bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced levels of MRE11 cause disease phenotypes distinct from ataxia telangiectasia-like disorder
Authors: Hartlerode Andrea J , Mostafa Ahmed M , Orban Steven K , Benedeck Rachel , Campbell Koral , Hoenerhoff Mark J , Ferguson David O , Sekiguchi JoAnn M 
Published: June 2024

Abstract
The MRE11/RAD50/NBS1 (MRN) complex plays critical roles in cellular responses to DNA double-strand breaks. MRN is involved in end binding and processing, and it also induces cell cycle checkpoints by activating the ataxia-telangiectasia mutated (ATM) protein kinase. Hypomorphic pathogenic variants in the MRE11, RAD50, or NBS1 genes cause autosomal recessive genome instability syndromes featuring variable degrees of dwarfism, neurological defects, anemia, and cancer predisposition. Disease-associated MRN alleles include missense and nonsense variants, and many cause reduced protein levels of the entire MRN complex. However, the dramatic variability in the disease manifestation of MRN pathogenic variants is not understood. We sought to determine if low protein levels are a significant contributor to disease sequelae and therefore generated a transgenic murine model expressing MRE11 at low levels. These mice display dramatic phenotypes including small body size, severe anemia, and impaired DNA repair. We demonstrate that, distinct from ataxia telangiectasia-like disorder caused by MRE11 pathogenic missense or nonsense variants, mice and cultured cells expressing low MRE11 levels do not display the anticipated defects in ATM activation. Our findings indicate that ATM signaling can be supported by very low levels of the MRN complex and imply that defective ATM activation results from perturbation of MRN function caused by specific hypomorphic disease mutations. These distinct phenotypic outcomes underline the importance of understanding the impact of specific pathogenic MRE11 variants, which may help direct appropriate early surveillance for patients with these complicated disorders in a clinical setting.
Overview of crosstalk between stromal and epithelial cells in the pathogenesis of adenomyosis and shared features with deep endometriotic nodules
Authors: Zipponi Margherita , Cacciottola Luciana , Dolmans Marie-Madeleine 
Published: June 2024

Abstract
Since the first description of adenomyosis more than 150 years ago, multiple hypotheses have attempted to explain its pathogenesis. Indeed, research over recent years has greatly enhanced our knowledge of the underlying causes. This has opened up avenues for the development of strategies for both disease prevention and treatment of its main symptoms, such as pelvic pain, heavy menstrual bleeding, and infertility. However, the current means are still largely ineffective, so it is vital that we shed light on the pathways involved. Dysregulated mechanisms and aberrant protein expression have been identified as contributing factors in interactions between endometrial epithelial and stromal cells, ultimately leading to the growth of adenomyotic lesions. These include collective cell migration, epithelial-to-mesenchymal transition, hormonal influence, and signaling from non-coding RNAs and extracellular vesicles. We provide a concise summary of the latest insights into the crosstalk between glands and stroma in ectopic adenomyotic lesion formation. While there is an abundance of literature on similarities between adenomyosis and deep endometriosis, there are insufficient data on the cytochemical, molecular, and pathogenetic mechanisms of these two disorders. However, various shared features, including alterations of cell adhesion molecules, abnormal hormone regulation, and the presence of cancer-driving mutations and epigenetic modifications, have been identified. Nevertheless, the pathogenic mechanisms that contribute to the cause and development of these enigmatic diseases have not been fully elucidated yet.
Resistance and adaptation to globalization: Case studies of the Japanese textile industry
Authors: Tomita Terumasa 
Published: June 2024

Abstract
In the age of economic globalization, industries and corporations are increasingly faced with new market realities owing to the intensification of international competition. This study posits that corporations either use resistance through political voice or decide to restructure to adapt to these realities. Three Japanese textile industries with poor competitiveness were selected as case studies and were observed from the perspective of corporate survival strategies. The towel industry in Imabari City, Ehime Prefecture, implemented resistance through a voice strategy; the glove industry in Higashikagawa City, Kagawa Prefecture, chose to move manufacturing overseas as an adjustment strategy; and the uniform industry in Kurashiki City, Okayama Prefecture, chose to utilize foreign workers as another adjustment strategy. These findings address the gap between prior research on ‘adaptation’ and research on political ‘resistance’ and demonstrate that variations exist in the strategies employed by less competitive industries.
Transcriptomic insights into the shift of trophic strategies in mixotrophic dinoflagellate Lepidodinium in the warming ocean
Authors: Chen Jiawei , Deng Lixia , Pang Mengwen , Li Yingdong , Xu Zhimeng , Zhang Xiaodong , Liu Hongbin 
Published: June 2024

