cross-sectional study was conducted among randomly selected 573 pregnant women who were attending antenatal care services at public health facilities. Bivariate and multivariable logistic regression models were used, and independent predictors were determined based on adjusted ORs with 95% CIs and p<0.05.

Results

Knowledge and practice of pregnant women on iodized utilization were 35.6% (95% CI 31.8 to 39.6%) and 37.7% (95% CI 32.1 to 42.9%), respectively. Living in urban areas (adjusted OR [AOR]=1.976, 95% CI 1.136 to 3.435) and having a higher level of education (AOR=2.018, 95% CI 1.037 to 3.930) were associated with having adequate knowledge. Having a diploma or higher education (AOR=2.684, 95% CI 1.137 to 6.340) and adequate knowledge about iodized salt utilization (AOR=2.095, 95% CI 1.273 to 3.447) were significantly associated with good practice.

Conclusions

The current study highlights the level of knowledge and practices of pregnant women on iodized salt. It emphasizes the necessity for targeted programs about the benefits of iodized salt and how to use it correctly, particularly for those with low literacy levels and those living in rural areas.
Attitudes towards wife-beating justification and its association with female genital mutilation – analysis of ever-married Somali women in the 2020 Somali Health and Demographic Survey
Authors: Mohamed Abdirahman Saeed , Bjertness Espen , Htet Aung Soe , Aye Win Thuzar , Madar Ahmed Ali
Published: June 2024

Background

In Somalia, despite its prohibition, female circumcision persists alongside significant intimate partner violence. This study examines the prevalence of wife-beating justification among Somali women and its link to the perception that female genital mutilation/cutting (FGM/C) is a religious obligation.

Methods

We studied 7726 married Somali women 15–49 y of age from the 2020 Somali Health and Demographic Survey. Using χ2 tests and logistic regression, we examined wife-beating justification by covariates and its connection to the perception that FGM/C is a religious obligation.

Results

The prevalence of women justifying wife-beating for any of six reasons was 56.5% (95% confidence interval [CI] 55.3 to 57.6). A higher prevalence of wife-beating justification was found among women 35–49 y of age (59.9% [95% CI 57.8 to 61.9]), without education (57.7% [95% CI 56.5 to 59.0]), rural residents (57.8% [95% CI 56.3 to 59.2]), with lower socio-economic status (60.4% [95% CI 58.7 to 62.1]) and married before age 18 y (58.4% [95% CI 56.7 to 60.1]). Adjusted for covariates, logistic regression analyses indicated a significant association between wife-beating justification and the belief that FGM/C is mandated by religion (adjusted odds ratio 1.40 [95% CI 1.17 to 1.68], p<0.001).

Conclusions

Wife-beating justification is alarmingly common among Somali women and significantly associated with the belief that FGM/C is mandated by religion. Further research is necessary to investigate the drivers behind the acceptance of domestic violence, its impact on women's mental health and well-being and its association with FGM/C acceptance.
Simplified and Detailed Evaluations of the Uncertainty of the Measurement of Microbiological Contamination of Pharmaceutical Products
Authors: Lourenço Felipe Rebello , Bettencourt da Silva Ricardo J N
Published: June 2024

Background

The control of the microbial contamination of pharmaceutical products (PP) is crucial to ensure their safety and efficacy. The validity of the monitoring of such contamination depends on the uncertainty of this quantification. Highly uncertain quantifications due to the variability of determinations or the magnitude of systematic effects affecting microbial growth or other analytical operations make analysis unfit for the intended use. The quantification of the measurement uncertainty expressing the combined effects of all random and systematic effects affecting the analysis allows for a sound decision about quantification adequacy for their intended use. The complexity of the quantification of microbial analysis uncertainty led to the development of simplified ways of performing this evaluation.

Objective

This work assesses the adequacy of the simplified quantification of the uncertainty of the determination of the microbial contamination of PP by log transforming microbial count and dilution factor of the test sample whose uncertainty is combined in a log scale using the uncertainty propagation law.

Methods

This assessment is performed by a parallel novel bottom-up and accurate evaluation of microbial analysis uncertainty involving the Monte Carlo method simulation of the Poisson log-normal distribution of counts and of the normally distributed measured volumes involved in the analysis. Systematic effects are assessed and corrected on results to compensate for their impact on the determinations. Poisson regression is used to predict precision affecting determinations on unknown test samples.

