bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guidelines for genetic testing in prostate cancer: a scoping review
Authors: Tuffaha Haitham , Edmunds Kim , Fairbairn David , Roberts Matthew J. , Chambers Suzanne , Smith David P. , Horvath Lisa , Arora Shiksha , Scuffham Paul 
Published: May 2023

Abstract
Background
Genetic testing, to identify pathogenic or likely pathogenic variants in prostate cancer, is valuable in guiding treatment decisions for men with prostate cancer and to inform cancer prevention and early detection options for their immediate blood relatives. There are various guidelines and consensus statements for genetic testing in prostate cancer. Our aim is to review genetic testing recommendations across current guidelines and consensus statements and the level of evidence supporting those recommendations.

Methods
A scoping review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for scoping review (PRISMA-ScR) guidelines. Electronic database searches and manual searches of grey literature, including websites of key organisations were conducted. Using the Population, Concept, Context (PCC) framework, this scoping review included: men with prostate cancer or men at high risk of prostate cancer and their biological families; existing guidelines and consensus statements with supporting evidence for genetic testing of men with prostate cancer from any geographical location worldwide.

Results
Of the 660 citations identified, 23 guidelines and consensus statements met the inclusion criteria for the scoping review. Based on different levels of evidence about who should be tested and how, a diverse range of recommendations were identified. There was general consensus among the guidelines and consensus statements that men with metastatic disease be offered genetic testing; however, there was less consensus in relation to genetic testing in localised prostate cancer. While there was some consensus in relation to which genes to test, recommendations varied regarding who to test, testing methods and implementation.

Conclusion
While genetic testing in prostate cancer is routinely recommended and numerous guidelines exist, there is still considerable lack of consensus regarding who should be tested and how they should be tested. Further evidence is needed to inform value-based genetic testing strategies for implementation in practice.
Numerical evidence for a small-scale dynamo approaching solar magnetic Prandtl numbers
Authors: Warnecke Jörn , Korpi-Lagg Maarit J. , Gent Frederick A. , Rheinhardt Matthias 
Published: May 2023

AbstractMagnetic fields on small scales are ubiquitous in the Universe. Although they can often be observed in detail, their generation mechanisms are not fully understood. One possibility is the so-called small-scale dynamo (SSD). Prevailing numerical evidence, however, appears to indicate that an SSD is unlikely to exist at very low magnetic Prandtl numbers (PrM) such as those that are present in the Sun and other cool stars. Here we have performed high-resolution simulations of isothermal forced turbulence using the lowest PrM values achieved so far. Contrary to earlier findings, the SSD not only turns out to be possible for PrM down to 0.0031 but also becomes increasingly easier to excite for PrM below about 0.05. We relate this behaviour to the known hydrodynamic phenomenon referred to as the bottleneck effect. Extrapolating our results to solar values of PrM indicates that an SSD would be possible under such conditions.
Symbioses shape feeding niches and diversification across insects
Authors: Cornwallis Charlie K. , van ’t Padje Anouk , Ellers Jacintha , Klein Malin , Jackson Raphaella , Kiers E. Toby , West Stuart A. , Henry Lee M. 
Published: May 2023

AbstractFor over 300 million years, insects have relied on symbiotic microbes for nutrition and defence. However, it is unclear whether specific ecological conditions have repeatedly favoured the evolution of symbioses, and how this has influenced insect diversification. Here, using data on 1,850 microbe–insect symbioses across 402 insect families, we found that symbionts have allowed insects to specialize on a range of nutrient-imbalanced diets, including phloem, blood and wood. Across diets, the only limiting nutrient consistently associated with the evolution of obligate symbiosis was B vitamins. The shift to new diets, facilitated by symbionts, had mixed consequences for insect diversification. In some cases, such as herbivory, it resulted in spectacular species proliferation. In other niches, such as strict blood feeding, diversification has been severely constrained. Symbioses therefore appear to solve widespread nutrient deficiencies for insects, but the consequences for insect diversification depend on the feeding niche that is invaded.
Flat band separation and robust spin Berry curvature in bilayer kagome metals
Authors: Di Sante Domenico , Bigi Chiara , Eck Philipp , Enzner Stefan , Consiglio Armando , Pokharel Ganesh , Carrara Pietro , Orgiani Pasquale , Polewczyk Vincent , Fujii Jun , King Phil D. C. , Vobornik Ivana , Rossi Giorgio , Zeljkovic Ilija , Wilson Stephen D. , Thomale Ronny , Sangiovanni Giorgio , Panaccione Giancarlo , Mazzola Federico 
Published: May 2023