Abstract
The shift between photoautotrophic and phagotrophic strategies in mixoplankton significantly impacts the planktonic food webs and biogeochemical cycling. Considering the projected global warming, studying how temperature impacts this shift is crucial. Here, we combined the transcriptome of in-lab cultures (mixotrophic dinoflagellate Lepidodinium sp.) and the metatranscriptome dataset of the global ocean to investigate the mechanisms underlying the shift of trophic strategies and its relationship with increasing temperatures. Our results showed that phagocytosis-related pathways, including focal adhesion, regulation of actin cytoskeleton, and oxidative phosphorylation, were significantly stimulated in Lepidodinium sp. when cryptophyte prey were added. We further compared the expression profiles of photosynthesis and phagocytosis genes in Lepidodinium sp. in the global sunlit ocean. Our results indicated that Lepidodinium sp. became more phagotrophic with increasing temperatures when the ambient chlorophyll concentration was &gt;0.3 mg.m−3 (~20.58% of the ocean surface) but became more photoautotrophic with increasing temperatures when the chlorophyll concentration was between 0.2 and 0.3 mg.m−3 (~11.47% of the ocean surface). Overall, we emphasized the crucial role of phagocytosis in phago-mixotrophy and suggested that the expression profile of phagocytosis genes can be a molecular marker to target the phagotrophic activity of mixoplankton in situ.
Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery
Authors: Huang Biyan , Xiao Yao , Zhang Yan 
Published: June 2024

Abstract
Selenocysteine (Sec) is encoded by the UGA codon that normally functions as a stop signal and is specifically incorporated into selenoproteins via a unique recoding mechanism. The translational recoding of UGA as Sec is directed by an unusual RNA structure, the SECIS element. Although archaea and eukaryotes adopt similar Sec encoding machinery, the SECIS elements have no similarities to each other with regard to sequence and structure. We analyzed &gt;400 Asgard archaeal genomes to examine the occurrence of both Sec encoding system and selenoproteins in this archaeal superphylum, the closest prokaryotic relatives of eukaryotes. A comprehensive map of Sec utilization trait has been generated, providing the most detailed understanding of the use of this nonstandard amino acid in Asgard archaea so far. By characterizing the selenoproteomes of all organisms, several selenoprotein-rich phyla and species were identified. Most Asgard archaeal selenoprotein genes possess eukaryotic SECIS-like structures with varying degrees of diversity. Moreover, euryarchaeal SECIS elements might originate from Asgard archaeal SECIS elements via lateral gene transfer, indicating a complex and dynamic scenario of the evolution of SECIS element within archaea. Finally, a roadmap for the transition of eukaryotic SECIS elements from archaea was proposed, and selenophosphate synthetase may serve as a potential intermediate for the generation of ancestral eukaryotic SECIS element. Our results offer new insights into a deeper understanding of the evolution of Sec insertion machinery.
Creating a next-generation phenotype library: the health data research UK Phenotype Library
Authors: Thayer Daniel S , Mumtaz Shahzad , Elmessary Muhammad A , Scanlon Ieuan , Zinnurov Artur , Coldea Alex-Ioan , Scanlon Jack , Chapman Martin , Curcin Vasa , John Ann , DelPozo-Banos Marcos , Davies Hannah , Karwath Andreas , Gkoutos Georgios V , Fitzpatrick Natalie K , Quint Jennifer K , Varma Susheel , Milner Chris , Oliveira Carla , Parkinson Helen , Denaxas Spiros , Hemingway Harry , Jefferson Emily 
Published: June 2024