Result

Simplified and detailed models of the uncertainty of the measurement of the microbial contamination of PP are provided, allowing objective comparisons of several determinations and those with a maximum contamination level.

Conclusions

This work concludes that triplicate determinations are required to produce results with adequately low uncertainty and that simplified uncertainty quantification underevaluates or overevaluates the uncertainty from determinations based on low or high colony numbers, respectively. Therefore, detailed uncertainty evaluations are advised for determinations between 50 and 200% of PP’s maximum admissible contamination value

Highlight

User-friendly tools for detailed and simplified evaluations of the uncertainty of the measurement of microbial contamination of PP are provided together with the understanding of when simplifications are adequate.
A MATLAB Toolbox for Findable, Accessible, Interoperable, and Reusable Atom Probe Data Science
Authors: Heller Martina , Ott Benedict , Dalbauer Valentin , Felfer Peter
Published: June 2024

Atom probe tomography (APT) data analytics have traditionally been based on manual analytics by researchers. As newer atom probes together with focused ion beam–based specimen preparation have opened APT to many more materials, yielding much more complex mass spectra, building up a systematic understanding of the pathway from raw data to final interpretation has increasingly become important. This demands a system in which the data and treatment can be traced, ideally by any interested party. Such an approach of findable, accessible, interoperable, and reusable (FAIR) data and analysis policies is becoming increasingly important, not just in APT. In this paper, we present a toolbox, written in MATLAB, which allows the user to store the raw and processed data in a standardized FAIR format (hierarchical data format 5) and process the data in a largely scriptable environment to minimize manual user input. This allows for the experiment data to be interchanged without owner explanations and the analysis to be reproduced. We have devised a metadata scheme that is extensible to other experiments in the materials science domain. With this toolbox, collective knowledge can be built up, and a large number of data sets can be analyzed in a fully automated fashion.
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase
Authors: Roy Priti , Walter Zachary , Berish Lauren , Ramage Holly , McCullagh Martin
Published: June 2024

The Orthoflavivirus NS3 helicase (NS3h) is crucial in virus replication, representing a potential drug target for pathogenesis. NS3h utilizes nucleotide triphosphate (ATP) for hydrolysis energy to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. Intermediate states along the ATP hydrolysis cycle and conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. Extensive molecular dynamics simulations of West Nile virus NS3h+ssRNA in the apo, ATP, ADP+Pi and ADP bound states were used to model the conformational ensembles along this cycle. Energetic and structural clustering analyses depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). Based on these results, MVIL mutants (D471L, D471N and D471E) were found to have a substantial reduction in ATPase activity and RNA replication compared to the wild-type. Simulations of the mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open ‘valve’ conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a ‘valve’ for the ATP-pocket, presenting a promising target for antiviral development.
ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction
Authors: Yancoskie Michelle N , Khaleghi Reihaneh , Gururajan Anirvinya , Raghunathan Aadarsh , Gupta Aryan , Diethelm Sarah , Maritz Corina , Sturla Shana J , Krishnan Marimuthu , Naegeli Hanspeter
Published: June 2024

The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C–containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C–>T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
Tuberculosis and Immune Reconstitution Inflammatory Syndrome in Patients With Inflammatory Bowel Disease and Anti-TNFα Treatment: Insights From a French Multicenter Study and Systematic Literature Review With Emphasis on Paradoxical Anti-TNFα Resumption
Authors: Amoura Ariane , Frapard Thomas , Treton Xavier , Surgers Laure , Beaugerie Laurent , Lafaurie Matthieu , Gornet Jean Marc , Lepeule Raphaël , Amiot Aurélien , Canouï Etienne , Abitbol Vered , Froissart Antoine , Vidon Mathias , Nguyen Yann , Lefort Agnès , Zarrouk Virginie
Published: June 2024

Background

The advent of anti–tumor necrosis factor α (anti-TNFα) has revolutionized the treatment of inflammatory bowel disease (IBD). However, susceptibility to active tuberculosis (TB) is associated with this therapy and requires its discontinuation. The risk of immune reconstitution inflammatory syndrome (IRIS) in this population is poorly understood, as is the safety of resuming anti-TNFα.

