bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical recurrence in patients with prostate cancer after primary definitive therapy: treatment based on risk stratification
Authors: Shore Neal D. , Moul Judd W. , Pienta Kenneth J. , Czernin Johannes , King Martin T. , Freedland Stephen J. 
Published: September 2023

Abstract
Background
Nearly one-third of patients with prostate cancer (PCa) experience biochemical recurrence (BCR) after primary definitive treatment. BCR increases the risk of distant metastasis and mortality in patients with prognostically unfavorable features. These patients are best managed with a tailored treatment strategy incorporating risk stratification using clinicopathological factors, next-generation imaging, and genomic testing.

Objective
This narrative review examines the utility of risk stratification for the management of patients with BCR in the context of clinical trial data, referencing the latest recommendations by European and US medical societies.

Methods
PubMed was searched for relevant studies published through May 21 2023 on treatment of patients with BCR after radical prostatectomy (RP) or external beam radiotherapy (EBRT).

Results
European and US guidelines support the risk-stratified management of BCR. Post-RP, salvage EBRT (with or without androgen deprivation therapy [ADT]) is an accepted treatment option for patients with BCR. Post-EBRT, local salvage therapies (RP, cryotherapy, high-intensity focused ultrasound, stereotactic body radiotherapy, and low-dose-rate and high-dose-rate brachytherapy) have demonstrated comparable relapse-free survival rates but differing adverse event profiles, short and long term. Local salvage therapies should be used for local-only relapses while ADT should be considered for regional or distant relapses. In practice, patients often receive ADT, with varying guidance for intermittent ADT vs. continuous ADT, due to consideration of quality-of-life effects.

Conclusions
Despite a lack of consensus for BCR treatment among guideline associations and medical societies, risk stratification of patients is essential for personalized treatment approaches, as it allows for an informed selection of therapeutic strategies and estimation of adverse events. In lower-risk disease, observation is recommended while in higher-risk disease, after failed repeat local therapy, ADT and/or clinical trial enrollment may be appropriate. Results from ongoing clinical studies of patients with BCR should provide consensus for management.
Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions
Authors: Singh Abhijeet , Schnürer Anna , Dolfing Jan , Westerholm Maria 
Published: September 2023

AbstractPropionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name ‘Candidatus Thermosyntrophopropionicum ammoniitolerans’ was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L−1 day−1 at hydrogen partial pressure 4–30 Pa and available energy was around −20 mol−1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.
Gasdermin D-mediated keratinocyte pyroptosis as a key step in psoriasis pathogenesis
Authors: Lian Ni , Chen Yujie , Chen Sihan , Zhang Ying , Chen Hao , Yang Yong , Gu Heng , Chen Qing , Li Min , Chen Xu 
Published: September 2023

AbstractGasdermin D (GSDMD)-mediated pyroptosis has a significant pro-inflammation characteristic due to dramatic secretion of pro-inflammatory substances. However, its role remains unclear in psoriasis as one chronic inflammatory skin disorder with high prevalence. We found that N-terminal GSDMD (N-GSDMD) was aberrantly expressed in epidermis of skin lesion in psoriasis patients and imiquimod-induced psoriasis-like dermatitis (IIPLD) mice. In epidermis of IIPLD mice and M5 (simulating psoriatic inflammatory challenge)-treated keratinocytes cultured in vitro, cleavage products of caspase-1, GSDMD and IL-1β were increased. M5-stimulated keratinocyte presented typical pyroptosis morphology accompanied with PI-staining. Gsdmd−/− keratinocytes could not present pyroptosis morphology while stimulated with M5. Electroporation of recombinant N-GSDMD could make the pyroptosis morphology reappear. In Gsdmd−/− mice or keratinocyte-specific Gsdmd conditional knockout mice, we observed the alleviation of psoriatic inflammation and epidermal aberrant expression of Ki-67 and differentiation markers (loricrin and keratin 5) after imiquimod stimulation. Transplanting skin tissue from control mice to Gsdmd−/− mice can evoke the response to imiquimod stimulation in the background of Gsdmd−/− mice (not limited in transplanting area). In M5-stimulated keratinocytes, disulfiram or GSDMD siRNA transfection can inhibit pyroptosis and eliminate disproportionate increases of Ki-67 and PI. We further validated that topically application of disulfiram (pyroptosis inhibitor) also alleviated IIPLD in mice. These findings indicate a novel mechanism that GSDMD-mediated keratinocyte pyroptosis facilitates hyperproliferation and aberrant differentiation induced by immune microenvironment in psoriatic skin inflammation, which contributes to pathogenesis of psoriasis. Our study provides an innovative insight that targeting pyroptosis can be considered as a therapeutic strategy against psoriasis.
Decoding the transcriptome of Duchenne muscular dystrophy to the single nuclei level reveals clinical-genetic correlations
Authors: Suárez-Calvet Xavier , Fernández-Simón Esther , Natera Daniel , Jou Cristina , Pinol-Jurado Patricia , Villalobos Elisa , Ortez Carlos , Monceau Alexandra , Schiava Marianela , Codina Anna , Verdu-Díaz José , Clark James , Laidler Zoe , Mehra Priyanka , Gokul-Nath Rasya , Alonso-Perez Jorge , Marini-Bettolo Chiara , Tasca Giorgio , Straub Volker , Guglieri Michela , Nascimento Andrés , Diaz-Manera Jordi 
Published: September 2023

