bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchically manufactured chiral plasmonic nanostructures with gigantic chirality for polarized emission and information encryption
Authors: Lee Yoon Ho , Won Yousang , Mun Jungho , Lee Sanghyuk , Kim Yeseul , Yeom Bongjun , Dou Letian , Rho Junsuk , Oh Joon Hak 
Published: November 2023

AbstractChiral metamaterials have received significant attention due to their strong chiroptical interactions with electromagnetic waves of incident light. However, the fabrication of large-area, hierarchically manufactured chiral plasmonic structures with high dissymmetry factors (g-factors) over a wide spectral range remains the key barrier to practical applications. Here we report a facile yet efficient method to fabricate hierarchical chiral nanostructures over a large area (>11.7 × 11.7 cm2) and with high g-factors (up to 0.07 in the visible region) by imparting extrinsic chirality to nanostructured polymer substrates through the simple exertion of mechanical force. We also demonstrate the application of our approach in the polarized emission of quantum dots and information encryption, including chiral quick response codes and anti-counterfeiting. This study thus paves the way for the rational design and fabrication of large-area chiral nanostructures and for their application in quantum communications and security-enhanced optical communications.
A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation
Authors: Ghanbarpour Alireza , Cohen Steven E. , Fei Xue , Kinman Laurel F. , Bell Tristan A. , Zhang Jia Jia , Baker Tania A. , Davis Joseph H. , Sauer Robert T. 
Published: November 2023

AbstractAAA+ proteases degrade intracellular proteins in a highly specific manner.E. coliClpXP, for example, relies on a C-terminal ssrA tag or other terminal degron sequences to recognize proteins, which are then unfolded by ClpX and subsequently translocated through its axial channel and into the degradation chamber of ClpP for proteolysis. Prior cryo-EM structures reveal that the ssrA tag initially binds to a ClpX conformation in which the axial channel is closed by a pore-2 loop. Here, we show that substrate-free ClpXP has a nearly identical closed-channel conformation. We destabilize this closed-channel conformation by deleting residues from the ClpX pore-2 loop. Strikingly, open-channel ClpXP variants degrade non-native proteins lacking degrons faster than the parental enzymes in vitro but degraded GFP-ssrA more slowly. When expressed inE. coli, these open channel variants behave similarly to the wild-type enzyme in assays of filamentation and phage-Mu plating but resulted in reduced growth phenotypes at elevated temperatures or when cells were exposed to sub-lethal antibiotic concentrations. Thus, channel closure is an important determinant of ClpXP degradation specificity.
Leveraging information between multiple population groups and traits improves fine-mapping resolution
Authors: Zhou Feng , Soremekun Opeyemi , Chikowore Tinashe , Fatumo Segun , Barroso Inês , Morris Andrew P. , Asimit Jennifer L. 
Published: November 2023

AbstractStatistical fine-mapping helps to pinpoint likely causal variants underlying genetic association signals. Its resolution can be improved by (i) leveraging information between traits; and (ii) exploiting differences in linkage disequilibrium structure between diverse population groups. Using association summary statistics, MGflashfm jointly fine-maps signals from multiple traits and population groups; MGfm uses an analogous framework to analyse each trait separately. We also provide a practical approach to fine-mapping with out-of-sample reference panels. In simulation studies we show that MGflashfm and MGfm are well-calibrated and that the mean proportion of causal variants with PP > 0.80 is above 0.75 (MGflashfm) and 0.70 (MGfm). In our analysis of four lipids traits across five population groups, MGflashfm gives a median 99% credible set reduction of 10.5% over MGfm. MGflashfm and MGfm only require summary level data, making them very useful fine-mapping tools in consortia efforts where individual-level data cannot be shared.
Site-selected in situ polymerization for living cell surface engineering
Authors: Zhong Yihong , Xu Lijia , Yang Chen , Xu Le , Wang Guyu , Guo Yuna , Cheng Songtao , Tian Xiao , Wang Changjiang , Xie Ran , Wang Xiaojian , Ding Lin , Ju Huangxian 
Published: November 2023

