bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urothelial carcinoma in situ with “early papillary formation” vs “lateral spread/shoulder lesion” of prior high-grade noninvasive papillary urothelial carcinoma: A survey of pathologist and urologist interpretations
Authors: Sangoi Ankur R , Shahabi Ali , Hirsch Michelle S , Kao Chia-Sui (Sunny) , Deebajah Mustafa , Barletta Justine A , Paner Gladell P , Smith Steven C , Grignon David J , Compérat Eva , Amin Mahul B , Maclean Fiona , Shah Rajal B , Iczkowski Kenneth A , Delprado Warick , Cheng Liang , Pan Chin-Chen , McKenney Jesse K , Ro Jae Y , Khani Francesca , Montironi Rodolfo , Robinson Brian D , Al-Ahmadie Hikmat , Epstein Jonathan I , Trpkov Kiril , Tretiakova Maria , Shen Steven S , Alanee Shaheen , Weight Christopher J , Akgul Mahmut , Williamson Sean R 
Published: December 2024

ABSTRACT

Objectives
Urothelial carcinoma in situ (CIS) with early papillary formation is terminology sometimes used to suggest incipient high-grade papillary urothelial carcinoma (PUC) but may lead to confusion between true CIS and lateral flat spread of PUC.

Methods
It remains unclear how pathologists and urologists interpret this scenario, so a survey was circulated to 68 pathologists (group 1 = 28 academic genitourinary pathologists; group 2 = 17 pathologists with a self-reported genitourinary focus; group 3 = 23 pathologists self-reported as not genitourinary specialists) and 32 urologists.

Results
Regarding atypical urothelial lesions that appear mainly flat but contain possible papillae, group 3 was more likely to label this as CIS compared with groups 1 and 2 (35% for group 3 vs 13% for groups 1 and 2), while groups 1 and 2 more often adopted another descriptive diagnosis, such as “CIS with early papillary features” (38% for groups 1 and 2 vs 13% for group 3). Among all 3 groups, group 1 was most likely to diagnose concomitant CIS and PUC in the same specimen but in different tissue fragments (58%). Pagetoid spread was reported to favor CIS predominantly by group 1 (61%). Urologists felt that the term lateral spread/shoulder was unclear (75%) and preferred early PUC (44%) or PUC with early growth (44%). Half (53%) of urologists felt that reporting CIS instead of lateral spread of PUC would change management.

Conclusions
Documentation of flat lesions lacks consensus among pathologists and may benefit from standardized terminology. Moreover, the distinction between CIS and early or lateral spread of PUC is not always clear to urologists and can influence disease management.
Development of a nano-specific safe-by-design module to identify risk management strategies
Authors: Ben Jeddi Hasnae , Goede Henk , Franken Remy , van Someren Eugene , Shandilya Neeraj , Vermoolen Ruby , Steck Josephine , Artous Sebastien , Hermosilla Jorge Salvador , Fransman Wouter 
Published: December 2024

Abstract
This article describes the development of a Safe-by-Design (SbD) module and its integration into an easy-to-use tool, named the Nano Exposure Quantifier—Safe-by-Design (NEQ-SbD) tool. The NEQ-SbD tool guides its user to lower the exposure to nanomaterials at the worksite where nanomaterials are manipulated or handled during a wide range of activities. This allows the tool user with an informed decision to assess airborne exposure and to select, compare, and identify appropriate risk management measures (RMM). The SbD module was developed using various information sources that can support and guide the SbD process, including the (i) RMM effectiveness based on analyses of an Exposure Control Efficacy Library (ECEL), (ii) RMM performance using a Computational Fluid Dynamics (CFD) model, (iii) e-cards based on a qualitative analysis of RMM information sources, and (iv) guidance for SbD strategy using an exposure directionality assessment. This information has been integrated in the user interface of the SbD module and NEQ-SbD tool to facilitate the SbD decision-making process. The SbD concept applied in the integrated NEQ-SbD tool introduces a comparison between a baseline exposure assessment and an (improved) SbD exposure assessment. The integrated NEQ-SbD tool consists of 4 modules including (i) a baseline exposure assessment, (ii) baseline results, (iii) SbD assessment, and (iv) SbD comparative results. The main purpose of the SbD module lies in guiding the user to the most sensitive (exposure) parameters and allowing a side-by-side comparison of potentially suitable RMMs. The integrated NEQ-SbD tool also offers a tiered approach and seamlessly shifts from a tier-1 to tier-2 uncertainty of an exposure assessment. The SbD module is illustrated using a worked example for the transfer of nano powders, showing the possibility of identifying SbD solutions for both safe-by-process and safe-by-material design purposes. The NEQ-SbD tool is a valuable tool for the SbD of nanomaterials and as a decision-making tool to support SbD risk management strategies that lead to minimizing health risks associated with occupational exposures.
Inhibition of shoot branching in Arabidopsis by the artificially biosynthesized canonical strigolactone
Authors: Mizutori Yuki , Nishiyama Kotaro , Seto Yoshiya 
Published: December 2024

