bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic detection of functional proteoform groups from bottom-up proteomic datasets
Authors: Bludau Isabell , Frank Max , Dörig Christian , Cai Yujia , Heusel Moritz , Rosenberger George , Picotti Paola , Collins Ben C. , Röst Hannes , Aebersold Ruedi 
Published: June 2021

AbstractTo a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that of the coding genome. Various processes create multiple distinct but related proteins per coding gene – so-called proteoforms – that expand the functional capacity of a cell. Evaluating proteoforms from classical bottom-up proteomics datasets, where peptides instead of intact proteoforms are measured, has remained difficult. Here we present COPF, a tool for COrrelation-based functional ProteoForm assessment in bottom-up proteomics data. It leverages the concept of peptide correlation analysis to systematically assign peptides to co-varying proteoform groups. We show applications of COPF to protein complex co-fractionation data as well as to more typical protein abundance vs. sample data matrices, demonstrating the systematic detection of assembly- and tissue-specific proteoform groups, respectively, in either dataset. We envision that the presented approach lays the foundation for a systematic assessment of proteoforms and their functional implications directly from bottom-up proteomic datasets.
Active coacervate droplets are protocells that grow and resist Ostwald ripening
Authors: Nakashima Karina K. , van Haren Merlijn H. I. , André Alain A. M. , Robu Irina , Spruijt Evan 
Published: June 2021

AbstractActive coacervate droplets are liquid condensates coupled to a chemical reaction that turns over their components, keeping the droplets out of equilibrium. This turnover can be used to drive active processes such as growth, and provide an insight into the chemical requirements underlying (proto)cellular behaviour. Moreover, controlled growth is a key requirement to achieve population fitness and survival. Here we present a minimal, nucleotide-based coacervate model for active droplets, and report three key findings that make these droplets into evolvable protocells. First, we show that coacervate droplets form and grow by the fuel-driven synthesis of new coacervate material. Second, we find that these droplets do not undergo Ostwald ripening, which we attribute to the attractive electrostatic interactions and translational entropy within complex coacervates, active or passive. Finally, we show that the droplet growth rate reflects experimental conditions such as substrate, enzyme and protein concentration, and that a different droplet composition (addition of RNA) leads to altered growth rates and droplet fitness. These findings together make active coacervate droplets a powerful platform to mimic cellular growth at a single-droplet level, and to study fitness at a population level.
Selective hydroboration of unsaturated bonds by an easily accessible heterotopic cobalt catalyst
Authors: Li Chuhan , Song Shuo , Li Yuling , Xu Chang , Luo Qiquan , Guo Yinlong , Wang Xiaoming 
Published: June 2021

AbstractHomogeneous earth-abundant metal catalysis based on well-defined molecular complexes has achieved great advance in synthetic methodologies. However, sophisticated ligand, hazardous activator and multistep synthesis starting from base metal salts are generally required for the generation of active molecular catalysts, which may hinder their broad application in large scale organic synthesis. Therefore, the development of metal cluster catalysts formed in situ from simple earth-abundant metal salts is of importance for the practical utilization of base metal resource, yet it is still in its infancy. Herein, a mixture of catalytic amounts of cobalt (II) iodide and potassium tert-butoxide is discovered to be highly active for selective hydroboration of vinylarenes and dihydroboration of nitriles, affording a good yield of diversified hydroboration products that without isolation can readily undergo further one pot transformations. It should be highlighted that the alkoxide-pinacolborane combination acts as an efficient activation strategy to activate cobalt (II) iodide for the generation of metastable heterotopic cobalt catalysts in situ, which is proposed to be catalytically active species.
A catalog of the diversity and ubiquity of bacterial microcompartments
Authors: Sutter Markus , Melnicki Matthew R. , Schulz Frederik , Woyke Tanja , Kerfeld Cheryl A. 
Published: June 2021

AbstractBacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which are incompatible with surrounding metabolism. BMCs consist of a selectively permeable shell, composed of three types of structurally conserved proteins, together with sequestered enzymes that vary among functionally distinct BMCs. Genes encoding shell proteins are typically clustered with those for the encapsulated enzymes. Here, we report that the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014, and the number of distinct BMC types has doubled. The new BMC types expand the range of compartmentalized catalysis and suggest that there is more BMC biochemistry yet to be discovered. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, experimental characterization, and development of BMC-based nanoarchitectures for biomedical and bioengineering applications.
Giant multiple caloric effects in charge transition ferrimagnet
Authors: Kosugi Yoshihisa , Goto Masato , Tan Zhenhong , Kan Daisuke , Isobe Masahiko , Yoshii Kenji , Mizumaki Masaichiro , Fujita Asaya , Takagi Hidenori , Shimakawa Yuichi 
Published: June 2021

AbstractCaloric effects of solids can provide us with innovative refrigeration systems more efficient and environment-friendly than the widely-used conventional vapor-compression cooling systems. Exploring novel caloric materials is challenging but critically important in developing future technologies. Here we discovered that the quadruple perovskite structure ferrimagnet BiCu3Cr4O12 shows large multiple caloric effects at the first-order charge transition occurring around 190 K. Large latent heat and the corresponding isothermal entropy change, 28.2 J K−1 kg−1, can be utilized by applying both magnetic fields (a magnetocaloric effect) and pressure (a barocaloric effect). Adiabatic temperature changes reach 3.9 K for the 50 kOe magnetic field and 4.8 K for the 4.9 kbar pressure, and thus highly efficient thermal controls are achieved in multiple ways.
Biodegradation of crude oil by immobilized Exiguobacterium sp. AO-11 and shelf life evaluation
Authors: Sakdapetsiri Chatsuda , Kaokhum Nitchakarn , Pinyakong Onruthai 
Published: June 2021

AbstractExiguobacterium sp. AO-11 was immobilized on bio-cord at 109 CFU g−1 carrier for the removal of crude oil from marine environments. To prepare a ready-to-use bioremediation product, the shelf life of the immobilized cells was calculated. Approximately 90% of 0.25% (v/v) crude oil removal was achieved within 9 days when the starved state of immobilized cells was used. The oil removal activity of the immobilized cells was maintained in the presence of oil dispersant (89%) and at pH values of 7–9. Meanwhile, pH, oil concentration and salinity affected the oil removal efficacy. The immobilized cells could be reused for at least 5 cycles. The Arrhenius equation describing the relationship between the rate of reaction and temperature was validated as a useful model of the kinetics of retention of activity by an immobilized biocatalyst. It was estimated that the immobilized cells could be stored in a non-vacuum bag containing phosphate buffer (pH 7.0) at 30 °C for 39 days to retain the cells at 107 CFU g−1 carrier and more than 50% degradation activity. These results indicated the potential of using bio-cord-immobilized crude oil-degrading Exiguobacterium sp. AO-11 as a bioremediation product in a marine environment.
Seroprevalence of SARS-CoV-2 antibodies in Saint Petersburg, Russia: a population-based study
Authors: Barchuk Anton , Skougarevskiy Dmitriy , Titaev Kirill , Shirokov Daniil , Raskina Yulia , Novkunkskaya Anastasia , Talantov Petr , Isaev Artur , Pomerantseva Ekaterina , Zhikrivetskaya Svetlana , Barabanova Lubov , Volkov Vadim 
Published: June 2021

AbstractProperly conducted serological survey can help determine infection disease true spread. This study aims to estimate the seroprevalence of SARS-CoV-2 antibodies in Saint Petersburg, Russia accounting for non-response bias. A sample of adults was recruited with random digit dialling, interviewed and invited for anti-SARS-CoV-2 antibodies. The seroprevalence was corrected with the aid of the bivariate probit model that jointly estimated individual propensity to agree to participate in the survey and seropositivity. 66,250 individuals were contacted, 6,440 adults agreed to be interviewed and blood samples were obtained from 1,038 participants between May 27 and June 26, 2020. Naïve seroprevalence corrected for test characteristics was 9.0% (7.2–10.8) by CMIA and 10.5% (8.6–12.4) by ELISA. Correction for non-response decreased estimates to 7.4% (5.7–9.2) and 9.1% (7.2–10.9) for CMIA and ELISA, respectively. The most pronounced decrease in bias-corrected seroprevalence was attributed to the history of any illnesses in the past 3 months and COVID-19 testing. Seroconversion was negatively associated with smoking status, self-reported history of allergies and changes in hand-washing habits. These results suggest that even low estimates of seroprevalence can be an overestimation. Serosurvey design should attempt to identify characteristics that are associated both with participation and seropositivity.
Insights into how environment shapes post-mortem RNA transcription in mouse brain
Authors: Bonadio Raphael Severino , Nunes Larissa Barbosa , Moretti Patricia Natália S. , Mazzeu Juliana Forte , Cagnin Stefano , Pic-Taylor Aline , de Oliveira Silviene Fabiana 
Published: June 2021

