bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient optimization of an accelerator neutron source for neutron capture therapy using genetic algorithms
Authors: Ge Yulin , Zhong Yao , Murata Isao , Tamaki Shingo , Yuan Nan , Sun Yanbing , Ma Wei , Zou Liping , Yang Zhen , Lu Liang 
Published: May 2024

AbstractBackgroundIn recent years, genetic algorithms have been applied in the field of nuclear technology design, producing superior optimization results compared to traditional methods. They can be employed in the design and optimization of beam shaping assemblies (BSA) BSA to obtain the desired neutron beams. But it should be noted that the direct combination of Monte Carlo methods with genetic algorithms requires a significant amount of computational resources and time.PurposeDesign and optimize BSA more efficiently to achieve neutron beams that meet specified recommendations.MethodsWe propose an approach of NSGA II with crucial variables which are identified by multivariate statistical techniques. This approach significantly reduces the problem sizes, thus reducing the time required for optimization. We illustrate this methodology using the example of BSA design for AB‐BNCT.ResultsThe computational efficiency has tripled with crucial variables. By using NSGA II, we obtained optimized models conforming to both the new and old version IAEA BNCT guidelines through a single optimization process and subjected them to phantom analysis. The results demonstrate that models obtained through this method can meet the IAEA recommendations with deep advantage depth (AD) and high absorbed ratio (AR).ConclusionThe genetic algorithm with crucial variables displays tremendous potential in addressing BSA optimization challenges.
Genetic and epigenetic alterations in precursor lesions of endometrial endometrioid carcinoma
Authors: Gotoh Osamu , Sugiyama Yuko , Tonooka Akiko , Kosugi Mayuko , Kitaura Sunao , Minegishi Ryu , Sano Masatoshi , Amino Sayuri , Furuya Rie , Tanaka Norio , Kaneyasu Tomoko , Kumegawa Kohei , Abe Akiko , Nomura Hidetaka , Takazawa Yutaka , Kanao Hiroyuki , Maruyama Reo , Noda Tetsuo , Mori Seiichi 
Published: May 2024

AbstractThe hyperplasia–carcinoma sequence is a stepwise tumourigenic programme towards endometrial cancer in which normal endometrial epithelium becomes neoplastic through non‐atypical endometrial hyperplasia (NAEH) and atypical endometrial hyperplasia (AEH), under the influence of unopposed oestrogen. NAEH and AEH are known to exhibit polyclonal and monoclonal cell growth, respectively; yet, aside from focal PTEN protein loss, the genetic and epigenetic alterations that occur during the cellular transition remain largely unknown. We sought to explore the potential molecular mechanisms that promote the NAEH–AEH transition and identify molecular markers that could help to differentiate between these two states. We conducted target‐panel sequencing on the coding exons of 596 genes, including 96 endometrial cancer driver genes, and DNA methylome microarrays for 48 NAEH and 44 AEH lesions that were separately collected via macro‐ or micro‐dissection from the endometrial tissues of 30 cases. Sequencing analyses revealed acquisition of the PTEN mutation and the clonal expansion of tumour cells in AEH samples. Further, across the transition, alterations to the DNA methylome were characterised by hypermethylation of promoter/enhancer regions and CpG islands, as well as hypo‐ and hyper‐methylation of DNA‐binding regions for transcription factors relevant to endometrial cell differentiation and/or tumourigenesis, including FOXA2, SOX17, and HAND2. The identified DNA methylation signature distinguishing NAEH and AEH lesions was reproducible in a validation cohort with modest discriminative capability. These findings not only support the concept that the transition from NAEH to AEH is an essential step within neoplastic cell transformation of endometrial epithelium but also provide deep insight into the molecular mechanism of the tumourigenic programme. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
ARAP3 protects from excessive formylated peptide‐induced microvascular leakage by acting on endothelial cells and neutrophils
Authors: Chu Julia Y , McCormick Barry , Sundaram Kruthika , Hardisty Gareth , Karmakar Utsa , Pumpe Caroline , Krull Elizabeth , Lucas Christopher D , Amado‐Azevedo Joana , Hordijk Peter L , Caporali Andrea , Mellor Harry , Baillie J Kenneth , Rossi Adriano G , Vermeren Sonja 
Published: May 2024