AbstractThe construction of polymer-based mimicry on cell surface to manipulate cell behaviors and functions offers promising prospects in the field of biotechnology and cell therapy. However, precise control of polymer grafting sites is essential to successful implementation of biomimicry and functional modulation, which has been overlooked by most current research. Herein, we report a biological site-selected, in situ controlled radical polymerization platform for living cell surface engineering. The method utilizes metabolic labeling techniques to confine the growth sites of polymers and designs a Fenton-RAFT polymerization technique with cytocompatibility. Polymers grown at different sites (glycans, proteins, lipids) have different membrane retention time and exhibit differential effects on the recognition behaviors of cellular glycans. Of particular importance is the achievement of in situ copolymerization of glycomonomers on the outermost natural glycan sites of cell membrane, building a biomimetic glycocalyx with distinct recognition properties.
An integrated study to decipher immunosuppressive cellular communication in the PDAC environment
Authors: AVŞAR Gülben , PİR Pınar 
Published: November 2023

AbstractPancreatic ductal adenocarcinoma (PDAC) is one the most aggressive cancers and characterized by a highly rigid and immunosuppressive tumor microenvironment (TME). The extensive cellular interactions are known to play key roles in the immune evasion, chemoresistance, and poor prognosis. Here, we used the spatial transcriptomics, scRNA-seq, and bulk RNA-seq datasets to enhance the insights obtained from each to decipher the cellular communication in the TME. The complex crosstalk in PDAC samples was revealed by the single-cell and spatial transcriptomics profiles of the samples. We show that tumor-associated macrophages (TAMs) are the central cell types in the regulation of microenvironment in PDAC. They colocalize with the cancer cells and tumor-suppressor immune cells and take roles to provide an immunosuppressive environment. LGALS9 gene which is upregulated in PDAC tumor samples in comparison to healthy samples was also found to be upregulated in TAMs compared to tumor-suppressor immune cells in cancer samples. Additionally, LGALS9 was found to be the primary component in the crosstalk between TAMs and the other cells. The widespread expression of P4HB gene and its interaction with LGALS9 was also notable. Our findings point to a profound role of TAMs via LGALS9 and its interaction with P4HB that should be considered for further elucidation as target in the combinatory immunotherapies for PDAC.
Carbon footprint and embodied nutrition evaluation of 388 recipes
Authors: Long Yin , Huang Liqiao , Fujie Rinakira , He Pan , Chen Zhiheng , Xu Xiaoyan , Yoshida Yoshikuni 
Published: November 2023

AbstractFood consumption, which delivers fundamental energy and essential nutrients to human beings, is crucial for achieving a series of sustainable goals. Alongside rising population growth and living standards, there has been a significant increase in food cultivation demands, supply chain complexities, and waste management. Therefore, to protect human health and the environment, promoting sustainable food systems and the uptake of sustainable dietary habits are vital. Yet, information on the environmental and health impact of dietary choices remains inconsistent across multiple evaluation methods, which fail to deliver essential ideas to consumers. In this study, we formulate an integrated approach using Environmentally Extended Input-Output analysis, covering the food supply chain from production to the distribution phase, complemented with a hybrid Life Cycle Assessment for cooking and disposal processes, to quantify the carbon footprint of specific recipes. Our dataset also includes the distinct nutritional values of each recipe. This dataset not only informs the food industry and recipe platforms, enabling more sustainable choices, but also helps individuals balance nutritional value with environmental impact, leading to more informed and sustainable dietary decisions.
Interaction networks of Escherichia coli replication proteins under different bacterial growth conditions
Authors: Morcinek-Orłowska Joanna , Walter Beata , Forquet Raphaël , Cysewski Dominik , Carlier Maxime , Mozolewski Michał , Meyer Sam , Glinkowska Monika 
Published: November 2023

AbstractIn this work we analyzed protein-protein interactions (PPIs) formed by E. coli replication proteins under three disparate bacterial growth conditions. The chosen conditions corresponded to fast exponential growth, slow exponential growth and growth cessation at the stationary phase. We performed affinity purification coupled with mass spectrometry (AP-MS) of chromosomally expressed proteins (DnaA, DnaB, Hda, SeqA, DiaA, DnaG, HolD, NrdB), tagged with sequential peptide affinity (SPA) tag. Composition of protein complexes was characterized using MaxQuant software. To filter out unspecific interactions, we employed double negative control system and we proposed qualitative and quantitative data analysis strategies that can facilitate hits identification in other AP-MS datasets. Our motivation to undertake this task was still insufficient understanding of molecular mechanisms coupling DNA replication to cellular growth. Previous works suggested that such control mechanisms could involve physical interactions of replication factors with metabolic or cell envelope proteins. However, the dynamic replication protein interaction network (PIN) obtained in this study can be used to characterize links between DNA replication and various cellular processes in other contexts.
Birds of a feather flock together: a dataset for Clock and Adcyap1 genes from migration genetics studies
Authors: Le Clercq Louis-Stéphane , Bazzi Gaia , Ferrer Obiol Joan , Cecere Jacopo G. , Gianfranceschi Luca , Grobler J. Paul , Kotzé Antoinette , Riutort León Marta , González-Solís Jacob , Rubolini Diego , Liedvogel Miriam , Dalton Desiré Lee 
Published: November 2023

