bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata
Authors: Ahmad Nadim , Ritz Manfred , Calchera Anjuli , Otte Jürgen , Schmitt Imke , Brueck Thomas , Mehlmer Norbert 
Published: October 2023

AbstractLichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high‐quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High‐quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.
Mesonephric‐like adenocarcinoma harbours characteristic copy number variations and a distinct DNA methylation signature closely related to mesonephric adenocarcinoma of the cervix
Authors: Kommoss Felix KF , Lee Cheng‐Han , Tessier‐Cloutier Basile , Gilks C Blake , Stewart Colin JR , von Deimling Andreas , Köbel Martin 
Published: October 2023

AbstractMesonephric‐like adenocarcinoma (MLA) of the female genital tract is an uncommon histotype that can arise in both the endometrium and the ovary. The exact cell of origin and histogenesis currently remain unknown. Here, we investigated whole genome DNA methylation patterns and copy number variations (CNVs) in a series of MLAs in the context of a large cohort of various gynaecological carcinoma types. CNV analysis of 19 MLAs uncovered gains of chromosomes 1q (18/19, 95%), 10 (15/19, 79%), 12 (14/19, 74%), and 2 (10/19, 53%), as well as loss of chromosome 1p (7/19, 37%). Gains of chromosomes 1q, 10, and 12 were also identified in the majority of mesonephric adenocarcinomas of the uterine cervix (MAs) as well as subsets of endometrioid carcinomas (ECs) and low‐grade serous carcinomas of the ovary (LGSCs) but only in a minority of serous carcinomas of the uterine corpus (USCs), clear cell carcinomas (CCCs), and tubo‐ovarian high‐grade serous carcinomas (HGSCs). While losses of chromosome 1p together with gains of chromosome 1q were also identified in both MA and LGSC, gains of chromosome 2 were almost exclusively identified in MLA and MA. Unsupervised hierarchical clustering and t‐SNE analysis of DNA methylation data (Illumina EPIC array) identified a co‐clustering for MLAs and MAs, which was distinct from clusters of ECs, USCs, CCCs, LGSCs, and HGSCs. Group‐wise comparisons confirmed a close epigenetic relationship between MLA and MA. These findings, in conjunction with the established histological and immunophenotypical overlap, suggest bona fide mesonephric differentiation, and support a more precise terminology of mesonephric‐type adenocarcinoma instead of MLA in these tumours. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
How to account for early overly small risk sets in the analysis of pregnancy outcome data?—Comparison of different methods for stabilizing the Aalen‐Johansen estimator
Authors: Stegherr Regina , Fietz Anne‐Katrin , Hoeltzenbein Maria , Dathe Katarina , Beyersmann Jan 
Published: October 2023

AbstractPurposeIn analyzing pregnancy data concerning drug exposure in the first trimester, the risk of spontaneous abortions is of primary interest. For estimating the cumulative incidence function, the Aalen–Johansen estimator is typically used, and competing risks such as induced abortion and livebirth are considered. However, the delayed study entry can lead to overly small risk sets for the first events. This results in large jumps in the estimated cumulative incidence function of spontaneous abortions or induced abortions using the Aalen–Johansen estimator, and consequently in an overestimation of the probability.MethodsSeveral approaches account for early overly small risk sets. The first approach is conditioning on the event time being greater than the event time causing the large jump. Second, the events can be ignored by censoring them. Third, the events can be postponed until a large enough number is at risk. These three approaches are compared.ResultsAll approaches are applied using data of 54 lacosamide‐exposed pregnancies. The Aalen–Johansen estimate of the probability of spontaneous abortion is 22.64%, which is relatively large for only three spontaneous abortions in the dataset. The conditional approach and the ignore approach have an estimated probability of 7.17%. In contrast, the estimate of the postpone approach is 16.45%. In this small sample, bootstrapped confidence intervals seem more accurate.ConclusionsIn the analyses of pregnancy data with rare events, the postpone approach is favorable as no events are excluded. However, the approach that ignores early events has the narrowest confidence interval.
Development of photocatalysis‐membrane separation reactor systems for aqueous pollutant removal
Authors: Zhang Junyang , Miao Yingchun , Huo Yuning , Li Hexing 
Published: October 2023

