bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hexokinase 2: The preferential target of trehalose‐6‐phosphate over hexokinase 1
Authors: Magalhães Rayne S. S. , Boechat Fernanda C. , Brasil Aline A. , Neto José. R. M. , Ribeiro Gabriela D. , Paranhos Luan H. , Neves de Souza Natália , Vieira Tuane , Outeiro Tiago F. , Neves Bianca C. , Eleutherio Elis C. A. 
Published: August 2022

AbstractCancer‐related metabolic features are in part maintained by hexokinase 2 upregulation, which leads to high levels of glucose‐6‐phosphate (G6P) and is needed to provide energy and biomass to support rapid proliferation. Using a humanized model of the yeast Saccharomyces cerevisiae, we explored how human hexokinase 2 (HK2) behaves under different nutritional conditions. At high glucose levels, yeast presents aerobic glycolysis through a regulatory mechanism known as catabolic repression, which exerts a metabolic adaptation like the Warburg effect. At high glucose concentrations, HK2 did not translocate into the nucleus and was not able to shift the metabolism toward a highly glycolytic state, in contrast to the effect of yeast hexokinase 2 (Hxk2), which is a crucial protein for the control of aerobic glycolysis in S. cerevisiae. During the stationary phase, when glucose is exhausted, Hxk2 is shuttled out of the nucleus, ceasing catabolic repression. Cells harvested at this condition display low glucose consumption rates. However, glucose‐starved cells expressing HK2 had an increased capacity to consume glucose. In those cells, HK2 localized to mitochondria, becoming insensitive to G6P inhibition. We also found that the sugar trehalose‐6‐phosphate (T6P) is a human HK2 inhibitor, like yeast Hxk2, but was not able to inhibit human HK1, the isoform that is ubiquitously expressed in almost all mammalian tissues. In contrast to G6P, T6P inhibited HK2 even when HK2 was associated with mitochondria. The binding of HK2 to mitochondria is crucial for cancer survival and proliferation. T6P was able to reduce the cell viability of tumor cells, although its toxicity was not impressive. This was expected as cell absorption of phosphorylated sugars is low, which might be counteracted using nanotechnology. Altogether, these data suggest that T6P may offer a new paradigm for cancer treatment based on specific inhibition of HK2.
Prediction of self‐diffusion coefficients of chemically diverse pure liquids by all‐atom molecular dynamics simulations
Authors: Baba Hiromi , Urano Ryo , Nagai Tetsuro , Okazaki Susumu 
Published: August 2022

AbstractMolecular self‐diffusion coefficients underlie various kinetic properties of the liquids involved in chemistry, physics, and pharmaceutics. In this study, 547 self‐diffusion coefficients are calculated based on all‐atom molecular dynamics (MD) simulations of 152 diverse pure liquids at various temperatures employing the OPLS4 force field. The calculated coefficients are compared with experimental data (424 extracted from the literature and 123 newly measured by pulsed‐field gradient nuclear magnetic resonance). The calculations well agree with the experimental values. The determination coefficient and root mean square error between the observed and calculated logarithmic self‐diffusion coefficients of the 547 entries are 0.931 and 0.213, respectively, demonstrating that the MD calculation can be an excellent industrial tool for predicting, for example, molecular transportation in liquids such as the diffusion of active ingredients in biological and pharmaceutical liquids. The self‐diffusion coefficients collected in this study are compiled into a database for broad researches including artificial intelligence calculations.
Asymmetric depth‐filtration: A versatile and scalable method for high‐yield isolation of extracellular vesicles with low contamination
Authors: Chernyshev Vasiliy S. , Chuprov‐Netochin Roman N. , Tsydenzhapova Ekaterina , Svirshchevskaya Elena V. , Poltavtseva Rimma A. , Merdalimova Anastasiia , Yashchenok Alexey , Keshelava Amiran , Sorokin Konstantin , Keshelava Varlam , Sukhikh Gennadiy T. , Gorin Dmitry , Leonov Sergey , Skliar Mikhail 
Published: August 2022