AbstractBirds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evidence, a systematic review and phylogenetic reanalysis was done. This descriptor outlines the methodology for sourcing, screening, and processing relevant literature and data. PRISMA guidelines were followed, ultimately including 66 studies, with 34 focusing on candidate genes at the genotype-phenotype interface. Studies were clustered using bibliographic coupling and citation network analysis, alongside scientometric analyses by publication year and location. Data was retrieved for allele data from databases, article supplements, and direct author communications. The dataset, version 1.0.2, encompasses data from 52 species, with 46 species for the Clock gene and 43 for the Adcyap1 gene. This dataset, featuring data from over 8000 birds, constitutes the most extensive cross-species collection for these candidate genes, used in studies investigating gene polymorphisms and seasonal bird migration.
Multiple impact effects of helium-driven shocks on thin fiber-metal laminates
Authors: Pai Anand , Rodriguez-Millan Marcos , Kini Chandrakant R. , Shenoy B. Satish 
Published: November 2023

AbstractFiber Metal Laminates (FMLs) have garnered considerable attention and are increasingly being utilized in the development of protective armors for explosion and ballistic scenarios. While most research has focused on assessing the response of FMLs to single impacts, real battlefield situations often require shielding structures to endure multiple impacts. Thus, this study revolves around the creation of hybrid FMLs designed for shock shielding purposes. The primary focus is on how these laminates withstand repetitive impacts from high-intensity shock waves, aiming to pinpoint the optimal sequence that offers the highest resistance against multiple shock impacts. To establish effective shielding, a multi-layered FML configuration is employed. This configuration incorporates AA6061-T6 facing plates, ballistic-grade synthetic materials like aramid/epoxy ply, and ultra-high molecular weight polyethylene (UHMWPE)/epoxy ply. Additionally, a paperboard/epoxy lamina is introduced to induce functional grading based on layerwise shock impedance mismatches. Shock impact experiments are conducted using a shock tube equipped with helium as the driver gas. Critical shock parameters, including Mach Number, positive impulse, and peak overpressure, are meticulously evaluated. For validation purposes, a numerical model is employed to project the damage profile as a function of radial distance across different laminate sequences. The study unveils that ply deformations are strongly influenced by the arrangement of core layers, particularly the positions of the paperboard and UHMWPE layers within the core structure. To contextualize the findings, the shock impact results obtained from this study are compared with those from prior experiments that employed nitrogen-driven shocks.
Association of serum uric acid with all-cause and cardiovascular mortality in obstructive sleep apnea
Authors: Yang Zhe , Lv Tian , Lv Xiaoheng , Wan Fangyuan , Zhou Hong , Wang Xiaoling , Zhang Lisan 
Published: November 2023

AbstractThe study investigated the association between Serum Uric Acid (SUA) levels and all-cause as well as cardiovascular mortality in patients with Obstructive Sleep Apnea (OSA). This prospective cohort study enrolled participants with OSA from four cycles of the National Health and Nutrition Examination Survey (NHANES) conducted between 2005 and 2008, and 2015–2018. A weighted Cox proportional hazards model was used to assess adjusted hazard ratios (aHRs) and their corresponding 95% confidence intervals (CI) for all-cause and cardiovascular mortality. Additionally, multivariable logistic regression and restricted cubic splines (RCS) models were employed to examine nonlinear relationships between SUA and all-cause and cardiovascular mortality. Among the 5,584 OSA participants included in the study, covering the four NHANES cycles and with a median follow-up of 4.333 years, a total of 537 deaths were observed, including 108 deaths attributed to cardiovascular disease. Comparing the fourth quartile (Q4) of uric acid levels, both the fifth quartile (Q5) (aHRs = 1.51, 95% CI [1.08, 2.12]) and the second quartile (Q2) (aHRs = 1.53, 95% CI [1.04, 2.25]) of uric acid levels were independently associated with an increased risk of all-cause mortality. Furthermore, comparing the fourth quartile (Q4) of uric acid levels, the second quartile (Q2) (aHRs = 2.40, 95% CI [1.08, 5.35]) of uric acid levels were independently associated with an increased risk of cardiovascular mortality. The RCS model demonstrated a U-shaped pattern in the association between SUA and all-cause mortality in OSA, with an inflection point observed at 5.83 mg/dl. The findings of this study suggest a U-shaped association between serum SUA levels and all-cause mortality and nonlinearity association between serum SUA levels and all-cause mortality. Further studies are warranted to determine the causal relationship between SUA levels and all-cause and cardiovascular mortality.
AI specialization for pathways of economic diversification
Authors: Mishra Saurabh , Koopman Robert , De Prato Giuditta , Rao Anand , Osorio-Rodarte Israel , Kim Julie , Spatafora Nikola , Strier Keith , Zaccaria Andrea 
Published: November 2023