AbstractObjectiveTo enable reproducible research at scale by creating a platform that enables health data users to find, access, curate, and re-use electronic health record phenotyping algorithms.Materials and MethodsWe undertook a structured approach to identifying requirements for a phenotype algorithm platform by engaging with key stakeholders. User experience analysis was used to inform the design, which we implemented as a web application featuring a novel metadata standard for defining phenotyping algorithms, access via Application Programming Interface (API), support for computable data flows, and version control. The application has creation and editing functionality, enabling researchers to submit phenotypes directly.ResultsWe created and launched the Phenotype Library in October 2021. The platform currently hosts 1049 phenotype definitions defined against 40 health data sources and &gt;200K terms across 16 medical ontologies. We present several case studies demonstrating its utility for supporting and enabling research: the library hosts curated phenotype collections for the BREATHE respiratory health research hub and the Adolescent Mental Health Data Platform, and it is supporting the development of an informatics tool to generate clinical evidence for clinical guideline development groups.DiscussionThis platform makes an impact by being open to all health data users and accepting all appropriate content, as well as implementing key features that have not been widely available, including managing structured metadata, access via an API, and support for computable phenotypes.ConclusionsWe have created the first openly available, programmatically accessible resource enabling the global health research community to store and manage phenotyping algorithms. Removing barriers to describing, sharing, and computing phenotypes will help unleash the potential benefit of health data for patients and the public.
Contemporary International Criminal Law After Critique
Authors: Burgis-Kasthala Michelle , Sander Barrie 
Published: June 2024

Abstract
Contemporary international criminal law (ICL) is a well-established field of scholarship and practice that wields significant influence in framing how certain events come to be understood and acted upon. Yet, as the field has increasingly captured the public’s attention and imagination, a body of critical scholarship has risen in prominence that seeks to test and challenge ICL’s underlying assumptions. In such a climate, this article suggests that ICL not only has moved beyond its inception and consolidation phases, but is beginning to emerge from its critical period towards a ‘post-critical’ phase where critique is becoming increasingly normalized within the field, with both reformist and structurally oriented reappraisals more readily acknowledged within ICL’s imaginary. Situated in this ‘post-critical’ moment, this article examines the extent to which the vocabulary and institutions of ICL may be productively (re-)engaged in the pursuit of emancipatory ends. After providing an overview of the strands of critique that have become increasingly prominent, we reflect on three avenues for engaging with the field of ICL ‘after critique’: first, critical engagement, centred on a commitment to revealing and detailing silenced and marginalized experiences and methods within the field itself; second, tactical and strategic engagement, which points to the ways in which actors choose to engage with imperfect legal frameworks for particular struggles; and finally, decolonial and abolitionist (dis-)engagement which takes as its point of departure the rejection of both colonial and carceral logics per se, especially in light of their historical and persisting patterns of patriarchal and racialized domination. Ultimately, in linking ICL with historical and contemporary anti-colonial and anti-carceral struggles, we seek not only to disrupt ICL progress narratives, but also to show how earlier, often-sidelined ways of imagining forms of harm and their repair may provide potentially more productive ways of engaging with ICL ‘after critique’.
Termite IPM in historic sites
Authors: Su Nan-Yao 
Published: June 2024

Abstract
Given the traditional use of wood, historical structures are susceptible to termite damage which can irreversibly affect their historical significance. Methods like drilling into the foundation for termiticide injection are impractical and potentially harmful to the structural integrity of these structures. Moreover, the location of these structures in ecologically sensitive areas prohibits the use of soil termiticides due to potential contamination of groundwater, rivers, or oceans. Termite Integrated Pest Management (IPM) strategies include baiting programs that use minimal quantities of benign insecticides to reduce environmental impact. This approach is consistent with the risk management component of termite IPM. Bait systems are proven to be effective in eliminating termite colonies, contributing to the benefit component of IPM by preserving the value of historical sites. This article discusses successful baiting interventions at notable locations such as the Statue of Liberty National Monument, New York, USA, the Christiansted National Historic Site in St. Croix, US Virgin Islands, and the Historic Tzu-Su Temple in Taiwan.
Advancing clinical trial equity through integration of telehealth and decentralized treatment
Authors: Brown Eleanor , Fisher George Albert , Shelton Andrew , Chang Daniel T , Pollom Erqi 
Published: June 2024