Abstract
Strigolactones (SLs) are apocarotenoid plant hormones that regulate shoot branching. The natural SLs can be divided into 2 groups, canonical and noncanonical SLs, according to those chemical structures. In a model plant, Arabidopsis thaliana, it has been thought to produce only noncanonical SLs. Moreover, in rice, it was suggested that canonical-SL such as 4-deoxyorobanchol (4DO) does not have a critical role in shoot branching inhibition. In this report, to understand the potential of canonical-SL in the shoot branching inhibition pathway in Arabidopsis, SL biosynthetic genes involved in canonical-SL production in other plant species were individually expressed in Arabidopsis. Our data clearly demonstrate that 5-deoxystrigol, but not 4DO, can inhibit shoot branching in Arabidopsis. Moreover, the results confirmed the important role of CLA methyltransferase in the shoot branching inhibition pathway in Arabidopsis.
Type I interferon and mitochondrial dysfunction are associated with dysregulated cytotoxic CD8+ T cell responses in juvenile systemic lupus erythematosus
Authors: Radziszewska Anna , Peckham Hannah , Restuadi Restuadi , Kartawinata Melissa , Moulding Dale , de Gruijter Nina M , Robinson George A , Butt Maryam , Deakin Claire T , Wilkinson Meredyth G Ll , Wedderburn Lucy R , Jury Elizabeth C , Rosser Elizabeth C , Ciurtin Coziana 
Published: December 2024

Abstract
Juvenile systemic lupus erythematosus (JSLE) is an autoimmune condition which causes significant morbidity in children and young adults and is more severe in its presentation than adult-onset SLE. While many aspects of immune dysfunction have been studied extensively in adult-onset SLE, there is limited and contradictory evidence of how cytotoxic CD8+ T cells contribute to disease pathogenesis and studies exploring cytotoxicity in JSLE are virtually non-existent. Here, we report that CD8+ T cell cytotoxic capacity is reduced in JSLE versus healthy controls, irrespective of treatment or disease activity. Transcriptomic and serum metabolomic analysis identified that this reduction in cytotoxic CD8+ T cells in JSLE was associated with upregulated type I interferon (IFN) signalling, mitochondrial dysfunction, and metabolic disturbances when compared to controls. Greater interrogation of the influence of these pathways on altered cytotoxic CD8+ T cell function demonstrated that JSLE CD8+ T cells had enlarged mitochondria and enhanced sensitivity to IFN-α leading to selective apoptosis of effector memory (EM) CD8+ T cells, which are enriched for cytotoxic mediator-expressing cells. This process ultimately contributes to the observed reduction in CD8+ T cell cytotoxicity in JSLE, reinforcing the growing evidence that mitochondrial dysfunction is a key pathogenic factor affecting multiple immune cell populations in type I IFN-driven rheumatic diseases.
Intravenous amino acid for kidney protection: current understanding and future perspectives
Authors: Kotani Yuki , Baiardo Redaelli Martina , Pruna Alessandro , Losiggio Rosario , Cocozza Susanna , Ti Lian Kah , Bradic Nikola , Comis Marco , Landoni Giovanni , Bellomo Rinaldo 
Published: December 2024