AbstractKagome materials have emerged as a setting for emergent electronic phenomena that encompass different aspects of symmetry and topology. It is debated whether the XV6Sn6 kagome family (where X is a rare-earth element), a recently discovered family of bilayer kagome metals, hosts a topologically non-trivial ground state resulting from the opening of spin–orbit coupling gaps. These states would carry a finite spin Berry curvature, and topological surface states. Here we investigate the spin and electronic structure of the XV6Sn6 kagome family. We obtain evidence for a finite spin Berry curvature contribution at the centre of the Brillouin zone, where the nearly flat band detaches from the dispersing Dirac band because of spin–orbit coupling. In addition, the spin Berry curvature is further investigated in the charge density wave regime of ScV6Sn6 and it is found to be robust against the onset of the temperature-driven ordered phase. Utilizing the sensitivity of angle-resolved photoemission spectroscopy to the spin and orbital angular momentum, our work unveils the spin Berry curvature of topological kagome metals and helps to define its spectroscopic fingerprint.
An integrated tumor, immune and microbiome atlas of colon cancer
Authors: Roelands Jessica , Kuppen Peter J. K. , Ahmed Eiman I. , Mall Raghvendra , Masoodi Tariq , Singh Parul , Monaco Gianni , Raynaud Christophe , de Miranda Noel F.C.C. , Ferraro Luigi , Carneiro-Lobo Tatiana C. , Syed Najeeb , Rawat Arun , Awad Amany , Decock Julie , Mifsud William , Miller Lance D. , Sherif Shimaa , Mohamed Mahmoud G. , Rinchai Darawan , Van den Eynde Marc , Sayaman Rosalyn W. , Ziv Elad , Bertucci Francois , Petkar Mahir Abdulla , Lorenz Stephan , Mathew Lisa Sara , Wang Kun , Murugesan Selvasankar , Chaussabel Damien , Vahrmeijer Alexander L. , Wang Ena , Ceccarelli Anna , Fakhro Khalid A. , Zoppoli Gabriele , Ballestrero Alberto , Tollenaar Rob A.E.M. , Marincola Francesco M. , Galon Jérôme , Khodor Souhaila Al , Ceccarelli Michele , Hendrickx Wouter , Bedognetti Davide 
Published: May 2023

AbstractThe lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.
Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China
Authors: Wang Zhan , Li Yinkun , Zheng Wengang , Ji Yuru , Duan Minjie , Ma Li 
Published: May 2023

AbstractAmmonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha−1 was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha−1 (52.7–56.5%) and when manure was added (72.7–99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha−1 (58.4–84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs’ community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs’ variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.
Machine learning-based predictive models for the occurrence of behavioral and psychological symptoms of dementia: model development and validation
Authors: Cho Eunhee , Kim Sujin , Heo Seok-Jae , Shin Jinhee , Hwang Sinwoo , Kwon Eunji , Lee SungHee , Kim SangGyun , Kang Bada 
Published: May 2023

AbstractThe behavioral and psychological symptoms of dementia (BPSD) are challenging aspects of dementia care. This study used machine learning models to predict the occurrence of BPSD among community-dwelling older adults with dementia. We included 187 older adults with dementia for model training and 35 older adults with dementia for external validation. Demographic and health data and premorbid personality traits were examined at the baseline, and actigraphy was utilized to monitor sleep and activity levels. A symptom diary tracked caregiver-perceived symptom triggers and the daily occurrence of 12 BPSD classified into seven subsyndromes. Several prediction models were also employed, including logistic regression, random forest, gradient boosting machine, and support vector machine. The random forest models revealed the highest area under the receiver operating characteristic curve (AUC) values for hyperactivity, euphoria/elation, and appetite and eating disorders; the gradient boosting machine models for psychotic and affective symptoms; and the support vector machine model showed the highest AUC. The gradient boosting machine model achieved the best performance in terms of average AUC scores across the seven subsyndromes. Caregiver-perceived triggers demonstrated higher feature importance values across the seven subsyndromes than other features. Our findings demonstrate the possibility of predicting BPSD using a machine learning approach.
Rapid ammonia build-up in small individually ventilated mouse cages cannot be overcome by adjusting the amount of bedding
Authors: Eskandarani Mahmud A. , Hau Jann , Kalliokoski Otto 
Published: May 2023