AbstractVascular permeability is temporarily heightened during inflammation, but excessive inflammation‐associated microvascular leakage can be detrimental, as evidenced in the inflamed lung. Formylated peptides regulate vascular leakage indirectly via formylated peptide receptor‐1 (FPR1)‐mediated recruitment and activation of neutrophils. Here we identify how the GTPase‐activating protein ARAP3 protects against formylated peptide‐induced microvascular permeability via endothelial cells and neutrophils. In vitro, Arap3−/− endothelial monolayers were characterised by enhanced formylated peptide‐induced permeability due to upregulated endothelial FPR1 and enhanced vascular endothelial cadherin internalisation. In vivo, enhanced inflammation‐associated microvascular leakage was observed in Arap3−/− mice. Leakage of plasma protein into the lungs of Arap3−/− mice increased within hours of formylated peptide administration. Adoptive transfer experiments indicated this was dependent upon ARAP3 deficiency in both immune and non‐immune cells. Bronchoalveolar lavages of formylated peptide‐challenged Arap3−/− mice contained neutrophil extracellular traps (NETs). Pharmacological inhibition of NET formation abrogated excessive microvascular leakage, indicating a critical function of NETs in this context. The observation that Arap3−/− mice developed more severe influenza suggests these findings are pertinent to pathological situations characterised by abundant formylated peptides. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Morphologic patterns observed in prostate biopsy cases with discrepant grade group and molecular risk classification
Authors: Greenland Nancy Y. , Cooperberg Matthew R. , Carroll Peter R. , Cowan Janet E. , Simko Jeffry P. , Stohr Bradley A. , Chan Emily 
Published: May 2024

AbstractBackgroundMolecular‐based risk classifier tests are increasingly being utilized by urologists and radiation oncologists to guide clinical decision making. The Decipher prostate biopsy test is a 22‐gene RNA biomarker assay designed to predict likelihood of high‐grade disease at radical prostatectomy and risk of metastasis and mortality. The test provides a risk category of low, intermediate, or high. We investigated histologic features of biopsies in which the Grade Group (GG) and Decipher risk category (molecular risk) were discrepant.MethodsOur institutional urologic outcomes database was searched for men who underwent prostate biopsies with subsequent Decipher testing from 2016 to 2020. We defined discrepant GG and molecular risk as either GG1‐2 with high Decipher risk category or GG ≥ 3 with low Decipher risk category. The biopsy slide on which Decipher testing was performed was re‐reviewed for GG and various histologic features, including % Gleason pattern 4, types of Gleason pattern 4 and 5, other “high risk” features (e.g., complex papillary, ductal carcinoma, intraductal carcinoma [IDC]), and other unusual and often “difficult to grade” patterns (e.g., atrophic carcinoma, mucin rupture, pseudohyperplastic carcinoma, collagenous fibroplasia, foamy gland carcinoma, carcinoma with basal cell marker expression, carcinoma with prominent vacuoles, and stromal reaction). Follow‐up data was also obtained from the electronic medical record.ResultsOf 178 men who underwent prostate biopsies and had Decipher testing performed, 41 (23%) had discrepant GG and molecular risk. Slides were available for review for 33/41 (80%). Of these 33 patients, 23 (70%) had GG1‐2 (GG1 n = 5, GG2 n = 18) with high Decipher risk, and 10 (30%) had GG ≥ 3 with low Decipher risk. Of the 5 GG1 cases, one case was considered GG2 on re‐review; no other high risk features were identified but each case showed at least one of the following “difficult to grade” patterns: 3 atrophic carcinoma, 1 collagenous fibroplasia, 1 carcinoma with mucin rupture, and 1 carcinoma with basal cell marker expression. Of the 18 GG2 high Decipher risk cases, 2 showed GG3 on re‐review, 5 showed large cribriform and/or other high risk features, and 10 showed a “difficult to grade” pattern. Of the 10 GG ≥ 3 low Decipher risk cases, 5 had known high risk features including 2 with large cribriform, 1 with IDC, and 1 with Gleason pattern 5.ConclusionsIn GG1‐2 high Decipher risk cases, difficult to grade patterns were frequently seen in the absence of other known high risk morphologic features; whether these constitute true high risk cases requires further study. In the GG ≥ 3 low Decipher risk cases, aggressive histologic patterns such as large cribriform and IDC were observed in half (50%) of cases; therefore, the molecular classifier may not capture all high risk histologic patterns.
Efficacy of a hydrogel spacer for improving quality of life in patients with prostate cancer undergoing low‐dose‐rate brachytherapy alone or in combination with intensity‐modulated radiotherapy: An observational study using propensity score matching
Authors: Nakai Yasushi , Tanaka Nobumichi , Asakawa Isao , Ohnishi Kenta , Miyake Makito , Yamaki Kaori , Torimoto Kazumasa , Fujimoto Kiyohide 
Published: May 2024