Methods

This French retrospective study (2010–2022) included all TB cases in patients with IBD who were treated with anti-TNFα in 6 participating centers. A systematic literature review was performed on TB-IRIS and anti-TNFα exposure.

Results

Thirty-six patients were included (median age, 35 years; IQR, 27–48). TB was disseminated in 86% and miliary in 53%. IRIS occurred in 47% after a median 45 days (IQR, 18–80). Most patients with TB-IRIS (93%) had disseminated TB. Miliary TB was associated with IRIS risk in univariate analysis (odds ratio, 7.33; 95% CI, 1.60–42.82; P = .015). Anti-TB treatment was longer in this population (median [IQR], 9 [9–12] vs 6 [6–9] months; P = .049). Anti-TNFα was resumed in 66% after a median 4 months (IQR, 3–10) for IBD activity (76%) or IRIS treatment (24%), with only 1 case of TB relapse. Fifty-two cases of TB-IRIS in patients treated with anti-TNFα were reported in the literature, complicating disseminating TB (85%) after a median 42 days (IQR, 21–90), with 70% requiring anti-inflammatory treatment. Forty cases of TB-IRIS or paradoxical reaction treated with anti-TNFα were also reported. IRIS was neurologic in 64%. Outcome was mostly favorable (93% recovery).

Conclusions

TB with anti-TNFα treatment is often complicated by IRIS of varying severity. Restarting anti-TNFα is a safe and effective strategy.
Mechanical force-activated CD109 on periodontal ligament stem cells governs osteogenesis and osteoclast to promote alveolar bone remodeling
Authors: Li Yang , Li Yi , Liu Chao , Yu Xinyi , Gan Ziqi , Xiang Lusai , Zheng Jinxuan , Meng Bowen , Yu Rongcheng , Chen Xin , Kou Xiaoxing , Cao Yang , Ai Tingting
Published: June 2024

Mechanical force-mediated bone remodeling is crucial for various physiological and pathological processes involving multiple factors, including stem cells and the immune response. However, it remains unclear how stem cells respond to mechanical stimuli to modulate the immune microenvironment and subsequent bone remodeling. Here, we found that mechanical force induced increased expression of CD109 on periodontal ligament stem cells (PDLSCs) in vitro and in periodontal tissues from the force-induced tooth movement rat model in vivo, accompanied by activated alveolar bone remodeling. Under mechanical force stimulation, CD109 suppressed the osteogenesis capacity of PDLSCs through the JAK/STAT3 signaling pathway, whereas it promoted PDLSC-induced osteoclast formation and M1 macrophage polarization through paracrine. Moreover, inhibition of CD109 in vivo by lentivirus-shRNA injection increased the osteogenic activity and bone density in periodontal tissues. On the contrary, it led to decreased osteoclast numbers and pro-inflammatory factor secretion in periodontal tissues and reduced tooth movement. Mechanistically, mechanical force-enhanced CD109 expression via the repression of miR-340-5p. Our findings uncover a CD109-mediated mechanical force response machinery on PDLSCs, which contributes to regulating the immune microenvironment and alveolar bone remodeling during tooth movement.
Reciprocal suppression between TGFβ signaling and TNF stimulation finetunes the macrophage inflammatory response
Authors: Xia Yuhan , Inoue Kazuki , Zheng Ting , Qin Yongli , Zhao Baohong
Published: June 2024