AbstractWe developed a novel asymmetric depth filtration (DF) approach to isolate extracellular vesicles (EVs) from biological fluids that outperforms ultracentrifugation and size‐exclusion chromatography in purity and yield of isolated EVs. By these metrics, a single‐step DF matches or exceeds the performance of multistep protocols with dedicated purification procedures in the isolation of plasma EVs. We demonstrate the selective transit and capture of biological nanoparticles in asymmetric pores by size and elasticity, low surface binding to the filtration medium, and the ability to cleanse EVs held by the filter before their recovery with the reversed flow all contribute to the achieved purity and yield of preparations. We further demonstrate the method's versatility by applying it to isolate EVs from different biofluids (plasma, urine, and cell culture growth medium). The DF workflow is simple, fast, and inexpensive. Only standard laboratory equipment is required for its implementation, making DF suitable for low‐resource and point‐of‐use locations. The method may be used for EV isolation from small biological samples in diagnostic and treatment guidance applications. It can also be scaled up to harvest therapeutic EVs from large volumes of cell culture medium.
Flavor differences of soybean and defatted soybean fermented soy sauce and its correlation with the enzyme profiles of the kojis
Authors: Tian Yi‐Fan , Chen Yu‐Xing , Tong Xing , Hou Sha , Zhao Mou‐Ming , Feng Yun‐Zi 
Published: August 2022

AbstractBACKGROUNDSoybeans and defatted soybeans, commonly used as protein ingredients, have different flavors of their fermented soy sauce. Clarifying the differences between the two soy sauces, as well as the formation mechanism, is an important prerequisite for improving the flavor of defatted soybean soy sauce. To this goal, the aroma characteristics of two soy sauces and their volatile profiles were compared by sensory evaluation and gas chromatography‐mass spectrometry, and eight enzyme activities and volatile profiles of matured koji were determined.RESULTSSensory results showed that the acids, fruity and cooked potato‐like attributes were higher in whole soybean fermented soy sauce, whereas defatted soybean soy sauce exhibited higher smoky and malty attributes, closely related to the contents of aroma‐active compounds in soy sauce, such as isobutyl acetate, 2/3‐methylbutanal, acetic acid and 2/3‐methylbutanoic acid. The content of most volatiles in the matured kojis showed a consistent trend with that of soy sauce: alcohols, acids, furan(one)s and ketones. Interestingly, acid protease and cellulase activities were 3.3 and 1.6 times higher in the whole soybean koji than in defatted soybean koji, respectively, whereas neutral protease, aminopeptidase, glucoamylase and β‐glucosidase were approximately 2.0 times higher in defatted soybean koji.CONCLUSIONIn summary, the flavor differences between soybean and defatted soybean fermented soy sauce were not only caused by the differences in the content of flavor precursors in the materials, but also closely related to the differences in the enzymatic profiles accumulated during the koji‐making process. © 2022 Society of Chemical Industry.
Presence of a resident species aids invader evolution
Authors: Lachapelle Josianne , Bestion Elvire , Jackson Eleanor E. , Schaum C.‐Elisa 
Published: August 2022

AbstractInteractions between phytoplankton species shape their physiological and evolutionary responses. Yet, studies addressing the evolutionary responses of phytoplankton in changing environments often lack an explicit element of biotic interactions. Here, we ask (1) how the presence of a locally adapted phytoplankton species will affect an invading phytoplankton species' evolutionary response to a physiologically challenging environment; (2) whether this response is conserved across environments varying in quality; and (3) which traits are associated with being a successful invader under climate change scenarios. In a conceptual first step to disentangle these broad questions, we experimentally evolved populations of fresh‐ and seawater phytoplankton in a novel salinity (the freshwater green algae Chlamydomonas in salt water, and the marine Ostreococcus in freshwater), either as mono‐cultures (colonizers) or as co‐cultures (invaders: invading a novel salinity occupied by a resident species, for example, Chlamydomonas invading salt water occupied by resident Ostreococcus) for 200 generations. We superimposed a temperature treatment (control (22°C), mild warming (26°C), drastic warming (32°C), and fluctuating (22°C/32°C) warming) as a representative aspect of climate change with the potential to ameliorate or deteriorate existing environmental conditions. Invaders had systematically lower extinction rates and evolved overall higher growth rates, as well as broader salinity and temperature preferences than colonizers. The invading species' evolutionary responses differed from those of colonizers in a replicable way across environments of differing quality. The evolution of small cell size and high reactive oxygen species tolerance may explain the invaders' higher fitness under the scenarios tested here.
Transmission Laser Welding of Similar and Dissimilar Semiconductor Materials
Authors: Sopeña Pol , Wang Andong , Mouskeftaras Alexandros , Grojo David 
Published: August 2022