AbstractBackgroundIt is unclear whether a hydrogel spacer can improve quality of life (QOL) in patients undergoing low‐dose‐rate brachytherapy (LDR‐BT) alone or in combination with intensity‐modulated radiotherapy (IMRT).MethodsWe enrolled patients with prostate cancer who underwent LDR‐BT alone with (n = 186) or without (n = 348) a hydrogel spacer, or underwent LDR‐BT in combination with IMRT with (n = 70) or without (n = 217) a hydrogel spacer. QOL was evaluated using Expanded Prostate Cancer Index Composite (EPIC) questionnaires at baseline and 1, 3, 6, 12, and 24 months after implantation. The groups were compared using propensity score matching analysis.ResultsAmong patients who underwent LDR‐BT alone, there were no differences regarding changes in urinary, bowel, sexual, or hormonal domain scores between the spacer and no‐spacer groups; however, the dose at the bowel was significantly lower in the spacer group than in the no‐spacer group. Among patients who underwent LDR‐BT in combination with IMRT, there were no differences regarding changes in urinary, sexual, or hormonal domain scores between the spacer and no‐spacer groups. However, the changes in the bowel domain score were significantly lower in the spacer group than in the no‐spacer group (p < 0.001).ConclusionsA hydrogel spacer may not improve impaired urinary, bowel, or sexual QOL in patients undergoing LDR‐BT alone. However, in patients undergoing LDR‐BT in combination with IMRT, a hydrogel spacer can improve impaired bowel QOL but not sexual or urinary QOL.
Overall and metastasis‐free survival of Afro‐Caribbean patients with biochemical recurrence after radical prostatectomy
Authors: Barriere Hugo , Kaulanjan Kévin , Stempfer Gautier , Mollard Philippe , Laguerre Mélanie , Senechal Cédric , Gourtaud Gilles , Roux Virginie , Sadreux Yvanne , Blanchet Pascal , Brureau Laurent 
Published: May 2024

AbstractIntroductionEarly salvage radiotherapy is indicated for patients with biochemical recurrence after radical prostatectomy. However, for various reasons, certain patients do not benefit from this treatment (OBS) or only at a late stage (LSR). There are few studies on this subject and none on a “high‐risk” population, such as patients of African descent. Our objective was to estimate the metastasis‐free (MFS) and overall survival (OS) of patients who did not receive salvage radiotherapy, and to identify risk factors of disease progression.Patients and MethodsThis was a single‐center retrospective study that included 154 patients, 99 in the OBS group and 55 in the LSR group. All were treated by total prostatectomy for localized prostate cancer between January 2000 and December 2020 and none received early salvage radiotherapy after biochemical recurrence.ResultsBaseline characteristics were similar between groups, except for the time to biochemical recurrence. The median follow‐up was 10.0 and 11.8 years for the OBS and LSR groups, respectively. The median time from surgery to LSR was 5.1 years. The two groups did not show a significant difference in MFS: 90.6% at 10 years for the OBS group and 93.3% for the LSR group. The median MFS was 19.8 and 19.6 years for the OBS and LSR groups respectively. OS for the OBS group was significantly higher than that for the LSR group (HR: 2.14 [1.07–4.29]; p = 0.03), with 10‐year OS of 95.9% for the OBS group and 76.1% for the LSR group. Median OS was 16 and 15.6 years for the OBS and LSR groups, respectively.ConclusionIn this study, we observed satisfactory metastasis‐free and OS rates relative to those reported in the scientific literature. The challenge is not to question the benefit of early salvage radiotherapy, but to improve the identification of patients at risk of progression through the development of molecular and genomic tests for more highly personalized medicine.
Exploratory and confirmatory factor analysis of emPHasis‐10: The health‐related quality‐of‐life measure in pulmonary hypertension
Authors: Rawlings Gregg H. , Gaskell Chris , Beail Nigel , Thompson Andrew , Armstrong Iain 
Published: May 2024