AbstractMost biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.
Peritumoral edema in breast cancer at preoperative MRI: an interpretative study with histopathological review toward understanding tumor microenvironment
Authors: Park Nora Jee-Young , Jeong Ji Yun , Park Ji Young , Kim Hye Jung , Park Chan Sub , Lee Jeeyeon , Park Ho Yong , Jung Jin Hyang , Kim Wan Wook , Chae Yee Soo , Lee Soo Jung , Kim Won Hwa 
Published: June 2021

AbstractPeritumoral edema (PE) of breast cancer at T2-weighted MR images is considered a poor prognostic sign and may represent the microenvironment surrounding the tumor; however, its histopathological mechanism remains unclear. The purpose of the study was to identify and describe detailed histopathological characteristics associated with PE at preoperative breast MRI in breast cancer patients. This retrospective study included breast cancer patients who had undergone preoperative MRI and surgery between January 2011 and December 2012. Two radiologists determined the presence of PE in consensus based on the signal intensity surrounding the tumor at T2-weighted images. The following detailed histopathological characteristics were reviewed by two breast pathologists using four-tiered grades; lymphovascular invasion, vessel ectasia, stromal fibrosis, growth pattern, and tumor budding. Tumor necrosis and tumor infiltrating lymphocytes were assessed using a percent scale. Baseline clinicopathological characteristics, including age and histologic grade, were collected. The associations between detailed histopathologic characteristics and PE were examined using multivariable logistic regression with odds ratio (OR) calculation. A total of 136 women (median age, 49 ± 9 years) were assessed; among them 34 (25.0%) had PE. After adjustment of baseline clinicopathological characteristics that were significantly associated with PE (age, T stage, N stage, histologic grade, and subtype, all Ps < 0.05), lymphovascular invasion (P = 0.009), vessel ectasia (P = 0.021), stromal fibrosis (P = 0.024), growth pattern (P = 0.036), and tumor necrosis (P < 0.001) were also associated with PE. In comparison with patients without PE, patients with PE were more likely to have a higher degree of lymphovascular invasion (OR, 2.9), vessel ectasia (OR, 3.3), stromal fibrosis (OR, 2.5), lesser degree of infiltrative growth pattern (OR, 0.4), and higher portion of tumor necrosis (OR, 1.4). PE of breast cancer at MRI is associated with detailed histopathological characteristics of lymphovascular invasion, vessel ectasia, stromal fibrosis, growth pattern, and tumor necrosis, suggesting a relevance for tumor microenvironment.
Significance of secretory leukocyte peptidase inhibitor in pleural fluid for the diagnosis of benign asbestos pleural effusion
Authors: Kishimoto Takumi , Kojima Yoko , Fujimoto Nobukazu 
Published: June 2021

AbstractSecretory leukocyte peptidase inhibitor (SLPI) is a biomarker present in the respiratory tract that protects against tissue destruction and aids in wound healing. We examined whether SLPI in pleural effusion can be used to distinguish benign asbestos pleural effusion (BAPE) from early-stage malignant pleural mesothelioma (MPM) and other diseases. We measured the levels of SLPI, hyaluronic acid (HA), soluble mesothelin-related peptides (SMRP), CCL2, galectin-3, and CYFRA21-1 in 51 patients with BAPE, 37 patients with early-stage MPM, 77 patients with pleural effusions due to non-small-cell lung cancer (LCa), and 74 patients with other pleural effusions. SLPI levels in the pleural fluid of patients with BAPE were significantly lower than those in patients with MPM, LCa, and other pleural effusions (p < 0.0001). The area under the curve (AUC) for SLPI’s ability to distinguish BAPE from MPM was 0.902, with a sensitivity of 82.4% and a specificity of 86.5%. This AUC was not only favourable but was better than the AUC for the ability of CYFRA21-1 to distinguish BAPE (0.853). The combination of SLPI and CYFRA21-1 achieved an AUC of 0.965 for the differentiation between BAPE and MPM. Pleural fluid SLPI as well as CYFRA21-1 and HA is useful as a biomarker to diagnose BAPE, which needs to be distinguished from early-stage MPM.
12α-Hydroxylated bile acid enhances accumulation of adiponectin and immunoglobulin A in the rat ileum
Authors: Yoshitsugu Reika , Liu Hongxia , Kamo Yoshie , Takeuchi Akari , Joe Ga-Hyun , Tada Koji , Kikuchi Keidai , Fujii Nobuyuki , Kitta Shinri , Hori Shota , Takatsuki Manami , Iwaya Hitoshi , Tanaka Yasutake , Shimizu Hidehisa , Ishizuka Satoshi 
Published: June 2021