AbstractDuchenne muscular dystrophy is a genetic disease produced by mutations in the dystrophin gene characterized by early onset muscle weakness leading to severe and irreversible disability. The cellular and molecular consequences of the lack of dystrophin in humans are only partially known, which is crucial for the development of new therapies aiming to slow or stop the progression of the disease. Here we have analyzed quadriceps muscle biopsies of seven DMD patients aged 2 to 4 years old and five age and gender matched controls using single nuclei RNA sequencing (snRNAseq) and correlated the results obtained with clinical data. SnRNAseq identified significant differences in the proportion of cell population present in the muscle samples, including an increase in the number of regenerative fibers, satellite cells, and fibro-adipogenic progenitor cells (FAPs) and a decrease in the number of slow fibers and smooth muscle cells. Muscle samples from the younger patients with stable mild weakness were characterized by an increase in regenerative fibers, while older patients with moderate and progressive weakness were characterized by loss of muscle fibers and an increase in FAPs. An analysis of the gene expression profile in muscle fibers identified a strong regenerative signature in DMD samples characterized by the upregulation of genes involved in myogenesis and muscle hypertrophy. In the case of FAPs, we observed upregulation of genes involved in the extracellular matrix regeneration but also several signaling pathways. Indeed, further analysis of the potential intercellular communication profile showed a dysregulation of the communication profile in DMD samples identifying FAPs as a key regulator of cell signaling in DMD muscle samples. In conclusion, our study has identified significant differences at the cellular and molecular levels in the different cell populations present in skeletal muscle samples of patients with DMD compared to controls.
Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart
Authors: Gafranek Jacob T. , D’Aniello Enrico , Ravisankar Padmapriyadarshini , Thakkar Kairavee , Vagnozzi Ronald J. , Lim Hee-Woong , Salomonis Nathan , Waxman Joshua S. 
Published: September 2023

AbstractHow two-chambered hearts in basal vertebrates have evolved from single-chamber hearts found in ancestral chordates remains unclear. Here, we show that the teleost sinus venosus (SV) is a chamber-like vessel comprised of an outer layer of smooth muscle cells. We find that in adult zebrafish nr2f1a mutants, which lack atria, the SV comes to physically resemble the thicker bulbus arteriosus (BA) at the arterial pole of the heart through an adaptive, hypertensive response involving smooth muscle proliferation due to aberrant hemodynamic flow. Single cell transcriptomics show that smooth muscle and endothelial cell populations within the adapting SV also take on arterial signatures. Bulk transcriptomics of the blood sinuses flanking the tunicate heart reinforce a model of greater equivalency in ancestral chordate BA and SV precursors. Our data simultaneously reveal that secondary complications from congenital heart defects can develop in adult zebrafish similar to those in humans and that the foundation of equivalency between flanking auxiliary vessels may remain latent within basal vertebrate hearts.
Monolithic FAPbBr3 photoanode for photoelectrochemical water oxidation with low onset-potential and enhanced stability
Authors: Yang Hao , Liu Yawen , Ding Yunxuan , Li Fusheng , Wang Linqin , Cai Bin , Zhang Fuguo , Liu Tianqi , Boschloo Gerrit , Johansson Erik M. J. , Sun Licheng 
Published: September 2023

AbstractDespite considerable research efforts on photoelectrochemical water splitting over the past decades, practical application faces challenges by the absence of efficient, stable, and scalable photoelectrodes. Herein, we report a metal-halide perovskite-based photoanode for photoelectrochemical water oxidation. With a planar structure using mesoporous carbon as a hole-conducting layer, the precious metal-free FAPbBr3 photovoltaic device achieves 9.2% solar-to-electrical power conversion efficiency and 1.4 V open-circuit voltage. The photovoltaic architecture successfully applies to build a monolithic photoanode with the FAPbBr3 absorber, carbon/graphite conductive protection layers, and NiFe catalyst layers for water oxidation. The photoanode delivers ultralow onset potential below 0 V versus the reversible hydrogen electrode and high applied bias photon-to-current efficiency of 8.5%. Stable operation exceeding 100 h under solar illumination by applying ultraviolet-filter protection. The photothermal investigation verifies the performance boost in perovskite photoanode by photothermal effect. This study is significant in guiding the development of photovoltaic material-based photoelectrodes for solar fuel applications.
Accounting for the climate benefit of temporary carbon storage in nature
Authors: Matthews H. Damon , Zickfeld Kirsten , Koch Alexander , Luers Amy 
Published: September 2023