AbstractBackgroundIn our rapidly expanding society, the demand for clean water has steadily emerged as one of the most critical issues, promoting the development of numerous water treatment strategies.AimsCoupling photocatalysis and membrane separation technology provides an energy saving and environment‐friendly as well as sustainable method for aqueous pollutants removal due to the synergetic enhanced pollutant removal efficiency and improved anti‐fouling performance. It is of great scientific and technical significance to construct multifunctional photocatalysis‐membrane separation reactor systems (PMRs) with both the high photocatalytic activity and the strong stability.DiscussionHerein, in order to introduce the recent advances of this field, we present a critical review on developments of PMRs for aqueous pollutant removal, which includes photocatalysts and membranes, advanced methods for designing PMRs. Meanwhile, the recent applications of PMRs in aqueous pollutant removal, antifouling strategies, and mechanisms have also been summarized, including the latest development of PMRs coupling with other treatment methods. Furthermore, future perspective of PMRs is outlooked and predicted.ConclusionPMRs, designed for the removal of aqueous pollutants, offer a more promising solution for the sustainable development of our society in the future.
International study of physicians' opinion on physician–patient sex concordance when treating athletes
Authors: Tsukahara Yuka , Novak Melissa , Takei Seira , Asif Irfan M. , Yamasawa Fumihiro , Torii Suguru , Akama Takao , Matsumoto Hideo , Day Carly 
Published: October 2023

AbstractBackgroundThe effect of physician–patient sex concordance in medicine has been reported in many studies. Whether physicians believe that the sex concordance between physician and athlete influences treatment has not been investigated.ObjectiveTo determine whether physicians believe that the sex concordance between physician and athlete influences treatment.DesignCross‐sectional study.SettingOnline survey.ParticipantsOne thousand one hundred ninety‐three sports medicine physicians in 51 countries. Participants were sports medicine physicians trained in orthopedics (n = 443 [37.1%]) and nonorthopedics (n = 750 [62.9%]).InterventionsNot applicable.Main Outcome MeasuresParticipants were asked to decide whether sex of the physician made them better suited to care for athletes of concordant or different sexes along with their personal background.ResultsOrthopedic sports medicine physicians agreed less than nonorthopedic sports medicine physicians regarding the statement “MALE sports medicine physicians are better suited than their female counterparts to care for MALE athletes” (odds ratio [OR] 0.56, 95% confidence interval [CI] 0.35–0.91, p = .02), and compared to sports medicine physicians based in Europe, those based in Asia agreed more to this statement (OR 7.91, 95% CI 4.60–13.60, p < .01). In addition, regarding the statement “FEMALE sports medicine physicians are better suited than their male counterparts to care for FEMALE athletes,” compared to sports medicine physicians based in Europe, those based in Asia (OR 9.12, 95% CI 5.63–14.79, p < .01) and North America (OR 2.18, 95% CI 1.46–3.25, p < .01) agreed more and orthopedic sports medicine physicians agreed less than nonorthopedic sports medicine physicians (OR 0.61, 95% CI 0.39–0.93, p = .02) to this statement.ConclusionsSports medicine physicians trained in orthopedics felt sex concordance was less important than physicians trained in other specialties. Asian sports medicine physicians believed sex concordance was more important compared to physicians in other regions.
Chromogenic detection of telomere lengths in situ aids the identification of precancerous lesions in the prostate
Authors: Ertunc Onur , Smearman Erica , Zheng Qizhi , Hicks Jessica L. , Brosnan‐Cashman Jacqueline A. , Jones Tracy , Gomes‐Alexandre Carolina , Trabzonlu Levent , Meeker Alan K. , De Marzo Angelo M. , Heaphy Christopher M. 
Published: October 2023

AbstractBackgroundTelomeres are terminal chromosomal elements that are essential for the maintenance of genomic integrity. The measurement of telomere content provides useful diagnostic and prognostic information, and fluorescent methods have been developed for this purpose. However, fluorescent‐based tissue assays are cumbersome for investigators to undertake, both in research and clinical settings.MethodsA robust chromogenic in situ hybridization (CISH) approach was developed to visualize and quantify telomere content at single cell resolution in human prostate tissues, both frozen and formalin‐fixed, paraffin‐embedded (FFPE).ResultsThis new assay (telomere chromogenic in situ hybridization [“Telo‐CISH”]) produces permanently stained slides that are viewable with a standard light microscope, thus avoiding the need for specialized equipment and storage. The assay is compatible with standard immunohistochemistry, thereby allowing simultaneous assessment of histomorphology, identification of specific cell types, and assessment of telomere status. In addition, Telo‐CISH eliminates the problem of autofluorescent interference that frequently occurs with fluorescent‐based methods. Using this new assay, we demonstrate successful application of Telo‐CISH to help identify precancerous lesions in the prostate by the presence of markedly short telomeres specifically in the luminal epithelial cells.ConclusionsIn summary, with fewer restrictions on the types of tissues that can be tested, and increased histologic information provided, the advantages presented by this novel chromogenic assay should extend the applicability of tissue‐based telomere length assessment in research and clinical settings.
RNAi‐mediated silencing of Mediterranean fruit fly (Ceratitis capitata) endogenous genes using orally‐supplied double‐stranded RNAs produced in Escherichia coli
Authors: Ortolá Beltrán , Urbaneja Alberto , Eiras Marcelo , Pérez‐Hedo Meritxell , Daròs José‐Antonio 
Published: October 2023