ABSTRACT
Acute kidney injury (AKI) is a common complication in critically ill and perioperative patients and is associated with mortality, morbidity, medical costs, and progression to chronic kidney function. Unfortunately, despite numerous research efforts, until recently, there was no AKI preventive therapy supported by level 1 evidence. Among the several factors that contribute to renal damage, two of the major triggers of AKI development are renal hypoperfusion and renal medullary hypoxia. The intravenous administration of a mixture of amino acids promotes the prevention of AKI through multiple mechanisms: the recruitment of renal functional reserve, increased renal blood flow, and improvements in renal oxygenation. Such mechanisms of action led to increased glomerular filtration rate and urine output in preclinical and pilot clinical studies. To test if these benefits on physiological parameters could be translated into clinically meaningful outcomes, a multicenter, randomized, placebo-controlled, trial was conducted in the cardiac surgery setting. Among 3511 adult patients undergoing elective cardiac surgery with cardiopulmonary bypass, intravenous amino acid administration, compared to placebo, significantly reduced the occurrence of AKI, providing the first level 1 evidence of an effective treatment for AKI prevention. In this review, we provide the epidemiology and pathophysiology of cardiac surgery-associated AKI and the concept of renal functional reserve. Then, we summarize the underlying mechanisms of intravenous amino acid infusion as a renoprotective strategy and its preclinical and clinical evidence. Finally, we discuss the existing evidence gaps and future directions of this promising intervention.
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images
Authors: Shahzad Muhammad , Shirazi Syed Hamad , Yaqoob Muhammad , Khan Zakir , Rasheed Assad , Ahmed Sheikh Israr , Hayat Asad , Zhou Huiyu 
Published: December 2024

Abstract
Visual analysis of peripheral blood smear slides using medical image analysis is required to diagnose red blood cell (RBC) morphological deformities caused by anemia. The absence of a complete anaemic RBC dataset has hindered the training and testing of deep convolutional neural networks (CNNs) for computer-aided analysis of RBC morphology. We introduce a benchmark RBC image dataset named Anemic RBC (AneRBC) to overcome this problem. This dataset is divided into two versions: AneRBC-I and AneRBC-II. AneRBC-I contains 1000 microscopic images, including 500 healthy and 500 anaemic images with 1224 × 960 pixel resolution, along with manually generated ground truth of each image. Each image contains approximately 1550 RBC elements, including normocytes, microcytes, macrocytes, elliptocytes, and target cells, resulting in a total of approximately 1 550 000 RBC elements. The dataset also includes each image’s complete blood count and morphology reports to validate the CNN model results with clinical data. Under the supervision of a team of expert pathologists, the annotation, labeling, and ground truth for each image were generated. Due to the high resolution, each image was divided into 12 subimages with ground truth and incorporated into AneRBC-II. AneRBC-II comprises a total of 12 000 images, comprising 6000 original and 6000 anaemic RBC images. Four state-of-the-art CNN models were applied for segmentation and classification to validate the proposed dataset.
Database URL: https://data.mendeley.com/datasets/hms3sjzt7f/1
Granulomatous inflammatory responses are elicited in the liver of PD-1 knockout mice by de novo genome mutagenesis
Authors: Nagaretnam Ilamangai , Kakimoto Yoshiya , Yoneshige Azusa , Takeuchi Fuka , Sakimura Takayuki , Sato Kanato , Osaki Yoshiro , Ishii Yuta , Ozaki Ai , Tamura Masaru , Hamada Michito , Shigeoka Toshiaki , Ito Akihiko , Ishida Yasumasa 
Published: December 2024

Abstract

Introduction
Programmed death-1 (PD-1) is a negative regulator of immune responses. Upon deletion of PD-1 in mice, symptoms of autoimmunity developed only after they got old. In a model experiment in cancer immunotherapy, PD-1 was shown to prevent cytotoxic T lymphocytes from attacking cancer cells that expressed neoantigens derived from genome mutations. Furthermore, the larger number of genome mutations in cancer cells led to more robust anti-tumor immune responses after the PD-1 blockade. To understand the common molecular mechanisms underlying these findings, we hypothesize that we might have acquired PD-1 during evolution to avoid/suppress autoimmune reactions against neoantigens derived from mutations in the genome of aged individuals.