AbstractLaser micro‐welding is an advanced manufacturing method today applied in various domains. However, important physical limitations have prevented so far to demonstrate its applicability in silicon (Si) and other technology‐essential semiconductors. Concentrating on circumventing the optical limits on the deliverable energy density at interfaces between narrow‐gap materials with intense infrared light, the first feasibility demonstration of transmission laser welding between Si workpieces using nanosecond laser pulses is made. A shear joining strength of 32 ± 10 MPa which compares very favorably to the complex process alternatives is obtained. Supported by experiments repeated on different material combinations including gallium arsenide, it is confirmed that this remarkable performance level is achievable for similar and dissimilar semiconductors. The demonstrations rely on a small footprint fiber laser, an aspect that holds great promises for the advent of a high‐efficiency flexible process beneficial for important technology developments including lab‐on‐a‐chip and hybrid semiconductor systems.
Printed Polymer‐Stabilized Chiral Nematic Liquid Crystal Privacy Windows
Authors: Li Mengmeng , Kamal Waqas , Orr Andrew C. J. , Castrejón‐Pita Alfonso A. , Elston Steve J. , Morris Stephen M. 
Published: August 2022

AbstractIn this paper, drop‐on‐demand (DoD) printing is demonstrated of polymer stabilized chiral nematic liquid crystal (PSCLC) privacy windows that can function in either a conventional mode (scattering to transparent) or reverse mode (transparent to scattering) with the application of an electric field. Inkjet printed droplets of the PSCLC mixture, with diameters of the order of 100–200 µm and sandwiched in LC layer thicknesses of ≈10–15 µm, are characterized in terms of their transmission as a function of the electric field amplitude and the response times for switching into and out of the scattering state. The results show that the printed droplets, and arrays thereof, exhibit similar electro‐optical properties to analogous thin‐film devices, but with the ability to incorporate bespoke features such as images and decorative patterns. Finally, the electro‐optical switching of a printed PSCLC privacy window whereby alphanumeric characters can be made to appear and disappear with the application of an electric field is demonstrated.
Exploration of the interchromosomal effects in preimplantation genetic testing for structural rearrangements based on next‐generation sequencing
Authors: Fan Junmei , Zhang Xueluo , Chen Yanhua , Zhang Junkun , Zhang Lei , Bi Xingyu , Wang Jinbao , Huang Xiang , Yan Meiqin , Wu Xueqing 
Published: August 2022

AbstractBackgroundTo investigate the interchromosomal effect (ICE) in chromosome translocation carriers.MethodsData on preimplantation genetic testing aneuploidy and structural rearrangements (translocation) were retrospectively collected and classified into a reciprocal translocation group, a Robertsonian translocation group and a control group. According to the carrier's gender and age, all cases underwent further subgroup difference analysis of de novo abnormal embryo rates and the number of chromosomes involved in de novo abnormal embryos.ResultsAmong the 283 couples who participated in this study, 1076 blastocysts from 352 cycles were collected, and 246 de novo abnormal embryos were included. There was a significant difference in the rate of de novo abnormal embryos among the three groups (p < .05) but no significant difference in the number of de novo abnormal chromosomes in the abnormal embryos (p > .05). Gender and age (classified by 35 years old) had no effect on the de novo abnormal embryo ratios among the translocation carriers (p > .05). However, the de novo abnormal ratio increased with age. The embryo constitution reflected no significant difference between the translocation groups (p > .05).ConclusionThe ICE was detected for the translocation carriers. The de novo abnormal embryo ratio increased with age. Gender had no effect on the de novo abnormal embryo ratio. Translocation status played a more important role than age and gender.
A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction
Authors: Zhu Baoli , Karwautz Clemens , Andrei Stefan , Klingl Andreas , Pernthaler Jakob , Lueders Tillmann 
Published: August 2022