AbstractThe growth in AI is rapidly transforming the structure of economic production. However, very little is known about how within-AI specialization may relate to broad-based economic diversification. This paper provides a data-driven framework to integrate the interconnection between AI-based specialization with goods and services export specialization to help design future comparative advantage based on the inherent capabilities of nations. Using detailed data on private investment in AI and export specialization for more than 80 countries, we propose a systematic framework to help identify the connection from AI to goods and service sector specialization. The results are instructive for nations that aim to harness AI specialization to help guide sources of future competitive advantage. The operational framework could help inform the public and private sectors to uncover connections with nearby areas of specialization.
Newly fabricated zinc oxide nanoparticles loaded materials for therapeutic nano delivery in experimental cryptosporidiosis
Authors: Hamdy Doaa A. , Ismail Mousa A. M. , El-Askary Hala M. , Abdel-Tawab Heba , Ahmed Marwa M. , Fouad Fatma M. , Mohamed Fatma 
Published: November 2023

AbstractCryptosporidiosis is a global health problem that threatens the lives of immunocompromised patients. This study targets to fabricate and investigate the efficiency of zinc oxide nanoparticles (ZnO-NPs), nitazoxanide (NTZ)-loaded ZnO-NPs, and Allium sativum (A. sativum)-loaded ZnO-NPs in treating cryptosporidiosis. Further FTIR, SEM, XRD, and zeta analysis were used for the characterization of ZnO-NPs and loaded materials. The morphology of loaded materials for ZnO-NPs changed into wrapped layers and well-distributed homogenous particles, which had a direct effect on the oocyst wall. The charge surface of all particles had a negative sign, which indicated well distribution into the parasite matrix. For anti-cryptosporidiosis efficiency, thirty immunosuppressed Cryptosporidium parvum-infected mice, classified into six groups, were sacrificed on the 21st day after infection with an evaluation of parasitological, histopathological, and oxidative markers. It was detected that the highest reduction percent of Cryptosporidium oocyst shedding was (81.5%) in NTZ, followed by (71.1%) in A. sativum-loaded ZnO-NPs-treated groups. Also, treatment with A. sativum and NTZ-loaded ZnO-NPs revealed remarkable amelioration of the intestinal, hepatic, and pulmonary histopathological lesions. Furthermore, they significantly produced an increase in GSH values and improved the changes in NO and MDA levels. In conclusion, this study is the first to report ZnO-NPs as an effective therapy for treating cryptosporidiosis, especially when combined with other treatments that enhance their antioxidant activity. It provides an economical and environment-friendly approach to novel delivery synthesis for antiparasitic applications.
Improved lipid production and component of mycosporine-like amino acids by co-overexpression of amt1 and aroB genes in Synechocystis sp. PCC6803
Authors: Eungrasamee Kamonchanock , Lindblad Peter , Jantaro Saowarath 
Published: November 2023