Abstract
Innovative strategies to increase clinical trial accessibility and equity are needed. We conducted a retrospective review of a phase II investigator-initiated trial to determine whether the modification of clinical trial design to decentralize study treatment can improve trial accessibility among underrepresented groups. Sociodemographic characteristics, including area deprivation indices, as well as study site travel distance, time, and costs were compared between enrolled participants who received chemotherapy locally and participants who did not. Participants who received chemotherapy locally lived substantially farther from the study site (median = 95.90 vs 25.20 miles, P = .004), faced a greater time burden traveling to the study site (median = 115.00 vs 34.00 minutes, P = .002), and had higher travel-related costs for a single trip to the study site (median = $62.81 vs $16.51, P = .004). This study highlights opportunities for alleviating financial and time burdens associated with clinical trial participation, promoting equity in clinical research.
Trial Registration: ClinicalTrials.gov identifier: NCT04380337.
(032) A REVIEW OF VESTIBULECTOMY PATHOLOGY FINDINGS AND A CALL TO ACTION TO STANDARDIZE PATHOLOGY REPORTING
Authors: Dumas K , Mikkilineni A , Odenwald E , Bahng J , Krapf J , Goldstein A , Cigna S 
Published: June 2024

Abstract

Introduction
There is no standardization for pathology reporting of vestibulectomy specimens. Our current understanding of neuroproliferative vestibulodynia is limited, but it is understood to be mediated by the accumulation c-afferent nociceptors and mast cells. Histopathology is fundamental to our understanding of disease mechanism and treatment. Given how much remains unknown about the histology, physiology, and neuroplasticity of the vestibule, it is imperative that we take every opportunity to fully examine this tissue and its complex role in pain.

Objective
Describe current pathology reporting practices for vestibulectomy specimens

Methods
Data was collected using Epic and Cerner report tools to identify any patients between 1/2017 to 10/2023 with a surgical history of vestibulectomy. Forty-five patients were identified & confirmed to have a history of vestibulectomy. Charts were reviewed to locate surgical pathology reports (available through hospital EMR, CRISP, or Care Everywhere).

Results
Pathology reports were available for 37 patients. Thirty-one of these reports (84%) were from our own institution; six reports were from outside hospitals. Marked variability in pathology reporting was noted between pathologists and institutions. All but one pathology report notes inflammation. The one report that does not include language about inflammation only notes “negative for dysplasia or malignancy”. Twenty-nine reports comment on the absence of dysplasia, including two reports from other institutions. All pathology reports from our institution (100%), note lymphoid infiltrate; however, this is not noted on any of the 6 pathology reports from other hospitals. Nineteen of the 31 specimens (61%) examined at our institution included specific stains to test for mast cells and nerve fibers. Nineteen specimens were evaluated with Giemsa staining and 8 specimens were evaluated with CD117 staining to assess for mast cell density (measured in mast cells/hpf). The range of mast cell density was 1/hpf to 25/hpf, and the average mast cell density was 8.1/hpf. All 19 specimens stained with S100 noted a relative increase in nerve fibers in the superficial dermis.

Conclusions
Histopathology is a window of opportunity to better understand the pathophysiology of neuroproliferative vestibulodynia. There is no standard when it comes to examining and reporting on vestibulectomy specimens. This results in reporting inconsistencies, which limits our ability to compile data and draw clinical conclusions. As surgeons we can collaborate to advance our understanding of the pathophysiology of vestibulodynia. This starts with communicating with our pathology colleagues, requesting appropriate stains, and setting a standard for reporting.