Impact statementMethane oxidizing microbes play a key role in reducing the emission of this potent greenhouse gas to the atmosphere. The known versatility of the recently discovered anaerobic Methylomirabilota methanotrophs is limited. Here, we report a novel uncultured Methylomirabilis species, Candidatus Methylomirabilis iodofontis, with the genetic potential of iodate respiration from biofilm in iodine‐rich cavern spring water. Star‐like cells resembling Methylomirabilis oxyfera were directly observed from the biofilm and a high‐quality metagenome‐assembled genome (MAG) of Ca. M. iodofontis was assembled. In addition to oxygenic denitrification and aerobic methane oxidation pathways, the M. iodofontis MAG also indicated its iodate‐reducing potential, a capability that would enable the bacterium to use iodate other than nitrite as an electron acceptor, a hitherto unrecognized metabolic potential of Methylomirabilota methanotrophs. The results advance the current understanding of the ecophysiology of anaerobic Methylomirabilota methanotrophs and may suggest an additional methane sink, especially in iodate‐rich ecosystems.
Design of a filtration system to improve the dose distribution of an accelerator‐based neutron capture therapy system
Authors: Hu Naonori , Tanaka Hiroki , Ono Koji 
Published: August 2022

AbstractPurposeThe aim of this study is to design and evaluate a neutron filtration system to improve the dose distribution of an accelerator‐based neutron capture therapy system.MethodsAn LiF‐sintered plate composed of 99%‐enriched 6Li was utilized to filter out low‐energy neutrons to increase the average neutron energy at the beam exit. A 5‐mm thick filter to fit inside a 12‐cm diameter circular collimator was manufactured, and experimental measurements were performed to measure the thermal neutron flux and gamma‐ray dose rate inside a water phantom. The experimental measurements were compared with the Monte Carlo simulation, particle, and heavy ion transport code system. Following the experimental verification, three filter designs were modeled, and the thermal neutron flux and the biologically weighted dose distribution inside a phantom were simulated. Following the phantom simulation, a dummy patient CT dataset was used to simulate a boron neutron capture therapy (BNCT) irradiation of the brain. A mock tumor located at 4, 6, 8 cm along the central axis and 4‐cm off‐axis was set, and the dose distribution was simulated for a maximum total biologically weighted brain dose of 12.5 Gy with a beam entering from the vertex.ResultsAll three filters improved the beam penetration of the accelerator‐based neutron source. Filter design C was found to be the most suitable filter, increasing the advantage depth from 9.1 to 9.9 cm. Compared with the unfiltered beam, the mean weighted dose in the tumor located at a depth of 8 cm along the beam axis was increased by ∼25%, and 34% for the tumor located at a depth of 8 cm and off‐axis by 4 cm.ConclusionA neutron filtration system for an accelerator‐based BNCT system was investigated using Monte Carlo simulation. The proposed filter design significantly improved the dose distribution for the treatment of deep targets in the brain.
Assessment of dose‐volume histogram precision for five clinical systems
Authors: Pepin Mark D. , Penoncello Gregory P. , Brom Kevin M. , Gustafson Jon M. , Long Kenneth M. , Rong Yi , Fong de los Santos Luis E. , Shiraishi Satomi 
Published: August 2022