Inflammation plays a crucial role in the development of various disease conditions or is closely associated with them. Inflammatory cytokines like TNF often engage in interactions with other cytokines and growth factors, including TGFβ, to orchestrate inflammatory process. Basal/endogenous TGFβ signaling is a universal presence, yet the precise way TNF communicates with TGFβ signaling to regulate inflammation and influence inflammatory levels in macrophages has remained elusive. To address this question, this study utilized genetic approaches and a combination of molecular and cellular methods, including conditional TGFβ receptor knockout mice, human cells, RNAseq, ATACseq and Cut & Run‐seq. The results reveal that the TGFβ signaling functions as a vital homeostatic pathway, curtailing uncontrolled inflammation in macrophages in response to TNF. Conversely, TNF employs two previously unrecognized mechanisms to suppress the TGFβ signaling. These mechanisms encompass epigenetic inhibition and RBP‐J‐mediated inhibition of the TGFβ signaling pathway by TNF. These mechanisms empower TNF to diminish the antagonistic influence exerted by the TGFβ signaling pathway, ultimately enhancing TNF's capacity to induce heightened levels of inflammation. This reciprocal suppression dynamic between TNF and the TGFβ signaling pathway holds unique physiopathological significance, as it serves as a crucial “braking” mechanism. The balance between TNF levels and the activity of the endogenous TGFβ signaling pathway plays a pivotal role in determining the overall extent of inflammation. The potential for therapeutically augmenting the TGFβ signaling pathway presents an intriguing avenue for countering the impact of TNF and, consequently, developing innovative strategies for inflammation control.
Scoping Review of Wounds in Hospitalized Adults with COVID-19 Over the First Three Years of the Pandemic
Authors: Bart Jennifer , Phillips Cristina , Bailey Meghan , Dunn Elizabeth C. , Ansell Margaret , DeCarvalho Magali R. , Lyon Debra E.
Published: June 2024

Objective

To synthesize the literature on skin failure and pressure injuries among hospitalized patients with COVID-19.

Data Sources

An electronic literature search using relevant keywords and controlled vocabulary was conducted in March 2023 on MEDLINE/PubMed, Embase, and CINAHL. Manual citation searches of included articles and grey literature, including the Wound, Ostomy, and Continence Nurses Society website were performed. Articles published in English between 2020 and April 2023 were considered.

Study Selection

Articles were included if they reported on COVID-19 positive hospitalized adults with wounds that were not present upon admission. A total of 31 articles met these criteria.

Data Extraction

Covidence was used to extract the data and was reviewed by multiple team members.

Data Synthesis

Of the 31 studies, 27 reported new onset skin lesions during hospitalization. Wounds were classified as pressure injuries, skin failure, livedo racemosea and/or, retiform purpura, and associated with microvascular thrombosisthrombotic vasculopathy. Most pressure injuries were associated with prone position and affected patients often had multiple comorbidities including hypertension, diabetes mellitus, end-stage renal disease, heart disease, and COPD. Four articles highlighted an increased risk of new onset wounds, and three emphasized the importance of distinguishing deep tissue pressure injuries from ischemic-related lesions in patients with COVID-19.

Conclusions

The evidence suggests an increased risk of ischemic lesions and pressure injuries (PI) in patients with COVID-19 infection. This phenomenon may have inflated the numbers of PI during the pandemic and adversely affected nursing quality measures in acute care environments.
An Allergic Reaction in Contrast-enhanced Ultrasound Lymphography for Lymphovenous Bypass Surgery
Authors: Rames Jess D. , Tran Nho V. , Hesley Gina K. , Fahradyan Vahe , Lee Christine U.
Published: June 2024

Lymphedema following oncologic intervention can cause significant lifelong morbidity for patients in whom conservative management fails. The associated swelling, discomfort, pain, and recurrent cellulitis greatly diminish quality of life. Surgical procedures, including suction-assisted lipectomy, lymphovenous anastomosis (LVA), and vascularized lymph node transfers, show effectiveness in both volume reduction in affected extremities and symptom relief. However, the success of procedures like LVA is dependent on effective preoperative lymphatic mapping to identify suitable vessels for anastomosis. Traditional superficial lymphatic mapping uses near infrared fluorescence indocyanine green (ICG) imaging. Moreover, recent advances in contrast-enhanced ultrasound (CEUS) lymphography increased lymphovenous bypass target identification for LVA in the extremities.7 CEUS lymphography uses microbubbles as a contrast-enhancing agent injected intradermally into the affected extremity with subsequent identification of superficial collecting lymphatic vessels using ultrasound. Although a recent report noted an uptick in severe and critical adverse drug reactions to an ultrasound contrast agent injected intravenously in stress echocardiography, adverse drug reactions associated with ultrasound contrast-enhancing agents in body ultrasound are rare. The safety profile and potential complications from CEUS lymphography in the lymphedema population have yet to be fully characterized. In this case report, the authors present the first cutaneous adverse drug event following a secondary exposure to the contrast used for CEUS imaging. Mechanisms and justifications for an immune-mediated process are explored, and a review of similar manifestations in other related contrast applications is discussed.