AbstractThe emPHasis‐10 is a health‐related quality of life (HRQoL) unidimensional measure developed specifically for adults with pulmonary hypertension. The tool has excellent psychometric properties and is well used in research and clinical settings. Its factor structure has not been examined, which may help to identity a complimentary approach to using the measure to examine patient functioning. We performed an exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) on a data set collected from 263 adults with PH recruited from a community setting. The EFA suggested the emPHasis‐10 consists of three underlying latent variables, which based on the loading of items, were termed “fatigue” (Items 3, 4, and 5), “independence” (Items 7, 8, 9, and 10), and “breathlessness” (Items 1, 2, and 6). All factors were found to have good internal consistency. “Independence” accounted for most of the variance (29%), followed by “breathlessness” (22%) and “fatigue” (19%). The CFA looked to confirm the fit of a three‐factor model. A higher‐order model was found to be the best fit consisting of HRQoL as a superordinate factor, for which the association between this factor and the 10 items was mediated through the three latent factors. Further analyses were performed testing the validity of the latent variables revealing all were significantly correlated with self‐reported measures of depression, anxiety, health‐anxiety, and dyspnea. Our analyses support the emPHasis‐10 as a measure of HRQoL, while also proposing the clinical utility of examining the three emergent factors, which could be used to glean additional insight into the respondent's functioning and inform care.
The PDI model system for parameterizing soil hydraulic properties
Authors: Peters Andre , Durner Wolfgang , Iden Sascha 
Published: May 2024

AbstractThe Peters–Durner–Iden (PDI) model system for describing soil hydraulic properties (SHP) has been developed over a decade. Inspired by Rien van Genuchten's seminal work, the PDI system focuses on an efficient and simple parameterization of water retention curves and hydraulic conductivity curves (HCC) across the entire soil moisture spectrum. By combining capillary and non‐capillary components for water retention and conductivity, it aims to reconcile mathematical simplicity and insights on water adsorption and film flow in soils. Recent developments have reduced the number of free parameters of the conductivity model to zero, enhancing the model's applicability in cases of limited data availability. The first reduction was achieved by a prediction of absolute non‐capillary conductivity based on the consideration of film and corner flow on the pore scale, and the second by a prediction of absolute capillary conductivity by a capillary bundle model. This allows a complete characterization of SHP over the entire moisture range with only four retention curve parameters. The inclusion of a maximum pore size in the capillary conductivity model prevents an unrealistic drop of the HCC near saturation. This paper provides a comprehensive overview of the PDI model system, emphasizing its conceptual features and mathematical details. An Excel sheet and a Python code stored in a repository are provided for accessibility.
Simulating bare soil evaporation for undisturbed soil cores—Using HYDRUS 3D simulation on X‐ray µCT determined soil macrostructures
Authors: Leuther Frederic , Diamantopoulos Efstathios 
Published: May 2024

AbstractEvaporation of soil water depends not only on climatic conditions, soil surface roughness, soil texture, and soil hydraulic properties but also on the soils’ macrostructure. Evaporation is characterized by water losses over time for a defined soil volume, where soils are assumed to be homogeneous in texture and structure. In this technical note, we investigated the potential and limitations of 3D modeling of evaporation processes on 250 cm3 soil cores with structural features ≥480 µm determined by X‐ray computed tomography. For this, we used isothermal Richards equation as the main governing equation, accounting also for isothermal vapor flow. We simulated two evaporation experiments with same soil texture but contrasting macrostructures, that is, the spatial arrangement of voxels classified as soil matrix and air‐filled voids, of a ploughed and non‐ploughed grassland soil with HYDRUS 3D. In both simulations, we fixed the potential evaporation rates to the experimental rates and evaluated simulation results with measured matric potential data at two depths (1.25 cm and 3.75 cm) continuously recorded at 10 min intervals. We could show that the simulations of bare soil evaporation were able to predict the tensiometer dynamics and water losses for the full experimental time of 7 days. The simulation provided unique spatial information of water content and flow velocities as a function of time, which are important when studying the effect of air‐filled macropores, macro‐connectivity of soil matrix, and water dynamics on soil evaporation.
Influence of geographical origin in the physical and bioactive parameters of single origin dark chocolate
Authors: Cartas José , Alvarenga Nuno , Partidário Ana , Lageiro Manuela , Roseiro Cristina , Gonçalves Helena , Leitão António Eduardo , Ribeiro Carlos Marques , Dias João 
Published: May 2024