AbstractPurposeTo investigate the dependency of dose‐volume histogram (DVH) behavior and precision on underlying discretization using shapes and dose distributions with known analytical DVHs for five commercial DVH calculators.MethodsDVHs and summary metrics were extracted from all five systems using synthetic cone and cylinder objects for which the true volume and DVH curves were known. Trends in the curves and metrics were explored by varying the underlying voxelization of the CT image, structure set, and dose grid as well by varying the geometry of the structure and direction of a linear dose gradient. Using synthetic structures allowed for comparison with ground truth DVH curves to assess their accuracy while an algorithm was additionally developed to assess the precision of each system. The precision was calculated with a novel algorithm that treats any “stair step” behavior in a DVH curve as an uncertainty band and calculates the width, characterized as a percent difference, of the band for various DVH metrics. The underlying voxelization was additionally changed and DVHs were extracted for two clinical examples. The details of how each system calculated DVHs were also investigated and tendencies in the calculated curves, metrics, and precision were related to choices made in the calculation methodology.ResultsCalculation methodology differences that had a noticeable impact on the DVH curves and summary metrics include supersampling beyond the input grids and interpretation of the superior and inferior ends of the structures. Among the systems studied, the median precision ranged from 0.902% to 3.22%, and interquartile ranges varied from 1.09% to 3.91%.ConclusionsCommercial dose‐evaluation solutions can calculate different DVH curves, structure volume measures, and dose statistics for the same input data due to differences in their calculation methodologies. This study highlights the importance of understanding and investigating the DVH calculation when considering a new clinical system and when using more than one system for data transfer.
Dual‐domain reconstruction network with V‐Net and K‐Net for fast MRI
Authors: Liu Xiaohan , Pang Yanwei , Jin Ruiqi , Liu Yu , Wang Zhenchang 
Published: August 2022

PurposeTo introduce a dual‐domain reconstruction network with V‐Net and K‐Net for accurate MR image reconstruction from undersampled k‐space data.MethodsMost state‐of‐the‐art reconstruction methods apply U‐Net or cascaded U‐Nets in the image domain and/or k‐space domain. Nevertheless, these methods have the following problems: (1) directly applying U‐Net in the k‐space domain is not optimal for extracting features; (2) classical image‐domain–oriented U‐Net is heavyweighted and hence inefficient when cascaded many times to yield good reconstruction accuracy; (3) classical image‐domain–oriented U‐Net does not make full use of information of the encoder network for extracting features in the decoder network; and (4) existing methods are ineffective in simultaneously extracting and fusing features in the image domain and its dual k‐space domain. To tackle these problems, we present 3 different methods: (1) V‐Net, an image‐domain encoder–decoder subnetwork that is more lightweight for cascading and effective in fully utilizing features in the encoder for decoding; (2) K‐Net, a k‐space domain subnetwork that is more suitable for extracting hierarchical features in the k‐space domain, and (3) KV‐Net, a dual‐domain reconstruction network in which V‐Nets and K‐Nets are effectively combined and cascaded.ResultsExtensive experimental results on the fastMRI dataset demonstrate that the proposed KV‐Net can reconstruct high‐quality images and outperform state‐of‐the‐art approaches with fewer parameters.ConclusionsTo reconstruct images effectively and efficiently from incomplete k‐space data, we have presented a dual‐domain KV‐Net to combine K‐Nets and V‐Nets. The KV‐Net achieves better results with 9% and 5% parameters than comparable methods (XPD‐Net and i‐RIM).
Improving Abundance Estimates of Spring–Summer Snake River Chinook Salmon for Fisheries Management
Authors: Coykendall D. Katharine , Delomas Thomas A. , Belnap Matthew , Campbell Matthew R. 
Published: August 2022

Abstract
The Columbia River basin is home to a run of spring–summer Chinook Salmon Oncorhynchus tshawytscha that returns to the Snake River drainage of Idaho, Oregon, and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River basin. However, Snake River spring–summer Chinook Salmon have experienced declines in abundance due to overfishing, habitat degradation, and dams. Several stocks are listed as threatened under the U.S. Endangered Species Act and are supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan, and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, PIT-tagged as juveniles and detected at Lower Granite Dam, to generate adult abundance estimates. In season, these estimates inform state and tribal harvest shares and ensure that broodstock needs are met. Postseason, they provide smolt-to-adult survival and return rates. Since 2012, parentage-based tagging (PBT) has provided an alternative method to estimate stock- and age-specific returns at Lower Granite Dam, since returning hatchery adults sampled at Lower Granite Dam can be assigned to their parents. We compared stock-specific abundance estimates between PIT- and PBT-derived methodologies for return years 2016–2019. Across all years, PIT tag estimates accounted for 65% of the PBT-based estimates at Lower Granite Dam across all age-groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT-based estimates should aide in-season harvest management and postseason run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.