bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic profiling of SARS-CoV-2-specific IgG responses elicited by an inactivated virus vaccine identifies peptides and proteins for predicting vaccination efficacy
Authors: Ma Ming-Liang , Shi Da-Wei , Li Yang , Hong Wei , Lai Dan-Yun , Xue Jun-Biao , Jiang He-Wei , Zhang Hai-Nan , Qi Huan , Meng Qing-Feng , Guo Shu-Juan , Xia De-Ju , Hu Jin-Jun , Liu Shuo , Li He-Yang , Zhou Jie , Wang Wei , Yang Xiao , Fan Xiong-Lin , Lei Qing , Chen Wei-Jun , Li Ce-Sheng , Yang Xiao-Ming , Xu Si-Hong , Wei Hong-Ping , Tao Sheng-Ce 
Published: August 2021

AbstractOne of the best ways to control COVID-19 is vaccination. Among the various SARS-CoV-2 vaccines, inactivated virus vaccines have been widely applied in China and many other countries. To understand the underlying protective mechanism of these vaccines, it is necessary to systematically analyze the humoral responses that are triggered. By utilizing a SARS-CoV-2 microarray with 21 proteins and 197 peptides that fully cover the spike protein, antibody response profiles of 59 serum samples collected from 32 volunteers immunized with the inactivated virus vaccine BBIBP-CorV were generated. For this set of samples, the microarray results correlated with the neutralization titers of the authentic virus, and two peptides (S1-5 and S2-22) were identified as potential biomarkers for assessing the effectiveness of vaccination. Moreover, by comparing immunized volunteers to convalescent and hospitalized COVID-19 patients, the N protein, NSP7, and S2-78 were identified as potential biomarkers for differentiating COVID-19 patients from individuals vaccinated with the inactivated SARS-CoV-2 vaccine. The comprehensive profile of humoral responses against the inactivated SARS-CoV-2 vaccine will facilitate a deeper understanding of the vaccine and provide potential biomarkers for inactivated virus vaccine-related applications.
The associations between whole grain and refined grain intakes and serum C-reactive protein
Authors: Taskinen Riikka E. , Hantunen Sari , Tuomainen Tomi-Pekka , Virtanen Jyrki K. 
Published: August 2021

Abstract
Background/objectives
Epidemiological studies suggest that whole grain intake has inverse associations with low-grade inflammation, but findings regarding refined grains are inconclusive. Our objective was to investigate whether consumption of whole or refined grains is associated with serum high sensitivity CRP (hs-CRP).

Subjects/methods
The study included 756 generally healthy men and women aged 53–73 years from the Kuopio Ischaemic Heart Disease Risk Factory Study, examined in 1999–2001. Dietary intakes were assessed using 4-day food records. ANCOVA and linear regression were used for analyses.

Results
The mean intake of whole and refined grains was 136 g/day (SD 80) and 84 g/day (SD 46), respectively. Higher whole grain intake was associated with lower hs-CRP concentration and higher refined grain intake with higher concentration after adjustment for lifestyle and dietary factors. Each 50 g/d higher whole grain intake was associated with 0.12 mg/L (95% Cl 0.02–0.21 mg/L) lower hs-CRP concentration and each 50 g/d higher refined grain intake with 0.23 mg/L (95% Cl 0.08–0.38) higher concentration. Adjustment for fibre from grains attenuated the associations especially with whole grains. There were no statistically significant interactions according to gender or BMI (P for interactions >0.065).

Conclusions
The results of this study suggest that higher intake of whole grains is associated with lower concentrations of hs-CRP and higher intake of refined grains is associated with higher concentrations. However, especially the association with whole grain intake was attenuated after adjusting for fibre intake from grains, suggesting that cereal fibre may partly explain the association.
Intellectual disability and microcephaly associated with a novel CHAMP1 mutation
Authors: Asakura Yuta , Osaka Hitoshi , Aoi Hiromi , Mizuguchi Takeshi , Matsumoto Naomichi , Yamagata Takanori 
Published: August 2021