AbstractWe previously reported that dietary supplementation with cholic acid (CA), the primary 12α-hydroxylated (12αOH) bile acid (BA), reduces plasma adiponectin concentration in rats. The aim of this study was to examine the distribution of adiponectin in the body of CA-fed rats and its influence on mucosal immunoglobulin A concentration in the intestine. Rats were fed a diet supplemented with or without CA (0.5 g CA/kg diet) for 13 weeks. A reduction in plasma adiponectin level was observed from week 3. At the end of the experiment, the CA diet reduced plasma adiponectin concentration both in the portal and aortic plasma. Accumulation of adiponectin was accompanied by an increase in cadherin-13 mRNA expression in the ileal mucosa of CA-fed rats. No increase was observed in adiponectin mRNA expression in the ileal and adipose tissues of the CA-fed rats. Immunoglobulin A concentration in the ileal mucosa was elevated in the CA-fed rats and was correlated with the ileal adiponectin concentration. 12αOH BAs may modulate mucosal immune response that are involved in the accumulation of adiponectin in the ileum.
Long-term body mass trajectories and hypertension by sex among Chinese adults: a 24-year open cohort study
Authors: Liu Ruru , Mi Baibing , Zhao Yaling , Dang Shaonong , Yan Hong 
Published: June 2021

AbstractEvidence was limited on trajectory of body mass index (BMI) through adulthood and its association with hypertension. We aimed to evaluate their association by sex in large-scale study. Data were obtained from the China Health and Nutrition Survey (CHNS) from 1991 to 2015. Latent class trajectory analysis (LCTA) was used to capture BMI change trajectories. Hazard risks (HRs) were estimated from Cox proportion hazard regression. Among 14,262 participants (mean age, 38.8; 47.8% men), 5138 hypertension occurred (2687 men and 2451 women) occurred during a mean follow-up 9.6 years. Four body mass trajectory groups were identified as BMI loss, stable, moderate and substantial gain. Appropriately half of participants (48.0%) followed 1 of the 2 BMI gain trajectories, where BMI increased at least 3 kg/m2 overtime. Compared with participants with stable BMI, those gaining BMI substantially had higher risk of hypertension by 65% (HR 1.65, 95% CI 1.45–1.86) in male and 83% (HR 1.83, 95% CI 1.58–2.12) in female. The HRs in BMI loss patterns were 0.74 (0.62–0.89) in men and 0.87 (0.75–1.00) in women. Our findings imply that majority of Chinese adults transited up to a higher BMI level during follow-up. Avoiding excessive weight gain and maintaining stable weight might be important for hypertension prevention.
Ternary logic decoder using independently controlled double-gate Si-NW MOSFETs
Authors: Han Seong-Joo , Han Joon-Kyu , Kim Myung-Su , Yun Gyeong-Jun , Yu Ji-Man , Tcho Il-Woong , Seo Myungsoo , Lee Geon-Beom , Choi Yang-Kyu 
Published: June 2021

