bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of proteins with different molecular structures under solution condition
Authors: Inoue Rintaro , Oda Takashi , Nakagawa Hiroshi , Tominaga Taiki , Saio Tomohide , Kawakita Yukinobu , Shimizu Masahiro , Okuda Aya , Morishima Ken , Sato Nobuhiro , Urade Reiko , Sato Mamoru , Sugiyama Masaaki 
Published: December 2020

AbstractIncoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, low flux of neutron beam, low signal to noise ratio of QENS spectrometers and unavailability of well-established analyzing method have been obstacles for studying internal dynamics under physiological condition (in solution). The recent progress of neutron source and spectrometer provide the fine iQENS profile with high statistics and as well the progress of computational technique enable us to quantitatively reveal the internal dynamic from the obtained iQENS profile. The internal dynamics of two proteins, globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution, were measured with the state-of-the art QENS spectrometer and then revealed with the newly developed analyzing method. It was clarified that the average relaxation rate of IDP was larger than that of GDP and the fraction of mobile H atoms of IDP was also much higher than that of GDP. Combined with the structural analysis and the calculation of solvent accessible surface area of amino acid residue, it was concluded that the internal dynamics were related to the highly solvent exposed amino acid residues depending upon protein’s structure.
Arrhythmogenic right ventricular cardiomyopathy in patients with biallelic JUP-associated skin fragility
Authors: Vahidnezhad Hassan , Youssefian Leila , Faghankhani Masoomeh , Mozafari Nikoo , Saeidian Amir Hossein , Niaziorimi Fatemeh , Abdollahimajd Fahimeh , Sotoudeh Soheila , Rajabi Fateme , Mirsafaei Liaosadat , Sani Zahra Alizadeh , Liu Lu , Guy Alyson , Zeinali Sirous , Kariminejad Ariana , Ho Reginald T. , McGrath John A. , Uitto Jouni 
Published: December 2020

AbstractArrhythmogenic right ventricular cardiomyopathy (ARVC), with skin manifestations, has been associated with mutations in JUP encoding plakoglobin. Genotype–phenotype correlations regarding the penetrance of cardiac involvement, and age of onset have not been well established. We examined a cohort of 362 families with skin fragility to screen for genetic mutations with next-generation sequencing-based methods. In two unrelated families, a previously unreported biallelic mutation, JUP: c.201delC; p.Ser68Alafs*92, was disclosed. The consequences of this mutation were determined by expression profiling both at tissue and ultrastructural levels, and the patients were evaluated by cardiac and cutaneous work-up. Whole-transcriptome sequencing by RNA-Seq revealed JUP as the most down-regulated gene among 21 skin fragility-associated genes. Immunofluorescence showed the lack of plakoglobin in the epidermis. Two probands, 2.5 and 22-year-old, with the same homozygous mutation, allowed us to study the cross-sectional progression of cardiac involvements in relation to age. The older patient had anterior T wave inversions, prolonged terminal activation duration (TAD), and RV enlargement by echocardiogram, and together with JUP mutation met definite ARVC diagnosis. The younger patient had no evidence of cardiac disease, but met possible ARVC diagnosis with one major criterion (the JUP mutation). In conclusion, we identified the same biallelic homozygous JUP mutation in two unrelated families with skin fragility, but cardiac findings highlighted age-dependent penetrance of ARVC. Thus, young, phenotypically normal patients with biallelic JUP mutations should be monitored for development of ARVC.
The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis
Authors: Oliveira Rute , Bush Matthew J. , Pires Sílvia , Chandra Govind , Casas-Pastor Delia , Fritz Georg , Mendes Marta V. 
Published: December 2020

AbstractExtracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ2–σ4 architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
The localization of non-backtracking centrality in networks and its physical consequences
Authors: Pastor-Satorras Romualdo , Castellano Claudio 
Published: December 2020

AbstractThe spectrum of the non-backtracking matrix plays a crucial role in determining various structural and dynamical properties of networked systems, ranging from the threshold in bond percolation and non-recurrent epidemic processes, to community structure, to node importance. Here we calculate the largest eigenvalue of the non-backtracking matrix and the associated non-backtracking centrality for uncorrelated random networks, finding expressions in excellent agreement with numerical results. We show however that the same formulas do not work well for many real-world networks. We identify the mechanism responsible for this violation in the localization of the non-backtracking centrality on network subgraphs whose formation is highly unlikely in uncorrelated networks, but rather common in real-world structures. Exploiting this knowledge we present an heuristic generalized formula for the largest eigenvalue, which is remarkably accurate for all networks of a large empirical dataset. We show that this newly uncovered localization phenomenon allows to understand the failure of the message-passing prediction for the percolation threshold in many real-world structures.
Deep orofacial phenotyping of population-based infants with isolated cleft lip and isolated cleft palate
Authors: Yow Mimi , Hermann Nuno V. , Wei Yuan , Karsten Agneta , Kreiborg Sven 
Published: December 2020