AbstractBACKGROUNDThe Mediterranean fruit fly (medfly), Ceratitis capitata Wiedemann, is a major pest affecting fruit and vegetable production worldwide, whose control is mainly based on insecticides. Double‐stranded RNA (dsRNA) able to down‐regulate endogenous genes, thus affecting essential vital functions via RNA interference (RNAi) in pests and pathogens, is envisioned as a more specific and environmentally‐friendly alternative to traditional insecticides. However, this strategy has not been explored in medfly yet.RESULTSHere, we screened seven candidate target genes by injecting in adult medflies gene‐specific dsRNA hairpins transcribed in vitro. Several genes were significantly down‐regulated, resulting in increased insect mortality compared to flies treated with a control dsRNA targeting the green fluorescent protein (GFP) complementary DNA (cDNA). Three of the dsRNAs, homologous to the beta subunit of adenosine triphosphate (ATP) synthase (ATPsynbeta), a vacuolar ATPase (V‐ATPase), and the ribosomal protein S13 (RPS13), were able to halve the probability of survival in only 48 h after injection. We then produced new versions of these three dsRNAs and that of the GFP control as circular molecules in Escherichia coli using a two‐self‐splicing‐intron‐based expression system and tested them as orally‐delivered insecticidal compounds against medfly adults. We observed a significant down‐regulation of V‐ATPase and RPS13 messenger RNAs (mRNAs) (approximately 30% and 90%, respectively) compared with the control medflies after 3 days of treatment. No significant mortality was recorded in medflies, but egg laying and hatching reduction was achieved by silencing V‐ATPase and RPS13.CONCLUSIONIn sum, we report the potential of dsRNA molecules as oral insecticide in medfly. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Rational design, synthesis and binding mechanisms of novel benzyl geranate derivatives as potential eco‐friendly aphid repellents
Authors: Pan Shi‐Xiang , Yang Zhao‐Kai , Liu Yan , Shi Zhuo , Qin Yao‐Guo , Qu Cheng , Li Xue‐Sheng , Zhou Zheng‐Xin , Luo Chen , Yang Xin‐Ling 
Published: October 2023

AbstractBACKGROUNDThe push–pull strategy is considered as a promising eco‐friendly method for pest management. Plant volatile organic compounds (PVOCs) act as semiochemicals constitute the key factor in implementing this strategy. Benzyl alcohol and geraniol, as functional PVOCs, were reported to regulate insect behavior, showing the potential application in pest control. Using geraniol as lead, a geraniol derivative 5i with fine repellent activity was discovered in our previous work. In order to explore novel, eco‐friendly aphid control agents, a series of benzyl geranate derivatives was designed and synthesized using 5i as the lead and benzyl alcohol as the active fragment.RESULTSBenzyl alcohol was firstly evaluated to have repellent activity to Acyrthosiphon pisum. Based on this repellent fragment, a series of novel benzyl geranate derivatives was rationally designed and synthesized using a scaffold‐hopping strategy. Among them, compound T9, with a binding affinity (Kd = 0.43 μm) and a substantial repellency of 64.7% against A. pisum, is the most promising compound. Molecule docking showed that hydrophobic and hydrogen‐bonding interactions substantially influenced the binding affinity of compounds with ApisOBP9. Additionally, T9 exhibited low‐toxicity to honeybees and ladybugs.CONCLUSIONUsing a simple scaffold‐hopping strategy combined with active fragment benzyl alcohol, a new derivative T9, with high aphid‐repellency and low‐toxicity to nontarget organisms, can be considered as a novel potential eco‐friendly aphid control agent for sustainable agriculture. © 2023 Society of Chemical Industry.
A performance assessment methodology with coupling between layers for LP‐DMC systems
Authors: Chen Xingyu , Li Lijuan , Yang Shipin 
Published: October 2023

AbstractFor the estimation of performance improvement potentials of LP‐DMC systems, a novel performance assessment methodology with the optimal benchmark considering the coupling between layers was proposed. The controlled variable tracking residuals and variable fluctuations are introduced as the coupling factors that the dynamic layer acts on the steady‐state layer. Correspondingly, the constraint scaling factor and fluctuation domain are introduced as the coupling factors that the steady‐state layer acts on the dynamic layer. The solutions of the two layers are interactive and iterative and eventually converge to optimal results. Then, the optimal results are utilized as the optimal criteria to define the assessment indexes of LP‐DMC. The experiment results in a simulation and an industrial process indicate the validity and rationality of the proposed methodology.
Sustainability assessment in cities in the eastern amazon
Authors: Lima Joana Alicia Pantoja , Progênio Mayke Feitosa , Costa Carlos Eduardo Aguiar de Souza , Crispim Diêgo Lima 
Published: October 2023