AbstractA ternary logic decoder (TLD) is demonstrated with independently controlled double-gate (ICDG) silicon-nanowire (Si-NW) MOSFETs to confirm a feasibility of mixed radix system (MRS). The TLD is essential component for realization of the MRS. The ICDG Si-NW MOSFET resolves the limitations of the conventional multi-threshold voltage (multi-Vth) schemes required for the TLD. The ICDG Si-NW MOSFETs were fabricated and characterized. Afterwards, their electrical characteristics were modeled and fitted semi-empirically with the aid of SILVACO ATLAS TCAD simulator. The circuit performance and power consumption of the TLD were analyzed using ATLAS mixed-mode TCAD simulations. The TLD showed a power-delay product of 35 aJ for a gate length (LG) of 500 nm and that of 0.16 aJ for LG of 14 nm. Thanks to its inherent CMOS-compatibility and scalability, the TLD based on the ICDG Si-NW MOSFETs would be a promising candidate for a MRS using ternary and binary logic.
Assessment of the gene mosaicism burden in blood and its implications for immune disorders
Authors: Solís-Moruno Manuel , Mensa-Vilaró Anna , Batlle-Masó Laura , Lobón Irene , Bonet Núria , Marquès-Bonet Tomàs , Aróstegui Juan I. , Casals Ferran 
Published: June 2021

AbstractThere are increasing evidences showing the contribution of somatic genetic variants to non-cancer diseases. However, their detection using massive parallel sequencing methods still has important limitations. In addition, the relative importance and dynamics of somatic variation in healthy tissues are not fully understood. We performed high-depth whole-exome sequencing in 16 samples from patients with a previously determined pathogenic somatic variant for a primary immunodeficiency and tested different variant callers detection ability. Subsequently, we explored the load of somatic variants in the whole blood of these individuals and validated it by amplicon-based deep sequencing. Variant callers allowing low frequency read thresholds were able to detect most of the variants, even at very low frequencies in the tissue. The genetic load of somatic coding variants detectable in whole blood is low, ranging from 1 to 2 variants in our dataset, except for one case with 17 variants compatible with clonal haematopoiesis under genetic drift. Because of the ability we demonstrated to detect this type of genetic variation, and its relevant role in disorders such as primary immunodeficiencies, we suggest considering this model of gene mosaicism in future genetic studies and considering revisiting previous massive parallel sequencing data in patients with negative results.
Topological phase transition between a normal insulator and a topological metal state in a quasi-one-dimensional system
Authors: Jangjan Milad , Hosseini Mir Vahid 
Published: June 2021

AbstractWe theoretically report the finding of a new kind of topological phase transition between a normal insulator and a topological metal state where the closing-reopening of bandgap is accompanied by passing the Fermi level through an additional band. The resulting nontrivial topological metal phase is characterized by stable zero-energy localized edge states that exist within the full gapless bulk states. Such states living on a quasi-one-dimensional system with three sublattices per unit cell are protected by hidden inversion symmetry. While other required symmetries such as chiral, particle-hole, or full inversion symmetry are absent in the system.
A new galling insect model enhances photosynthetic activity in an obligate holoparasitic plant
Authors: Murakami Ryo , Ushima Ryo , Sugimoto Ryoma , Tamaoki Daisuke , Karahara Ichirou , Hanba Yuko , Wakasugi Tatsuya , Tsuchida Tsutomu 
Published: June 2021

AbstractInsect-induced galls are microhabitats distinct from the outer environment that support inhabitants by providing improved nutrients, defence against enemies, and other unique features. It is intriguing as to how insects reprogram and modify plant morphogenesis. Because most of the gall systems are formed on trees, it is difficult to maintain them in laboratories and to comprehend the mechanisms operative in them through experimental manipulations. Herein, we propose a new model insect,Smicronyx madaranus, for studying the mechanisms of gall formation. This weevil forms spherical galls on the shoots ofCuscuta campestris, an obligate parasitic plant. We established a stable system for breeding and maintaining this ecologically intriguing insect in the laboratory, and succeeded in detailed analyses of the gall-forming behaviour, gall formation process, and histochemical and physiological features. ParasiticC. campestrisdepends on host plants for its nutrients, and usually shows low chlorophyll content and photosynthetic activity. We demonstrate thatS. madaranus-induced galls have significantly increased CO2absorbance. Moreover, chloroplasts and starch accumulated in gall tissues at locations inhabited by the weevil larvae. These results suggest that the gall-inducing weevils enhance the photosynthetic activity inC. campestris, and modify the plant tissue to a nutrient-rich shelter for them.