AbstractMutations in a number of genes related to chromosomal segregation reportedly cause developmental disorders, e.g., chromosome alignment-maintaining phosphoprotein 1 (CHAMP1). We report on an 8-year-old Japanese girl who presented with a developmental disorder and microcephaly and carries a novel nonsense mutation in CHAMP1. Therefore, CHAMP1 mutation should be considered as a differential diagnosis of global developmental delay and microcephaly.
A hierarchical approach to removal of unwanted variation for large-scale metabolomics data
Authors: Kim Taiyun , Tang Owen , Vernon Stephen T. , Kott Katharine A. , Koay Yen Chin , Park John , James David E. , Grieve Stuart M. , Speed Terence P. , Yang Pengyi , Figtree Gemma A. , O’Sullivan John F. , Yang Jean Yee Hwa 
Published: August 2021

AbstractLiquid chromatography-mass spectrometry-based metabolomics studies are increasingly applied to large population cohorts, which run for several weeks or even years in data acquisition. This inevitably introduces unwanted intra- and inter-batch variations over time that can overshadow true biological signals and thus hinder potential biological discoveries. To date, normalisation approaches have struggled to mitigate the variability introduced by technical factors whilst preserving biological variance, especially for protracted acquisitions. Here, we propose a study design framework with an arrangement for embedding biological sample replicates to quantify variance within and between batches and a workflow that uses these replicates to remove unwanted variation in a hierarchical manner (hRUV). We use this design to produce a dataset of more than 1000 human plasma samples run over an extended period of time. We demonstrate significant improvement of hRUV over existing methods in preserving biological signals whilst removing unwanted variation for large scale metabolomics studies. Our tools not only provide a strategy for large scale data normalisation, but also provides guidance on the design strategy for large omics studies.
Blurring the boundary between homogenous and heterogeneous catalysis using palladium nanoclusters with dynamic surfaces
Authors: Cano Israel , Weilhard Andreas , Martin Carmen , Pinto Jose , Lodge Rhys W. , Santos Ana R. , Rance Graham A. , Åhlgren Elina Harriet , Jónsson Erlendur , Yuan Jun , Li Ziyou Y. , Licence Peter , Khlobystov Andrei N. , Alves Fernandes Jesum 
Published: August 2021

AbstractUsing a magnetron sputtering approach that allows size-controlled formation of nanoclusters, we have created palladium nanoclusters that combine the features of both heterogeneous and homogeneous catalysts. Here we report the atomic structures and electronic environments of a series of metal nanoclusters in ionic liquids at different stages of formation, leading to the discovery of Pd nanoclusters with a core of ca. 2 nm surrounded by a diffuse dynamic shell of atoms in [C4C1Im][NTf2]. Comparison of the catalytic activity of Pd nanoclusters in alkene cyclopropanation reveals that the atomically dynamic surface is critically important, increasing the activity by a factor of ca. 2 when compared to compact nanoclusters of similar size. Catalyst poisoning tests using mercury and dibenzo[a,e]cyclooctene show that dynamic Pd nanoclusters maintain their catalytic activity, which demonstrate their combined features of homogeneous and heterogeneous catalysts within the same material. Additionally, kinetic studies of cyclopropanation of alkenes mediated by the dynamic Pd nanoclusters reveal an observed catalyst order of 1, underpinning the pseudo-homogeneous character of the dynamic Pd nanoclusters.
DNA dynamics and computation based on toehold-free strand displacement
Authors: Kang Hong , Lin Tong , Xu Xiaojin , Jia Qing-Shan , Lakerveld Richard , Wei Bryan 
Published: August 2021

AbstractWe present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.
Access to cationic polyhedral carboranes via dynamic cage surgery with N-heterocyclic carbenes
Authors: Vrána Jan , Holub Josef , Samsonov Maksim A. , Růžičková Zdeňka , Cvačka Josef , McKee Michael L. , Fanfrlík Jindřich , Hnyk Drahomír , Růžička Aleš 
Published: August 2021