AbstractIsolated orofacial clefts (OFC) are common with poorly understood aetiology. Heterogeneous phenotypes and subphenotypes confound aetiological variant findings. To improve OFC phenome understanding, population-based, consecutive, pre-treatment infants with isolated unilateral cleft lip (UCL, n = 183) and isolated cleft palate (CP, n = 83) of similar ancestry were grouped for deep phenotyping. Subphenotypes stratified by gender and cleft severity were evaluated for primary dental malformations and maturation using radiographs. We found that cleft severity and tooth agenesis were inadequate to distinguish heterogeneity in infants with UCL and CP. Both groups featured slow dental maturity, significantly slower in males and the UCL phenotype. In 32.8% of infants with UCL, supernumerary maxillary lateral incisors were present on the cleft lip side, but not in infants with CP, suggesting a cleft dental epithelium and forme fruste cleft dentoalveolus of the UCL subphenotype. The findings underscored the importance of deep phenotyping to disclose occult OFC subphenotypes.
Chronic effects of high-intensity functional training on motor function: a systematic review with multilevel meta-analysis
Authors: Wilke Jan , Mohr Lisa 
Published: December 2020

AbstractHigh-intensity functional training (HIFT) has become a popular method in the sports and fitness sector. In contrast to unimodal approaches such as strength or endurance training, it has been hypothesized to induce concurrent adaptations in multiple markers of motor function. However, to date, the effectiveness of HIFT in this regard has not been studied. The present systematic review quantified the chronic effects of HIFT on motor function in healthy individuals. A multilevel meta-analysis with a robust random effects meta-regession model was used to pool the standardized mean differences (SMD) between (a) HIFT and (b) no-exercise (NEX) as well as conventional endurance, resistance and balance training for outcomes of muscle strength, endurance capacity and balance. The influence of possible effect modifiers such as program duration, session duration, age or sex was examined in a moderator analysis. Seventeen papers with moderate to high methodological quality (PEDro scale) were identified. Compared to NEX, HIFT had small to moderate positive effects on endurance capacity (SMD: 0.42, 95% CI 0.07–0.78, p = 0.03) and strength (0.60, 95% CI 0.02–1.18, p = 0.04) but no effect on balance (SMD: − 0.10, 95% CI − 1.13 to 0.92, p = 0.42). Regarding endurance, HIFT showed similar effectiveness as moderate-intensity endurance training (SMD: − 0.11, 95% CI − 1.17 to 0.95, p = 0.75) and high-intensity interval endurance training (SMD: − 0.15, 95% CI − 1.4 to 1.1, p = 0.66). No comparisons of HIFT vs. classical resistance or balance training were found. Moderator analyses revealed no influence of most effect modifiers. However, regarding endurance, females seemed to respond more strongly to HIFT in the comparison to NEX (p < .05). HIFT appears to represent an appropriate method to induce chronic improvements in motor function. While being superior to NEX and non-inferior to endurance training, current evidence does not allow a comparison against resistance and balance training. The impact of possible effect moderators should be further elucidated in future research.
Combination treatment with a PI3K/Akt/mTOR pathway inhibitor overcomes resistance to anti-HER2 therapy in PIK3CA-mutant HER2-positive breast cancer cells
Authors: Fujimoto Yumi , Morita Tomoko Yamamori , Ohashi Akihiro , Haeno Hiroshi , Hakozaki Yumi , Fujii Masanori , Kashima Yukie , Kobayashi Susumu S. , Mukohara Toru 
Published: December 2020

AbstractAmplification and/or overexpression of human epidermal growth factor receptor 2 (HER2) are observed in 15–20% of breast cancers (HER2+ breast cancers), and anti-HER2 therapies have significantly improved prognosis of patients with HER2+ breast cancer. One resistance mechanism to anti-HER2 therapies is constitutive activation of the phosphoinositide 3-kinase (PI3K) pathway. Combination therapy with small-molecule inhibitors of AKT and HER2 was conducted in HER2+ breast cancer cell lines with or without PIK3CA mutations, which lead to constitutive activation of the PI3K pathway. PIK3CA mutations played important roles in resistance to single-agent anti-HER2 therapy in breast cancer cell lines. Combination therapy of a HER2 inhibitor and an AKT inhibitor, as well as other PI3K pathway inhibitors, could overcome the therapeutic limitations associated with single-agent anti-HER2 treatment in PIK3CA-mutant HER2+ breast cancer cell lines. Furthermore, expression of phosphorylated 4E-binding protein 1 (p4EBP1) following the treatment correlated with the antiproliferative activities of the combination, suggesting that p4EBP1 may have potential as a prognostic and/or efficacy-linking biomarkers for these combination therapies in patients with HER2+ breast cancer. These findings highlight potential clinical strategies using combination therapy to overcome the limitations associated with single-agent anti-HER2 therapies in patients with HER2+ breast cancer.
Laboratory analysis of Au–Pd bimetallic nanoparticles synthesized with Citrus limon leaf extract and its efficacy on mosquito larvae and non-target organisms
Authors: Minal Savy Panamkuttiyiel , Prakash Soam 
Published: December 2020