AbstractDark chocolate presents exclusive characteristics that make it a food product with worldwide consumption and also as an ingredient in several food industries. Although chocolate is an energy-dense food, it is also rich in bioactive compounds and recent studies have demonstrated health benefits from a moderate consumption. Therefore, the quantification of the bioactive compounds of different types of cocoa, from different geographical origins, is of great importance to recognize the importance of single origin dark chocolate from the nutritional point of view. Dark chocolate produced from Amelonado variety presented higher values of hardness (5592 g), plastic viscosity (2.87 Pa.s) and yield value (12.91 Pa). Both dark chocolates from Peru, Piura Blanco and Chuncho, presented higher results in total phenolic content, total antioxidant capacity, caffeine and vitamin E. Additionally, sample Piura Blanco presented a higher content of theobromine (720.7 mg/100 g), lactic acid (1153.2 mg/100 g), succinic acid (679.4 mg/100 g) and oxalic acid (468.5 mg/100 g). On the other hand, chocolate from São Tomé presented a higher content of sucrose (38.22%) and SFA (62.38% of total fat). The results obtained demonstrate the existence of heterogeneity in cocoa varieties, supporting decision-makers in the selection of the most suitable cocoa for specific market needs.
First-trimester serum biomarkers in twin pregnancies and adverse obstetric outcomes–a single center cohort study
Authors: Queirós Alexandra , Gomes Laura , Pereira Inês , Charepe Nádia , Plancha Marta , Rodrigues Sofia , Cohen Álvaro , Alves Marta , Papoila Ana Luísa , Simões Teresinha 
Published: May 2024

Abstract
Purpose
This study aimed to determine the association of first-trimester maternal serum biomarkers with preterm birth (PTB), fetal growth restriction (FGR) and hypertensive disorders of pregnancy (HDP) in twin pregnancies.

Methods
This is a retrospective cohort study of twin pregnancies followed at Maternidade Dr. Alfredo da Costa, Lisbon, Portugal, between January 2010 and December 2022. We included women who completed first-trimester screening in our unit and had ongoing pregnancies with two live fetuses, and delivered after 24 weeks. Maternal characteristics, pregnancy-associated plasma protein-A (PAPP-A) and β-human chorionic gonadotropin (β-hCG) levels were analyzed for different outcomes: small for gestational age (SGA), gestational hypertension (GH), early and late-onset pre-eclampsia (PE), as well as the composite outcome of PTB associated with FGR and/or HDP. Univariable, multivariable logistic regression analyses and receiver-operating characteristic curve were used.

Results
466 twin pregnancies met the inclusion criteria. Overall, 185 (39.7%) pregnancies were affected by SGA < 5th percentile and/or HDP. PAPP-A demonstrated a linear association with gestational age at birth and mean birth weight. PAPP-A proved to be an independent risk factor for SGA and PTB (< 34 and < 36 weeks) related to FGR and/or HDP. None of the women with PAPP-A MoM > 90th percentile developed early-onset PE or PTB < 34 weeks.

Conclusion
A high serum PAPP-A (> 90th percentile) ruled out early-onset PE and PTB < 34 weeks. Unless other major risk factors for hypertensive disorders are present, these women should not be considered candidates for aspirin prophylaxis. Nevertheless, close monitoring of all TwP for adverse obstetric outcomes is still recommended.
A commentary on studies of brain iron accumulation during ageing
Authors: Hackett Mark J. 
Published: May 2024

AbstractBrain iron content is widely reported to increase during “ageing”, across multiple species from nematodes, rodents (mice and rats) and humans. Given the redox-active properties of iron, there has been a large research focus on iron-mediated oxidative stress as a contributor to tissue damage during natural ageing, and also as a risk factor for neurodegenerative disease. Surprisingly, however, the majority of published studies have not investigated brain iron homeostasis during the biological time period of senescence, and thus knowledge of how brain homeostasis changes during this critical stage of life largely remains unknown. This commentary examines the literature published on the topic of brain iron homeostasis during ageing, providing a critique on limitations of currently used experimental designs. The commentary also aims to highlight that although much research attention has been given to iron accumulation or iron overload as a pathological feature of ageing, there is evidence to support functional iron deficiency may exist, and this should not be overlooked in studies of ageing or neurodegenerative disease.
Graphical abstract