AbstractIndicators are important tools that help monitor and assess sustainability, providing crucial information for public management. This study aimed to analyze the behavior of municipalities in eastern amazon (State of Pará), through sustainability indicators that cover social, economic, environmental and basic sanitation dimensions, applying the statistical method of multivariate analysis. For the selection of indicators, a checklist of academic papers on sustainability was carried out. For the composition of the clusters, the Ward method was applied. To validate the number of groups, the Pakhira‐Bandyopadhyay‐Maulik (PBM) index was used, obtaining 2 groups for the sanitation and general dimensions, 3 for environmental and social and 7 groups for economic. In this study, it was possible to demonstrate that several municipalities have deficiencies related to access to water supply and mainly sewage collection and treatment, causing various consequences for the population, as they do not comply with the commitments of the Sustainable Development Goals.
Size Dependent Phase Transformation of Liquid Gallium
Authors: Liu Jinyun , Song Lijian , He Zidong , Wang Shengding , Zhang Wuxu , Yang Huali , Li Fali , Li Shengbin , Wang Jianing , Xiao Huiyun , Xu Dan , Liu Yiwei , Wu Yuanzhao , Wang Jun‐Qiang , Shui Xiaoxue , Hu Yuan‐Chao , Shang Jie , Li Run‐Wei 
Published: October 2023

AbstractAs the most popular liquid metal (LM), gallium (Ga) and its alloys are emerging as functional materials due to their unique combination of fluidic and metallic properties near room temperature. As an important branch of utilizing LMs, micro‐ and submicron‐particles of Ga‐based LM are widely employed in wearable electronics, catalysis, energy, and biomedicine. Meanwhile, the phase transition is crucial not only for the applications based on this reversible transformation process, but also for the solidification temperature at which fluid properties are lost. While Ga has several solid phases and exhibits unusual size‐dependent phase behavior. This complex process makes the phase transition and undercooling of Ga uncontrollable, which considerably affects the application performance. In this work, extensive (nano‐)calorimetry experiments are performed to investigate the polymorph selection mechanism during liquid Ga crystallization. It is surprisingly found that the crystallization temperature and crystallization pathway to either α −Ga or β −Ga can be effectively engineered by thermal treatment and droplet size. The polymorph selection process is suggested to be highly relevant to the capability of forming covalent bonds in the equilibrium supercooled liquid. The observation of two different crystallization pathways depending on the annealing temperature may indicate that there exist two different liquid phases in Ga.
High‐Affinity Host–Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures
Authors: Narayanan Raghu Pradeep , Prasad Abhay , Buchberger Alex , Zou Lei , Bernal‐Chanchavac Julio , MacCulloch Tara , Fahmi Nour Eddine , Yan Hao , Zhang Fei , Webber Matthew J. , Stephanopoulos Nicholas 
Published: October 2023

AbstractThe combination of multiple orthogonal interactions enables hierarchical complexity in self‐assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host–guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 1010 m−1, directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower‐affinity β‐cyclodextrin–adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high‐affinity CB[7]–adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high‐affinity CB[7]–guest recognition as an orthogonal axis to drive self‐assembly in DNA nanotechnology.
3D Magnetic Metal‐Organic Frameworks Current Collectors Accelerate the Lithium‐Ion Diffusion Rate for Superlong Cyclic Lithium Metal Anode
Authors: Chen Haibo , Hu Jing , Li Hang , Zhang Jianli , Chen Qiang , Hou Guangya , Tang Yiping 
Published: October 2023

AbstractLithium, is the most ideal anode material for lithium‐based batteries. However, the overgrowth of lithium dendrites and the low lithium‐ion diffusion rate at low temperatures limit the further application of lithium metal anodes. Here, the applied magnetic field is introduced inside the lithium metal anode by using a novel magnetic metal‐organic framework as a current collector. The magnetic field can improve the conductivity of this novel current collector, thus accelerating the diffusion of lithium ions in the battery, an advantage that is particularly prominent at low temperatures. In addition, the current collector can stabilize the solid electrolyte interface and inhibit the growth of lithium dendrites, resulting in excellent electrochemical performance. The symmetrical cell at room temperature can exceed 4600 h with a hysteresis voltage of only 9 mV. After 300 cycles at room temperature, the capacity of full cell is still 142 mA h g−1, and it remains stable for 380 cycles at 5 °C (capacity above 120 mA h g−1). The strategy of constructing novel current collector with magnetic field can promote the further application of lithium batteries in extreme conditions such as low temperatures.