AbstractThe current study provides novel results on the synthesis of bimetallic nanoparticles (BNPs) of gold and palladium (Au–Pd) with an eco-friendly and non-toxic aqueous leaf extract of plant Citrus limon. The BNPs were characterized and toxicity bioassay was examined on the larvae of the pathogen vectors such as Anopheles stephensi and Aedes aegypti mosquitoes. The predation efficiency test was evaluated on the invertebrate non-target organisms such as natural predatory nymphs of dragonfly and damselfly. The results of material characterization using UV VIS spectroscopy confirmed the synthesis of Au–Pd BNPs with the appearance of the SPR bands. FT-IR spectroscopy indicates the presence of functional groups containing high amounts of nitro compounds and amines on the surface of BNPs. TEM result shows the presence of spherical polydisperse Au–Pd BNPs in the sample. The XRD pattern displayed the semi-crystalline nature and the changes in the hydrodynamic size and surface potential was determined for the sample at 0 h, 24 h, 48 h, and 72 h of synthesis through DLS and ZP analysis. Au–Pd BNPs Bioassay provided the effective lethal concentrations (LC50) against the I–IV instar larvae of An. stephensi and Ae. aegypti after 24 h, 48 h, and 72 h of exposure. The LC50 obtained from the larvicidal bioassay was used to test its effect on the predation efficiency of the selected nymphs which showed increased predation from 40 to 48 h of exposure as compared to the negative control. Hereby, we conclude that Au–Pd BNPs bioassay shows toxic mosquito larvicidal activity at the selected concentration with no lethal effect on the predation efficiency of the selected stage of the predatory non-target aquatic invertebrate insects.
Catalytic oxidation of small organic molecules by cold plasma in solution in the presence of molecular iron complexes†
Authors: Śmiłowicz Dariusz , Kogelheide Friederike , Schöne Anna Lena , Stapelmann Katharina , Awakowicz Peter , Metzler-Nolte Nils 
Published: December 2020

AbstractThe plasma-mediated decomposition of volatile organic compounds has previously been investigated in the gas phase with metal oxides as heterogeneous catalysts. While the reactive species in plasma itself are well investigated, very little is known about the influence of metal catalysts in solution. Here, we present initial investigations on the time-dependent plasma-supported oxidation of benzyl alcohol, benzaldehyde and phenol in the presence of molecular iron complexes in solution. Products were identified by HPLC, ESI-MS, FT-IR, and $$^{1}\hbox {H NMR}$$

1

H NMR

spectroscopy. Compared to metal-free oxidation of the substrates, which is caused by reactive oxygen species and leads to a mixture of products, the metal-mediated reactions lead to one product cleanly, and faster than in the metal-free reactions. Most noteworthy, even catalytic amounts of metal complexes induce these clean transformations. The findings described here bear important implications for plasma-supported industrial waste transformations, as well as for plasma-mediated applications in biomedicine, given the fact that iron is the most abundant redox-active metal in the human body.
Synthesis and thermal decomposition kinetics of moisture curable polyurethane films as a reinforcing material for cultural relics
Authors: Zhao Xing , Wang Liqin , Guo Lang , Ma Yanni , Wang Ziming , Niu Qing , Zheng Liping 
Published: December 2020