Methods
To test the hypothesis, we introduced random mutations into the genome of young PD-1–/– and PD-1+/+ mice. We employed two different procedures of random mutagenesis: administration of a potent chemical mutagen N-ethyl-N-nitrosourea (ENU) into the peritoneal cavity of mice and deletion of MSH2, which is essential for the mismatch-repair activity in the nucleus and therefore for the suppression of accumulation of random mutations in the genome.

Results
We observed granulomatous inflammatory changes in the liver of the ENU-treated PD-1 knockout (KO) mice but not in the wild-type (WT) counterparts. Such lesions also developed in the PD-1/MSH2 double KO mice but not in the MSH2 single KO mice.

Conclusion
These results support our hypothesis about the physiological function of PD-1 and address the mechanistic reasons for immune-related adverse events observed in cancer patients having PD-1-blockade immunotherapies.
Management of dyslipidaemia in patients with comorbidities—facing the challenge
Authors: Frühwald Lisa , Fasching Peter , Dobrev Dobromir , Kaski Juan Carlos , Borghi Claudio , Wassmann Sven , Huber Kurt , Semb Anne Grete , Agewall Stefan , Drexel Heinz 
Published: December 2024

Abstract
This review aims to examine the evidence on the benefits and risks of lipid-lowering drugs in patients with liver disease. Elevated liver enzyme levels often lead to cautious discontinuation of these drugs, potentially withholding from patients their benefit in reducing cardiovascular disease morbidity and mortality. Using a literature search of PubMed, we examine the efficacy and safety profiles of various lipid-lowering agents, including statins, ezetimibe, bempedoic acid, PCSK9 inhibitors, fibrates, and icosapent ethyl, focusing particularly on their potential side effects related to liver health. A major challenge in the assessment of drug-induced hepatotoxicity is the fact that it relies heavily on case reports rather than real-world evidence. There is currently a lack of robust evidence on lipid-lowering therapy in people with pre-existing liver disease. Nevertheless, we have attempted to summarize the available data for all the drugs mentioned in order to provide guidance for the treatment of patients with liver dysfunction. This review highlights the need for further research to optimize treatment strategies for patients with coexisting liver and cardiovascular disease.
Bioaugmentation to enhance degradation of acetochlor and pretilachlor in water and sediment under anaerobic conditions
Authors: Duc Ha Danh , Oanh Nguyen Thi 
Published: December 2024

Abstract
Chloroacetamide herbicides are widely used to control weeds globally. In this study, three acetochlor-degrading mixed cultures using nitrate, sulfate, and ferric iron as electron acceptors were isolated and determined for their degradation under anaerobic conditions. The degradation rates of all mixed pure cultures in a mineral medium were not much different at 1 µM, while the rates at 50 µM were in the order: mixed culture using nitrate &gt; sulfate &gt; ferric iron as electron acceptors, giving 6.70, 6.13, and 4.85 µM/day, respectively. During acetochlor degradation, 2-ethyl-6-methyl-N-(ethoxymethyl)acetanilide, N-2-ethylphenyl acetamide, and 2-ethylaniline were transiently produced. Interestingly, the mixture of all cultures synergistically degraded pretilachlor although no individual strains could degrade the compound. Toluene and 2-ethylaniline were metabolites of pretilachlor degradation by the acetochlor-degrading bacteria. However, pretilachlor inhibited the acetochlor degradation by acetochlor-degrading bacteria. The inoculation of both acetochlor- and pretilachlor-degrading bacteria resulted in 91.4 ± 2.1% of acetochlor and 82.4 ± 2.6% of pretilachlor being utilized for 7 days. Moreover, the introduction of these degrading bacteria accelerated the degradation of both substrates contaminating water and sediment collected from a pond. This study provides insights into anaerobic degradation by pure cultures using different electron acceptors.
A novel method for telomere length detection in fission yeast
Authors: Mohamed Hadeel A B Elnaim , Agus Hizlan Hincal , Palabiyik Bedia 
Published: December 2024