AbstractPolyhedral boranes and heteroboranes appear almost exclusively as neutral or anionic species, while the cationic ones are protonated at exoskeletal heteroatoms or they are instable. Here we report the reactivity of 10-vertex closo-dicarbadecaboranes with one or two equivalents of N-heterocyclic carbene to 10-vertex nido mono- and/or bis-carbene adducts, respectively. These complexes easily undergo a reaction with HCl to give cages of stable and water soluble 10-vertex nido-type cations with protonation in the form of a BHB bridge or 10-vertex closo-type cations containing one carbene ligand when originating from closo-1,10-dicarbadecaborane. The reaction of a 10-vertex nido mono-carbene adduct with phosphorus trichloride gives nido-11-vertex 2-phospha-7,8-dicarbaundecaborane, which undergoes an oxidation of the phosphorus atom to P = O, while the product of a bis-carbene adduct reaction is best described as a distorted C2B6H8 fragment bridged by the (BH)2PCl2+ moiety.
Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota
Authors: Galindo Luis Javier , López-García Purificación , Torruella Guifré , Karpov Sergey , Moreira David 
Published: August 2021

AbstractCompared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living flagellated stages (zoospores) remain poorly known and their phylogenetic position is often unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchytrids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.
The killifish visual system as an in vivo model to study brain aging and rejuvenation
Authors: Vanhunsel Sophie , Bergmans Steven , Beckers An , Etienne Isabelle , Van houcke Jolien , Seuntjens Eve , Arckens Lut , De Groef Lies , Moons Lieve 
Published: August 2021

AbstractWorldwide, people are getting older, and this prolonged lifespan unfortunately also results in an increased prevalence of age-related neurodegenerative diseases, contributing to a diminished life quality of elderly. Age-associated neuropathies typically include diseases leading to dementia (Alzheimer’s and Parkinson’s disease), as well as eye diseases such as glaucoma and age-related macular degeneration. Despite many research attempts aiming to unravel aging processes and their involvement in neurodegeneration and functional decline, achieving healthy brain aging remains a challenge. The African turquoise killifish (Nothobranchius furzeri) is the shortest-lived reported vertebrate that can be bred in captivity and displays many of the aging hallmarks that have been described for human aging, which makes it a very promising biogerontology model. As vision decline is an important hallmark of aging as well as a manifestation of many neurodegenerative diseases, we performed a comprehensive characterization of this fish’s aging visual system. Our work reveals several aging hallmarks in the killifish retina and brain that eventually result in a diminished visual performance. Moreover, we found evidence for the occurrence of neurodegenerative events in the old killifish retina. Altogether, we introduce the visual system of the fast-aging killifish as a valuable model to understand the cellular and molecular mechanisms underlying aging in the vertebrate central nervous system. These findings put forward the killifish for target validation as well as drug discovery for rejuvenating or neuroprotective therapies ensuring healthy aging.
Degradation of ancient Maya carved tuff stone at Copan and its bacterial bioconservation
Authors: Elert Kerstin , Ruiz-Agudo Encarnación , Jroundi Fadwa , Gonzalez-Muñoz Maria Teresa , Fash Barbara W. , Fash William L. , Valentin Nieves , de Tagle Alberto , Rodriguez-Navarro Carlos 
Published: August 2021

AbstractMuch stone sculptural and architectural heritage is crumbling, especially in intense tropical environments. This is exemplified by significant losses on carvings made of tuff stone at the Classic Maya site of Copan. Here we demonstrate that Copan stone primarily decays due to stress generated by humidity-related clay swelling resulting in spalling and material loss, a damaging process that appears to be facilitated by the microbial bioweathering of the tuff stone minerals (particularly feldspars). Such a weathering process is not prevented by traditional polymer- and alkoxysilane-based consolidants applied in the past. As an alternative to such unsuccessful conservation treatments, we prove the effectiveness of a bioconservation treatment based on the application of a sterile nutritional solution that selectively activates the stone´s indigenous bacteria able to produce CaCO3 biocement. The treatment generates a bond with the original matrix to significantly strengthen areas of loss, while unexpectedly, bacterial exopolymeric substances (EPS) impart hydrophobicity and reduce clay swelling. This environmentally-friendly bioconservation treatment is able to effectively and safely preserve fragile stones in tropical conditions, opening the possibility for its widespread application in the Maya area, and elsewhere.
Learning spin liquids on a honeycomb lattice with artificial neural networks
Authors: Li Chang-Xiao , Yang Sheng , Xu Jing-Bo 
Published: August 2021