AbstractIn situ consolidation is the most common treatment to conserve cultural relics, but materials for preserving fragile organic cultural relics in humid archaeological excavation sites are scarce. To solve the problem, a moisture-curable polyurethane (MCPU) prepolymer was synthesized by reacting isophorone diisocyanate with polyethylene glycol 600. The standard acetone–dibutylamine method, Fourier transform infrared spectroscopy, gel chromatography and thermogravimetric analysis were utilized to determine the change in isocyanate groups before and after the reaction, the prepolymer molecular weight, the thermal decomposition kinetic parameters and the MCPU film lifetime. The results showed that the number-average molecular weight of the prepolymer was 749, and the weight average molecular weight was 1684. Isophorone groups in the prepolymer react with moisture in the air to form colorless, transparent, flexible films. The thermal decomposition of the MCPU films was a first-order reaction, and the decomposition process consisted of two stages. The Dakin equation was used to obtain the thermal aging equation lg t = 4600.82/T − 8.07, meaning that at 15 °C, the sample has an approximately 150-year lifetime. A new conservation material was developed, and its thermal decomposition kinetics were studied, which are significant for the conservation of fragile organic cultural relics in humid environments.
Dietary fiber components, microstructure, and texture of date fruits (Phoenix dactylifera, L.)
Authors: Kamal-Eldin Afaf , George Navomy , Sobti Bhawna , AlRashidi Nouf , Ghnimi Sami , Ali Abdul Aziz , Andersson Annica A. M. , Andersson Roger , Antony Asha , Hamed Fathalla 
Published: December 2020

AbstractDate fruits vary widely in the hardness of their edible parts and they are classified accordingly into soft, semi-dry, and dry varieties. Fruit texture, a significant parameter in determining consumer acceptance, is related to the tissue structure and chemical composition of the fruit, mainly the ratio of sucrose to reducing sugars. This study aimed to understand the relationship between the chemical composition, microstructure, and texture profile of 10 major Emirati date fruits. The soluble sugars, glucose and fructose, represent ca 80 g/100 g of the fruits on the basis of dry weight (DW) while the dietary fiber contents varied 5.2–7.4 g/100 dg D.W. with lignin being the main determinant of the variability. The textures of the samples were studied using instrumental texture profile analysis. While no correlation was found between the soluble sugar and texture parameters in this study, the different fiber constituents correlated variably with the different parameters of date fruit texture. Lignin, arabinoxylan, galactomannan, and pectin were found to correlate significantly with fruit hardness and the related parameters, gumminess and chewiness. Both lignin and arabinoxylan correlated with resilience, and arabinoxylan exhibited a strong correlation with cohesiveness.
Acclimation temperature affects thermal reaction norms for energy reserves in Drosophila
Authors: Klepsatel Peter , Girish Thirnahalli Nagaraj , Gáliková Martina 
Published: December 2020

AbstractOrganisms have evolved various physiological mechanisms to cope with unfavourable environmental conditions. The ability to tolerate non-optimal thermal conditions can be substantially improved by acclimation. In this study, we examined how an early-life acclimation to different temperatures (19 °C, 25 °C and 29 °C) influences thermal reaction norms for energy stores inDrosophilaadults. Our results show that acclimation temperature has a significant effect on the amount of stored fat and glycogen (and their relative changes) and the optimal temperature for their accumulation. Individuals acclimated to 19 °C had, on average, more energy reserves than flies that were initially maintained at 25 °C or 29 °C. In addition, acclimation caused a shift in optimal temperature for energy stores towards acclimation temperature. We also detected significant population differences in this response. The effect of acclimation on the optimal temperature for energy stores was more pronounced in flies from the temperate climate zone (Slovakia) than in individuals from the tropical zone (India). Overall, we found that the acclimation effect was stronger after acclimation to low (19 °C) than to high (29 °C) temperature. The observed sensitivity of thermal reaction norms for energy reserves to acclimation temperature can have important consequences for surviving periods of food scarcity, especially at suboptimal temperatures.
In situ modelling of biofilm formation in a hydrothermal spring cave
Authors: Anda Dóra , Szabó Attila , Kovács-Bodor Petra , Makk Judit , Felföldi Tamás , Ács Éva , Mádl-Szőnyi Judit , Borsodi Andrea K. 
Published: December 2020

AbstractAttachment of microorganisms to natural or artificial surfaces and the development of biofilms are complex processes which can be influenced by several factors. Nevertheless, our knowledge on biofilm formation in karstic environment is quite incomplete. The present study aimed to examine biofilm development for a year under controlled conditions in quasi-stagnant water of a hydrothermal spring cave located in the Buda Thermal Karst System (Hungary). Using a model system, we investigated how the structure of the biofilm is formed from the water and also how the growth rate of biofilm development takes place in this environment. Besides scanning electron microscopy, next-generation DNA sequencing was used to reveal the characteristic taxa and major shifts in the composition of the bacterial communities. Dynamic temporal changes were observed in the structure of bacterial communities. Bacterial richness and diversity increased during the biofilm formation, and 9–12 weeks were needed for the maturation. Increasing EPS production was also observed from the 9–12 weeks. The biofilm was different from the water that filled the cave pool, in terms of the taxonomic composition and metabolic potential of microorganisms. In these karstic environments, the formation of mature biofilm appears to take place relatively quickly, in a few months.