Abstract
Fission yeast is the ideal model organism for studying telomere maintenance in higher eukaryotes. Telomere length has been directly correlated with life expectancy and the onset of aging-related diseases in mammals. In this study, we developed a novel simple, and reproducible method to measure the telomere length, by investigating the effect of caffeine and cisplatin on the telomere length in fission yeast. Hydroxyurea-synchronized fission yeast cells were exposed to 62 µM cisplatin and 8.67 mM caffeine treatments for 2 h, then their telomere lengths were evaluated with two different methods. First, the quantitative polymerase chain reaction (qPCR) assay was used as a confirmative method, where telomere length was determined relative to a single-copy gene in the genome. Second, the newly developed method standard polymerase chain reaction (PCR)/ImageJ assay assessed the telomere length based on the amplified PCR band intensity using a set of telomere primers, reflecting telomeric sequence availability in the genome. Both methods show a significant decrease and a notable telomere lengthening in response to cisplatin and caffeine treatments, respectively. The finding supports the accuracy and productivity of the standard PCR/ImageJ assay as it can serve as a quick screening tool to study the effect of suspected chemotherapeutic and antiaging drugs on telomere length in fission yeast.
Acute Severe Ulcerative Colitis and Cytomegalovirus During Pregnancy: A Case Report
Authors: Lelong Margaux , Bourreille Arnaud , Mosnier Jean-François , Trang-Poisson Caroline , Le Berre Catherine 
Published: December 2024

Lay Summary
This is the first case report of cytomegalovirus colitis following viral reactivation during pregnancy in a patient hospitalized for acute severe ulcerative colitis and treated with ganciclovir despite its teratogenic risk given her corticosteroid-refractory nature, with favorable outcomes after 3 years.
Listening and Preparing the Society to Engage: The Case of the Colombian Truth Commission and Its Legacy Strategy
Authors: Prada Ramírez María Paula , Wingender Leslie 
Published: December 2024

ABSTRACT
Reflections on the Colombian Truth Commission are timely to answer a question less explored in the transitional justice literature related to how transitional justice processes have been popularized and made accessible to the broader public, and moreover, how the various stakeholders have extended the fruits of transitional justice. In this note from the field, we offer our practitioner perspectives on the key enabling conditions and strategic moments in the development of the Commission’s legacy strategy that contributed to these outcomes. We examine how the Commission’s ethical and political framing of the listening exercises and its overall institutional structure led to a long-term peacebuilding project that continues to mobilize today through the work of the Trabajo en red con aliados or the Network of Allies. We unpack the key factors that foster ongoing mobilization of civil society and local government actors engaged in debating, implementing and grappling with the recommendations of the final report. This note provides new information for the debate about the value of networks and partnerships related to facing the truth and moving towards non-recurrence in transitional justice endeavors.
Host plant selection and performance of ambrosia beetles in flood-stressed versus ethanol-injected trees provide implications for management strategies
Authors: Cambronero-Heinrichs Juan Carlos , Ranger Christopher M , Santoiemma Giacomo , Cavaletto Giacomo , Carloni Francesca , Battisti Andrea , Meggio Franco , Rassati Davide 
Published: December 2024

Abstract
Ambrosia beetles (Curculionidae: Scolytinae and Platypodinae) are fungus-farming woodborers that can cause damage to the trees they colonize. Some of these beetles target stressed plants that emit ethanol, and management strategies have proposed using ethanol-injected trees as trap trees to monitor or divert dispersing adult females away from valuable crops. In this study, we used container-grown trees from 8 species to compare the effect of ethanol injection versus flooding on ambrosia beetle host selection and colonization success. Our aims were to understand whether ethanol injection is a suitable technique for different ambrosia beetle species and whether its effectiveness varies depending on the tree species used. In addition, we quantified the amount of ethanol in tree tissues to understand whether ethanol concentration could reflect observed differences among treatments and tree species. Our findings demonstrated that ethanol-injected trees were significantly more selected by both Xyleborinus saxesenii and Xylosandrus spp. and that significantly more adult beetles of both taxa emerged from ethanol-injected than flood-stressed trees. In addition, we showed that ethanol injection can trigger attacks by X. saxesenii and Xylosandrus spp. on a variety of deciduous tree species, nullifying the effects of the species-specific characteristics observed on flood-stressed trees, which can only partially be attributed to the amount of ethanol within the plant. This supported the idea that practitioners can potentially select any species of deciduous trees in management programs for ambrosia beetles based on ethanol-injected trees.