AbstractImplementing homologous overexpression of the amt1 (A) and aroB (B) genes involved in ammonium transporter and the synthesis of mycosporine-like amino acids (MAAs) and aromatic amino acids, respectively, we created three engineered Synechocystis sp. PCC6803 strains, including Ox-A, Ox-B, and Ox-AB, to study the utilization of carbon and nitrogen in cyanobacteria for the production of valuable products. With respect to amt1 overexpression, the Ox-A and Ox-AB strains had a greater growth rate under (NH4)2SO4 supplemented condition. Both the higher level of intracellular accumulation of lipids in Ox-A and Ox-AB as well as the increased secretion of free fatty acids from the Ox-A strain were impacted by the late-log phase of cell growth. It is noteworthy that among all strains, the Ox-B strain undoubtedly spotted a substantial accumulation of glycogen as a consequence of aroB overexpression. Additionally, the ammonium condition drove the potent antioxidant activity in Ox strains with a late-log phase, particularly in the Ox-B and Ox-AB strains. This was probably related to the altered MAA component inside the cells. The higher proportion of P4-fraction was induced by the ammonium condition in both Ox-B and Ox-AB, while the noted increase of the P1 component was found in the Ox-A strain.
Biodistribution and function of coupled polymer-DNA origami nanostructures
Authors: Joseph Noah , Shapiro Anastasia , Gillis Ella , Barkey Shirin , Abu-Horowitz Almogit , Bachelet Ido , Mizrahi Boaz 
Published: November 2023

AbstractSpatial control over the distribution of therapeutics is a highly desired feature, which could limit the side effects of many drugs. Here we describe a nanoscale agent, fabricated from a coupled polymer-DNA origami hybrid that exhibits stability in serum and slow diffusion through tissues, in a manner correlating with shape and aspect ratio. Coupling to fragments of polyethylene glycol (PEG) through polyamine electrostatic interactions resulted in marked stability of the agents in-vivo, with > 90% of the agents maintaining structural integrity 5 days following subcutaneous injection. An agent functionalized with aptamers specific for human tumor necrosis factor TNF-alpha, significantly abrogated the inflammatory response in a delayed-type hypersensitivity model in humanized TNF-alpha mice. These findings highlight polymer-DNA hybrid nanostructures as a programmable and pharmacologically viable update to mainstream technologies such as monoclonal antibodies, capable of exerting an additional layer of control across the spatial dimension of drug activity.
Extended planar defects of oxygen vacancies in ferroelectric $$\hbox {BaTiO}_3$$ and impact on ferroelectricity
Authors: Qiu Shaohui , Fu Huaxiang 
Published: November 2023

AbstractExtended defects of vacancies in ferroelectrics (FE), where vacancies spread over an extended space, are of critical importance in terms of understanding the long-standing problems such as polarization fatigue and aging. However, extended defects in FEs are poorly understood. Here we investigate the extended planar oxygen vacancies in ferroelectric $$\hbox {BaTiO}_3$$

BaTiO
3

using density functional theory and the modern theory of polarization. Oxygen vacancies of different charge states, namely $${\textrm{V}}^{2+}_{{\textrm{O}}}$$

V

O

2
+

, $${\textrm{V}}^{1+}_{{\textrm{O}}}$$

V

O

1
+

, and $${\textrm{V}}^{0}_{{\textrm{O}}}$$

V

O
0

, are studied. We obtain interesting results such as: (i) The formation energy of planar $${\textrm{V}}^{2+}_{{\textrm{O}}}$$

V

O

2
+

vacancies can be very small (merely 0.54 eV) even under the oxygen-rich condition, which is considerably smaller than the formation energy (4.0 eV) of planar $${\textrm{V}}^{0}_{{\textrm{O}}}$$

V

O
0

vacancies; (ii) Planar $${\textrm{V}}^{2+}_{{\textrm{O}}}$$

V

O

2
+

vacancies drastically reduce the ferroelectric polarization in $$\hbox {BaTiO}_3$$

BaTiO
3

by more than one order of magnitude, which provides a pivotal (theoretical) evidence that the planar oxygen vacancies could be the origin of polarization fatigue and imprinting. The polarization dead layer caused by planar oxygen vacancies is shown to be around 72 Å. Microscopic origin and insight, based on the local Ti-O relative displacements, are provided to understand these interesting phenomena.
Effects of extracted oil of fermented Tartary buckwheat on lipid-lowering, inflammation modulation, and gut microbial regulation in mice
Authors: Yang Xin , Zhu Anran , Li Xuanchen , He Shengling , Zhu Yi , Anyan Wen , Qin Likang , Zeng Haiying 
Published: November 2023

This study investigated the composition of Tartary buckwheat oil fermented by Monascus purpureus and extracted under supercritical CO2 conditions (FTBO), and evaluated its effects on lipid-lowering, inflammation modulation, and gut microbial regulation in mice.