Disclosure
Any of the authors act as a consultant, employee or shareholder of an industry for: Patty Brisben Foundation.
(033) ABSENCE OF GENDER-AFFIRMING HYSTERECTOMIES FROM HYSTERECTOMY SEXUAL FUNCTION OUTCOMES LITERATURE
Authors: De Moya A , Watson K , Rowen T 
Published: June 2024

Abstract

Introduction
Gender affirming healthcare is a multidisciplinary field that includes (but is not limited to) the following interventions: hormonal therapy and gender affirming surgery (chest surgery, hysterectomy, oophorectomy, metoidioplasty, phalloplasty, etc.). Gender-affirming hormone therapy has been shown to positively impact orgasm duration and satisfaction level among both transgender men and women. Research on sexual wellbeing after gender affirming surgery (GAS) indicates positive effects on sexual health outcomes; however, the literature lacks sufficient studies to make evidence-based recommendations.

Objective
To synthesize and review the current state of literature on sexual outcomes following gender affirming hysterectomies as background to inform a planned study on this topic.

Methods
This project is a literature review of peer-reviewed journal articles on sexual function and pleasure outcomes following hysterectomies, with a particular focus on gender affirming hysterectomies. We considered various cohort studies, systematic reviews, position statements, and meta-analyses in our review.

Results
No research currently exists on sexual function or orgasm experience after gender affirming hysterectomy. Current literature exploring sexual function post-hysterectomy only includes cisgender populations (indications typically include cancer risk reduction, pelvic pain, and/or abnormal uterine bleeding). Studies have found mixed results regarding sexual function in cisgender women post-hysterectomy and/or oophorectomy, including changes to anxiety and depression, sexual health and wellness, both in a positive and negative direction. Other analyses found no significant change in sexual function post-hysterectomy in cisgender women. Based on these findings, hysterectomies have mixed effects on sexual satisfaction & function in cisgender populations but there is no data to guide transgender populations.

Conclusions
More research is needed on sexual health outcomes (i.e., sexual pleasure, arousal, and orgasm) after gender affirming surgery, as very few studies examine the role of sexual function, including desire, arousal, pain and orgasm in patients’ lives post-GAS. No studies investigate sexual satisfaction post-gender affirming hysterectomy despite it being an important GAS for transgender men. Research on this procedure in this specific population will inform evidence-based practices and recommendations, elucidate sex outcomes when the main indication for a hysterectomy is gender affirmation, and advance our understanding of sexual pleasure overall. This author team is initiating a study to address this critical question.

Disclosure
No.
(100) MASTURBATION: AN UNDERUTILIZED TREATMENT?
Authors: Dubinskaya A , Toubi K , Anger J , Eilber K 
Published: June 2024

Abstract

Introduction
Certain types of masturbation have been shown to affect genital and genitourinary health. However, the full range of health benefits associated with masturbation and its various forms remains inadequately studied.

Objective
This study aimed to investigate the literature addressing utilization of masturbation for various health conditions among females.

Methods
We conducted a systematic literature review of PubMed, Embase, and Medline from January 1980 to November 2023, adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search incorporated keywords such as “masturbation,” “sexual pleasure,” “benefits of masturbation,” “sexual self-stimulation,” “solo sex,” “onanism,” and “self-pleasure.” Inclusion criteria for the analysis were clinical trials, cohort studies, and reviews with cisgender women over 18 years old as participants, and masturbation utilized as an intervention. Exclusion criteria were case reports, surveys, studies involving men, or those with a history of gender dysphoria.

Results
A total of 176 studies were initially identified. Only five studies met all inclusion and exclusion criteria. Among these, four were clinical trials, and one was a systematic review. All but one study investigated the role of masturbation in the ability to orgasm with or without a partner. Orgasmic function was noted to be improved among participants in these four studies. One study investigated the endocrine changes associated with orgasm and found a significant elevation in post-orgasmic prolactin, similar to men. Participants in all the studies were cisgender women aged 18 to 55, predominantly heterosexual. The intervention duration ranged from 10 minutes per session to multiple sessions over the course of five weeks, with only one study specifying the mode of masturbation (vibrators). Four of the studies used erotica and pornography as augmentation to masturbation, and a partner was involved in the intervention in two of the studies. Only one study employed formal quantitative methods for outcome assessment.

Conclusions
Masturbation has primarily been investigated as an intervention for orgasmic dysfunction. There is a significant need for studies examining different types of masturbation and their effects on general and genitourinary health.

Disclosure
No.