AbstractWe sought to investigate if varying levels of bedding had an effect on intra-cage ammonia levels in individually ventilated mouse cages (Euro Standard Types II and III). Employing a routine 2 week cage-changing interval, our goal is to keep ammonia levels under 50 ppm. In smaller cages used for breeding or for housing more than four mice, we measured problematic levels of intra-cage ammonia, and a considerable proportion of these cages had ammonia levels at more than 50 ppm toward the end of the cage-change cycle. These levels were not reduced significantly when the levels of absorbent wood chip bedding was either increased or decreased by 50%. The mice in both cage types II and III were housed at comparable stocking densities, yet ammonia levels in larger cages remained lower. This finding highlights the role of cage volume, as opposed to simply the floor space, in controlling air quality. With the current introduction of newer cage designs that employ an even smaller headspace, our study urges caution. With individually ventilated cages, problems with intra-cage ammonia may go undetected, and we may opt to utilize insufficient cage-changing intervals. Few modern cages have been designed to account for the amounts and types of enrichment that are used (and, in parts of the world, mandated) today, adding to the problems associated with decreasing cage volumes.
Extraordinary clinical response to ibrutinib in low-grade ovarian cancer guided by organoid drug testing
Authors: Gray Heidi J. , Chatterjee Payel , Rosati Rachele , Appleyard Lauren R. , Durenberger Grace J. , Diaz Robert L. , Swan Hallie A. , Peretti Danielle , Pollastro Maddy , Ainge Trevor , Kapeli Katannya , Pereira Shalini , Margossian Astrid L. , Banda Kalyan , Goff Barbara A. , Swisher Elizabeth M. , Bernard Brady , Kemp Christopher J. , Grandori Carla 
Published: May 2023

AbstractLow-grade serous ovarian cancer (LGSOC) typically responds poorly to standard platinum-based chemotherapy and new therapeutic approaches are needed. We describe a remarkable response to targeted therapy in a patient with platinum-resistant, advanced LGSOC who had failed standard-of-care chemotherapy and two surgeries. The patient was in rapid decline and entering hospice care on home intravenous (i.v.) opioid analgesics and a malignant bowel obstruction requiring a G-tube. Genomic analysis of the patient’s tumor did not indicate obvious therapeutic options. In contrast, a CLIA-certified drug sensitivity assay of an organoid culture derived from the patient’s tumor identified several therapeutic choices, including Bruton’s tyrosine kinase (BTK) inhibitor ibrutinib, as well as the EGFR inhibitors afatinib and erlotinib. Following off-label administration of daily ibrutinib as monotherapy, the patient had an exceptional clinical turnaround over the following 65 weeks with normalization of CA-125 levels, resolution of the malignant bowel obstruction, halting of pain medications, and improvement of performance status from ECOG 3 to ECOG 1. After 65 weeks of stable disease, the patient’s CA-125 levels began to rise, at which point the patient discontinued ibrutinib and began taking afatinib as monotherapy. The patient’s CA-125 levels remained stable for an additional 38 weeks but due to anemia and rising CA-125 levels, the patient switched to erlotinib and is currently being monitored. This case highlights the clinical utility of ex vivo drug testing of patient-derived tumor organoids as a new functional precision medicine approach to identify effective personalized therapies for patients who have failed standard-of-care treatments.
Refined high-content imaging-based phenotypic drug screening in zebrafish xenografts
Authors: Sturtzel C. , Grissenberger S. , Bozatzi P. , Scheuringer E. , Wenninger-Weinzierl A. , Zajec Z. , Dernovšek J. , Pascoal S. , Gehl V. , Kutsch A. , Granig A. , Rifatbegovic F. , Carre M. , Lang A. , Valtingojer I. , Moll J. , Lötsch D. , Erhart F. , Widhalm G. , Surdez D. , Delattre O. , André N. , Stampfl J. , Tomašič T. , Taschner-Mandl S. , Distel M. 
Published: May 2023

AbstractZebrafish xenotransplantation models are increasingly applied for phenotypic drug screening to identify small compounds for precision oncology. Larval zebrafish xenografts offer the opportunity to perform drug screens at high-throughput in a complex in vivo environment. However, the full potential of the larval zebrafish xenograft model has not yet been realized and several steps of the drug screening workflow still await automation to increase throughput. Here, we present a robust workflow for drug screening in zebrafish xenografts using high-content imaging. We established embedding methods for high-content imaging of xenografts in 96-well format over consecutive days. In addition, we provide strategies for automated imaging and analysis of zebrafish xenografts including automated tumor cell detection and tumor size analysis over time. We also compared commonly used injection sites and cell labeling dyes and show specific site requirements for tumor cells from different entities. We demonstrate that our setup allows us to investigate proliferation and response to small compounds in several zebrafish xenografts ranging from pediatric sarcomas and neuroblastoma to glioblastoma and leukemia. This fast and cost-efficient assay enables the quantification of anti-tumor efficacy of small compounds in large cohorts of a vertebrate model system in vivo. Our assay may aid in prioritizing compounds or compound combinations for further preclinical and clinical investigations.
Highly pH-stable lanthanide MOFs: a tunable luminescence and ratiometric luminescent probe for sulfamethazine
Authors: Zhang Xu , Liu Dongyan , Yu Jiahui , Li Xin , Zheng Hanwen , Zhou Yanan , Huang Cuiying , Zhu Yanyu , Jiao Chengqi , Sun Zhengang 
Published: May 2023