AbstractMachine learning methods provide a new perspective on the study of many-body system in condensed matter physics and there is only limited understanding of their representational properties and limitations in quantum spin liquid systems. In this work, we investigate the ability of the machine learning method based on the restricted Boltzmann machine in capturing physical quantities including the ground-state energy, spin-structure factor, magnetization, quantum coherence, and multipartite entanglement in the two-dimensional ferromagnetic spin liquids on a honeycomb lattice. It is found that the restricted Boltzmann machine can encode the many-body wavefunction quite well by reproducing accurate ground-state energy and structure factor. Further investigation on the behavior of multipartite entanglement indicates that the residual entanglement is richer in the gapless phase than the gapped spin-liquid phase, which suggests that the residual entanglement can characterize the spin-liquid phases. Additionally, we confirm the existence of a gapped non-Abelian topological phase in the spin liquids on a honeycomb lattice with a small magnetic field and determine the corresponding phase boundary by recognizing the rapid change of the local magnetization and residual entanglement.
Effects of irrigation and nitrogen on chlorophyll content, dry matter and nitrogen accumulation in sugar beet (Beta vulgaris L.)
Authors: Wang Ning , Fu Fengzhen , Wang Hongrong , Wang Peng , He Shuping , Shao Hongying , Ni Zhen , Zhang Xingmei 
Published: August 2021

AbstractA 2-year field experiment was conducted to analyze the growth conditions, physical features, yield, and nitrogen use efficiency (NUE) of sugar-beet under limited irrigation conditions in northeast of China. A cultivar H003 was used as plant materials; six treatments (C1–C6) were included: C1, no nitrogen applied, rain-fed; C2, nitrogen (120.00 kg ha−1), rain-fed; C3, no nitrogen applied, hole irrigation for seeding; C4, nitrogen (120.00 kg ha−1), hole irrigation for seeding; C5, no nitrogen applied, hole irrigation for seeding; and C6, nitrogen (120.00 kg ha−1), hole irrigation for seeding, and irrigation at foliage rapid growth stage. The irrigation supply was only 500 mL/plant once. Results showed C6 showed the highest chlorophyll content, dry matter accumulation, yield, etc. and had the best NUE among all the treatments. In conclusion, under the routine fertilization conditions of northeast of China, the cultivation measure of hole irrigation 500 mL/plant for seeding combined with irrigation 500 mL/plant at foliage rapid growth stage greatly improved sugar-beet yield and NUE.
Cost-effectiveness of adjunctive negative pressure wound therapy in paediatric burn care: evidence from the SONATA in C randomised controlled trial
Authors: Frear Cody C. , Griffin Bronwyn R. , Cuttle Leila , Kimble Roy M. , McPhail Steven M. 
Published: August 2021

AbstractNegative pressure wound therapy (NPWT) has been shown to improve clinical outcomes for children with burns by accelerating wound re-epithelialisation. Its effects on healthcare costs, however, remain poorly understood. The aim of this study was to evaluate the cost-effectiveness of NPWT from a healthcare provider perspective using evidence from the SONATA in C randomised controlled trial, in which 101 children with small-area burns were allocated to either standard care (silver-impregnated dressings) or standard care in combination with adjunctive NPWT. The primary outcome, time to re-epithelialisation, was assessed through a blinded photographic review. Resource usage and costs were prospectively recorded for each participant for up to 6 months. Incremental cost-effectiveness ratios and dominance probabilities were estimated and uncertainty quantified using bootstrap resampling. Mean costs per participant—including dressings, labour, medication, scar management, and theatre operations—were lower in the NPWT group (AUD $903.69) relative to the control group (AUD $1669.01). There was an 89% probability that NPWT was dominant, yielding both faster re-epithelialisation and lower overall costs. Findings remained robust to sensitivity analyses employing alternative theatre costs and time-to-re-epithelialisation estimates for grafted patients. In conclusion, adjunctive NPWT is likely to be a cost-effective and dominant treatment for small-area paediatric burns (ANZCTR.org.au:ACTRN12618000256279).
Combined genetic and chemical screens indicate protective potential for EGFR inhibition to cardiomyocytes under hypoxia
Authors: Heliste Juho , Jokilammi Anne , Vaparanta Katri , Paatero Ilkka , Elenius Klaus 
Published: August 2021