AbstractNature-based climate solutions can contribute to climate mitigation, but the vulnerability of land carbon to disturbances means that efforts to slow or reverse land carbon loss could result in only temporary storage. The challenge of accounting for temporary storage is a key barrier to the implementation of nature-based climate mitigation strategies. Here we offer a solution to this challenge using tonne-year accounting, which integrates the amount of carbon over the time that it remains in storage. We show that tonne-years of carbon storage are proportional to degree-years of avoided warming, and that a physically based tonne-year accounting metric could effectively quantify and track the climate benefit of temporary carbon storage. If the world can sustain an increasing number of tonne-years alongside rapid fossil fuel CO2 emissions reductions, then the resulting carbon storage (even if only temporary) would have considerable and lasting climate value by lowering the global temperature peak.
Genotoxic effects of base and prime editing in human hematopoietic stem cells
Authors: Fiumara Martina , Ferrari Samuele , Omer-Javed Attya , Beretta Stefano , Albano Luisa , Canarutto Daniele , Varesi Angelica , Gaddoni Chiara , Brombin Chiara , Cugnata Federica , Zonari Erika , Naldini Matteo Maria , Barcella Matteo , Gentner Bernhard , Merelli Ivan , Naldini Luigi 
Published: September 2023

AbstractBase and prime editors (BEs and PEs) may provide more precise genetic engineering than nuclease-based approaches because they bypass the dependence on DNA double-strand breaks. However, little is known about their cellular responses and genotoxicity. Here, we compared state-of-the-art BEs and PEs and Cas9 in human hematopoietic stem and progenitor cells with respect to editing efficiency, cytotoxicity, transcriptomic changes and on-target and genome-wide genotoxicity. BEs and PEs induced detrimental transcriptional responses that reduced editing efficiency and hematopoietic repopulation in xenotransplants and also generated DNA double-strand breaks and genotoxic byproducts, including deletions and translocations, at a lower frequency than Cas9. These effects were strongest for cytidine BEs due to suboptimal inhibition of base excision repair and were mitigated by tailoring delivery timing and editor expression through optimized mRNA design. However, BEs altered the mutational landscape of hematopoietic stem and progenitor cells across the genome by increasing the load and relative proportions of nucleotide variants. These findings raise concerns about the genotoxicity of BEs and PEs and warrant further investigation in view of their clinical application.
Integration of spatial and single-cell data across modalities with weakly linked features
Authors: Chen Shuxiao , Zhu Bokai , Huang Sijia , Hickey John W. , Lin Kevin Z. , Snyder Michael , Greenleaf William J. , Nolan Garry P. , Zhang Nancy R. , Ma Zongming 
Published: September 2023

Abstract
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori ‘linked’ features. We describe matching X-modality via fuzzy smoothed embedding (MaxFuse), a cross-modal data integration method that, through iterative coembedding, data smoothing and cell matching, uses all information in each modality to obtain high-quality integration even when features are weakly linked. MaxFuse is modality-agnostic and demonstrates high robustness and accuracy in the weak linkage scenario, achieving 20~70% relative improvement over existing methods under key evaluation metrics on benchmarking datasets. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, MaxFuse enabled the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis
Authors: Gu Zhoulin , Gong Junyi , Zhu Zhou , Li Zhen , Feng Qi , Wang Changsheng , Zhao Yan , Zhan Qilin , Zhou Congcong , Wang Ahong , Huang Tao , Zhang Lei , Tian Qilin , Fan Danlin , Lu Yiqi , Zhao Qiang , Huang Xuehui , Yang Shihua , Han Bin 
Published: September 2023

AbstractExploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica–indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica–japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.
Monitoring of carbon-water fluxes at Eurasian meteorological stations using random forest and remote sensing
Authors: Xie Mingjuan , Ma Xiaofei , Wang Yuangang , Li Chaofan , Shi Haiyang , Yuan Xiuliang , Hellwich Olaf , Chen Chunbo , Zhang Wenqiang , Zhang Chen , Ling Qing , Gao Ruixiang , Zhang Yu , Ochege Friday Uchenna , Frankl Amaury , De Maeyer Philippe , Buchmann Nina , Feigenwinter Iris , Olesen Jørgen E. , Juszczak Radoslaw , Jacotot Adrien , Korrensalo Aino , Pitacco Andrea , Varlagin Andrej , Shekhar Ankit , Lohila Annalea , Carrara Arnaud , Brut Aurore , Kruijt Bart , Loubet Benjamin , Heinesch Bernard , Chojnicki Bogdan , Helfter Carole , Vincke Caroline , Shao Changliang , Bernhofer Christian , Brümmer Christian , Wille Christian , Tuittila Eeva-Stiina , Nemitz Eiko , Meggio Franco , Dong Gang , Lanigan Gary , Niedrist Georg , Wohlfahrt Georg , Zhou Guoyi , Goded Ignacio , Gruenwald Thomas , Olejnik Janusz , Jansen Joachim , Neirynck Johan , Tuovinen Juha-Pekka , Zhang Junhui , Klumpp Katja , Pilegaard Kim , Šigut Ladislav , Klemedtsson Leif , Tezza Luca , Hörtnagl Lukas , Urbaniak Marek , Roland Marilyn , Schmidt Marius , Sutton Mark A. , Hehn Markus , Saunders Matthew , Mauder Matthias , Aurela Mika , Korkiakoski Mika , Du Mingyuan , Vendrame Nadia , Kowalska Natalia , Leahy Paul G. , Alekseychik Pavel , Shi Peili , Weslien Per , Chen Shiping , Fares Silvano , Friborg Thomas , Tallec Tiphaine , Kato Tomomichi , Sachs Torsten , Maximov Trofim , di Cella Umberto Morra , Moderow Uta , Li Yingnian , He Yongtao , Kosugi Yoshiko , Luo Geping 
Published: September 2023

AbstractSimulating the carbon-water fluxes at more widely distributed meteorological stations based on the sparsely and unevenly distributed eddy covariance flux stations is needed to accurately understand the carbon-water cycle of terrestrial ecosystems. We established a new framework consisting of machine learning, determination coefficient (R2), Euclidean distance, and remote sensing (RS), to simulate the daily net ecosystem carbon dioxide exchange (NEE) and water flux (WF) of the Eurasian meteorological stations using a random forest model or/and RS. The daily NEE and WF datasets with RS-based information (NEE-RS and WF-RS) for 3774 and 4427 meteorological stations during 2002–2020 were produced, respectively. And the daily NEE and WF datasets without RS-based information (NEE-WRS and WF-WRS) for 4667 and 6763 meteorological stations during 1983–2018 were generated, respectively. For each meteorological station, the carbon-water fluxes meet accuracy requirements and have quasi-observational properties. These four carbon-water flux datasets have great potential to improve the assessments of the ecosystem carbon-water dynamics.
Environmental impact assessment of rice mill waste valorisation to glucose through biorefinery platform
Authors: Abu-Bakar Nurul Ain , Roslan Ahmad Muhaimin , Hassan Mohd Ali , Rahman Mohammad Hariz Abdul , Ibrahim Khairul Nadiah , Abd Rahman Muhammad Daaniyall , Mohamad Rozyanti 
Published: September 2023

AbstractEnvironmental impact assessment of glucose production from paddy milling waste, known as empty and partially filled paddy grain (EPFG) in Malaysia, was performed using life cycle assessment (LCA). Three scenarios were conducted based on system expansion of the process. The LCA was conducted using ReCiPe methodology at midpoint and endpoint levels. The results indicate that enzymatic hydrolysis phase is the hotspot in the conversion system due to enzyme production. In addition, the agriculture phase also contributed to negative impacts, especially towards climate change. An improved environmental load was observed in scenario 2 when all EPFG fractionation was utilised to replace fossil-based electricity. Sensitivity analysis showed an increase in glucose yield leads to reduced environmental impact. Thus, the LCA study suggests that the conversion process of EPFG could further benefit and improve the paddy industry waste management with low impact contribution to the environment compared to other feedstock used for glucose production.
Optimal control of quantum state preparation and entanglement creation in two-qubit quantum system with bounded amplitude
Authors: Li Xikun 
Published: September 2023

AbstractWe consider the optimal control problem in a two-qubit system with bounded amplitude. Two cases are studied: quantum state preparation and entanglement creation. Cost functions, fidelity and concurrence, are optimized over bang-off controls for various values of the total duration, respectively. For quantum state preparation problem, three critical time points are determined accurately, and optimal controls are estimated. A better estimation of the quantum speed limit is obtained, so is the time-optimal control. For entanglement creation problem, two critical time points are determined, one of them is the minimal time to achieve maximal entanglement (unit concurrence) starting from the product state. In addition, the comparisons between bang-off and chopped random basis (CRAB) are made.