A series of isostructural Ln-MOFs were synthesized. By adjusting the molar ratio of Ln3+, the doped Ln-MOFs show changes in emission colors. Meanwhile, the Tb-MOF exhibits ratiometric luminescence sensing of SMZ in mariculture water and human urine.
Studies of large‐scale DC connected photovoltaic power system based on multi‐modular cascaded DC‐DC converter
Authors: Liu Fei , Chen Yushuo , Shi Jian , Qu Lu , Zi Zhenning , Yu Zhanqing 
Published: May 2023

AbstractDC collection and transmission is one of the major development directions of large‐scale photovoltaic (PV) power system. In order to achieve low‐cost, high‐efficiency and long‐distance transmission of PV power, this paper adopted a DC grid‐connected topology by using multi‐modular cascaded DC‐DC converters, forming an input‐independent and output‐series (IIOS) system. In this system, an LLC type DC‐DC converter based on IGCT and magnetically integrated transformer was proposed in this paper, which can significantly increase the capacity, efficiency and power density of DC‐DC converter. And the equalization unit based on half‐bridge topology was adopted for the case of uneven irradiation of the PV inputs. In addition, this paper proposed an equalization control method based on the Nearest Level Modulation (NLM), which greatly simplifies the design of the acquisition and control system. Furthermore, the parametric design of a 50MW PV system was presented, and the simulation was carried out to verify the feasibility and advantages of the system in this paper. The proposed IIOS system is more suitable for high‐capacity, long‐distance PV power transmission, which can serve as a reference for the development of large‐scale photovoltaic systems.
Near‐field electrospinning fabrication of piezoelectric polymer microfiber sensors for detection of weak mechanical excitation
Authors: Jiang Hanxiao , Luo Xingsheng , Chen Qiusong , Xu Fan , Zhu Guodong , Jiang Zaixiu , Guliakova Anna A. 
Published: May 2023

AbstractCollection and conversion of widespread mechanical energy is one promising way to alleviate environmental pollution and energy crisis. Piezoelectric materials can effectively realise this conversion between mechanical and electrical energies. Here, via near‐field electrospinning, piezoelectric poly(vinylidene fluoride) microfibers were fabricated on flexible polyethylene terephthalate substrate. Bending measurement indicated that open‐circuit voltage response from piezoelectric microfibers was strain dependent but insensitive to bending frequency. The microfiber sensor could detect acoustic signals with sound pressure level between 70 and 120 dB and the recorded acoustic frequency was well consistent with the nominal frequency. Light wind from a low‐power hand fan was also detected by this microfiber sensor. This simply structured and highly flexible piezoelectric microfiber sensor provided a promising and low‐cost fabrication measure for weak mechanical excitation sensing.
Feasibility of structure inversions for gravity-mode pulsators
Authors: Vanlaer V. , Aerts C. , Bellinger E. P. , Christensen-Dalsgaard J. 
Published: May 2023

Context. Gravity-mode asteroseismology has significantly improved our understanding of mixing in intermediate mass stars. However, theoretical pulsation periods of stellar models remain in tension with observations, and it is often unclear how the models of these stars should be further improved. Inversions provide a path forward by directly probing the internal structure of these stars from their pulsation periods, quantifying which parts of the model are in need of improvement. This method has been used with success in the case of solar-like pulsators, but has not yet been applied to main-sequence gravity-mode pulsators.
Aims. Our aim is to determine whether structure inversions for gravity-mode pulsators are feasible. We focus on the case of slowly rotating slowly pulsating B-type (SPB) stars.
Methods. We computed and analyzed dipole mode kernels for three variables pairs: (ρ, c), (N2, c), and (N2, ρ). We assessed the potential of these kernels by predicting the oscillation frequencies of a model after perturbing its structure. We then tested two inversion methods, regularized least squares (RLS) and subtractive optimally localized averages (SOLA), using a model grid computed with the MESA stellar evolution code and the GYRE pulsation code.
Results. We find that changing the stellar structure affects the oscillation frequencies in a nonlinear way. The oscillation modes for which this nonlinear dependency is the strongest are in resonance with the near-core peak in the buoyancy frequency. The near-core region of the star can be probed with SOLA, while RLS requires fine tuning to obtain accurate results. Both RLS and SOLA are strongly affected by the nonlinear dependencies on the structure differences, as these methods are based on a first-order approximation. These inversion methods need to be modified for meaningful applications of inversions to SPB stars.
Conclusions. Our results show that inversions of gravity-mode pulsators are possible in principle, but that the typical inversion methods developed for solar-like oscillators are not applicable. Future work should focus on developing nonlinear inversion methods.