AbstractThe return of blood flow to ischemic heart after myocardial infarction causes ischemia–reperfusion injury. There is a clinical need for novel therapeutic targets to treat myocardial ischemia–reperfusion injury. Here we screened for targets for the treatment of ischemia–reperfusion injury using a combination of shRNA and drug library analyses in HL-1 mouse cardiomyocytes subjected to hypoxia and reoxygenation. The shRNA library included lentiviral constructs targeting 4625 genes and the drug library 689 chemical compounds approved by the Food and Drug Administration (FDA). Data were analyzed using protein–protein interaction and pathway analyses. EGFR inhibition was identified as a cardioprotective mechanism in both approaches. Inhibition of EGFR kinase activity with gefitinib improved cardiomyocyte viability in vitro. In addition, gefitinib preserved cardiac contractility in zebrafish embryos exposed to hypoxia-reoxygenation in vivo. These findings indicate that the EGFR inhibitor gefitinib is a potential candidate for further studies of repurposing the drug for the treatment of myocardial infarction.
Efficacy of lenvatinib for unresectable hepatocellular carcinoma based on background liver disease etiology: multi-center retrospective study
Authors: Hiraoka Atsushi , Kumada Takashi , Tada Toshifumi , Tani Joji , Kariyama Kazuya , Fukunishi Shinya , Atsukawa Masanori , Hirooka Masashi , Tsuji Kunihiko , Ishikawa Toru , Takaguchi Koichi , Itobayashi Ei , Tajiri Kazuto , Shimada Noritomo , Shibata Hiroshi , Ochi Hironori , Kawata Kazuhito , Yasuda Satoshi , Toyoda Hidenori , Aoki Tomoko , Tanaka Takaaki , Ohama Hideko , Nouso Kazuhiro , Tsutsui Akemi , Nagano Takuya , Itokawa Norio , Arai Taeang , Okubo Tomomi , Imai Michitaka , Koizumi Yohei , Nakamura Shinichiro , Joko Koji , Hiasa Yoichi , Kudo Masatoshi ,   The Real-life Practice Experts for HCC (RELPEC) Study Group and HCC 48 Group (hepatocellular carcinoma experts from 48 clinics in Japan)
Published: August 2021

AbstractIt was recently reported that hepatocellular carcinoma (HCC) patients with non-alcoholic steatohepatitis (NASH) are not responsive to immune-checkpoint inhibitor (ICI) treatment. The present study aimed to evaluate the therapeutic efficacy of lenvatinib in patients with non-alcoholic fatty liver disease (NAFLD)/NASH-related unresectable-HCC (u-HCC). Five hundred thirty u-HCC patients with Child–Pugh A were enrolled, and divided into the NAFLD/NASH (n = 103) and Viral/Alcohol (n = 427) groups. Clinical features were compared in a retrospective manner. Progression-free survival (PFS) was better in the NAFLD/NASH than the Viral/Alcohol group (median 9.3 vs. 7.5 months, P = 0.012), while there was no significant difference in overall survival (OS) (20.5 vs. 16.9 months, P = 0.057). In Cox-hazard analysis of prognostic factors for PFS, elevated ALT (≥ 30 U/L) (HR 1.247, P = 0.029), modified ALBI grade 2b (HR 1.236, P = 0.047), elevated AFP (≥ 400 ng/mL) (HR 1.294, P = 0.014), and NAFLD/NASH etiology (HR 0.763, P = 0.036) were significant prognostic factors. NAFLD/NASH etiology was not a significant prognostic factor in Cox-hazard analysis for OS (HR0.758, P = 0.092), whereas AFP (≥ 400 ng/mL) (HR 1.402, P = 0.009), BCLC C stage (HR 1.297, P = 0.035), later line use (HR 0.737, P = 0.014), and modified ALBI grade 2b (HR 1.875, P < 0.001) were significant. Lenvatinib can improve the prognosis of patients affected by u-HCC irrespective of HCC etiology or its line of treatment.