bluuebunny/crossref_metadata_2025_split huggingface dataset:
ERRFI1 induces apoptosis of hepatocellular carcinoma cells in response to tryptophan deficiency
Authors: Cui Mingqing , Liu Dan , Xiong Wujun , Wang Yugang , Mi Jun 
Published: October 2021

AbstractTryptophan metabolism is an essential regulator of tumor immune evasion. However, the effect of tryptophan metabolism on cancer cells remains largely unknown. Here, we find that tumor cells have distinct responses to tryptophan deficiency in terms of cell growth, no matter hepatocellular carcinoma (HCC) cells, lung cancer cells, or breast cancer cells. Further study shows that ERRFI1 is upregulated in sensitive HCC cells, but not in resistant HCC cells, in response to tryptophan deficiency, and ERRFI1 expression level positively correlates with HCC patient overall survival. ERRFI1 knockdown recovers tryptophan deficiency-suppressed cell growth of sensitive HCC cells. In contrast, ERRFI1 overexpression sensitizes resistant HCC cells to tryptophan deficiency. Moreover, ERRFI1 induces apoptosis by binding PDCD2 in HCC cells, PDCD2 knockdown decreases the ERRFI1-induced apoptosis in HCC cells. Thus, we conclude that ERRFI1-induced apoptosis increases the sensitivity of HCC cells to tryptophan deficiency and ERRFI1 interacts with PDCD2 to induce apoptosis in HCC cells.
The ethical landscape(s) of non-invasive prenatal testing in England, France and Germany: findings from a comparative literature review
Authors: Perrot Adeline , Horn Ruth 
Published: October 2021

AbstractSince 2019, England, France and Germany have started offering NIPT as a publicly funded second-tier test for common chromosomal aneuploidies (trisomy 21, 18 and/or 13). Despite these benefits, the introduction of NIPT into routine prenatal care also raises a number of ethical concerns. In this paper, we analyse how these issues are discussed differently across countries, echoing the different socio-political particularities and value-systems that shape the use and regulation of NIPT in a specific country. The international comparison between England, France and Germany shows how each country defines the principle of reproductive autonomy and weighs it against other principles and values, such as, human dignity, disability rights and the duty of care of health professionals. In terms of methodology, our literature review focuses on arguments and regulations of prenatal testing and reproductive choices (specifically on NIPT), through the investigation of regulatory, parliamentary, scientific, medical, association, institutional and media sources. The comparative review helps to better understand ethical questions discussed with regard to NIPT, and, more broadly, to prenatal genomic testing, and the limits associated with reproductive autonomy in the three countries studied. Whereas reproductive autonomy is valued in each country, it is understood and implemented differently depending on the socio-cultural context, and on what other principles are evoked and how they are defined.
A moisture-tolerant route to unprotected α/β-amino acid N-carboxyanhydrides and facile synthesis of hyperbranched polypeptides
Authors: Tian Zi-You , Zhang Zhengchu , Wang Shuo , Lu Hua 
Published: October 2021

AbstractA great hurdle in the production of synthetic polypeptides lies in the access of N-carboxyanhydrides (NCA) monomers, which requires dry solvents, Schlenk line/gloveboxe, and protection of side-chain functional groups. Here we report a robust method for preparing unprotected NCA monomers in air and under moisture. The method employs epoxy compounds as ultra-fast scavengers of hydrogen chloride to allow assisted ring-closure and prevent NCA from acid-catalyzed decomposition under moist conditions. The broad scope and functional group tolerance of the method are demonstrated by the facile synthesis of over 30 different α/β-amino acid NCAs, including many otherwise inaccessible compounds with reactive functional groups, at high yield, high purity, and up to decagram scales. The utility of the method and the unprotected NCAs is demonstrated by the facile synthesis of two water-soluble polypeptides that are promising candidates for drug delivery and protein modification. Overall, our strategy holds great potential for facilitating the synthesis of NCA and expanding the industrial application of synthetic polypeptides.
Thermally active nanoparticle clusters enslaved by engineered domain wall traps
Authors: Tierno Pietro , Johansen Tom H. , Straube Arthur V. 
Published: October 2021

AbstractThe stable assembly of fluctuating nanoparticle clusters on a surface represents a technological challenge of widespread interest for both fundamental and applied research. Here we demonstrate a technique to stably confine in two dimensions clusters of interacting nanoparticles via size-tunable, virtual magnetic traps. We use cylindrical Bloch walls arranged to form a triangular lattice of ferromagnetic domains within an epitaxially grown ferrite garnet film. At each domain, the magnetic stray field generates an effective harmonic potential with a field tunable stiffness. The experiments are combined with theory to show that the magnetic confinement is effectively harmonic and pairwise interactions are of dipolar nature, leading to central, strictly repulsive forces. For clusters of magnetic nanoparticles, the stationary collective states arise from the competition between repulsion, confinement and the tendency to fill the central potential well. Using a numerical simulation model as a quantitative map between the experiments and theory we explore the field-induced crystallization process for larger clusters and unveil the existence of three different dynamical regimes. The present method provides a model platform for investigations of the collective phenomena emerging when strongly confined nanoparticle clusters are forced to move in an idealized, harmonic-like potential.
Orchestrating and sharing large multimodal data for transparent and reproducible research
Authors: Mammoliti Anthony , Smirnov Petr , Nakano Minoru , Safikhani Zhaleh , Eeles Christopher , Seo Heewon , Nair Sisira Kadambat , Mer Arvind S. , Smith Ian , Ho Chantal , Beri Gangesh , Kusko Rebecca ,   Massive Analysis Quality Control (MAQC) Society Board of Directors, Shraddha Thakkar , Sansone Susanna-Assunta , Tong Weida , Wolfinger Russ D. , Mason Christopher E. , Jones Wendell , Dopazo Joaquin , Furlanello Cesare , Lin Eva , Yu Yihong , Martin Scott , Hafner Marc , Haibe-Kains Benjamin 
Published: October 2021

AbstractReproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA (orcestra.ca), which provides a flexible framework for the reproducible processing of multimodal biomedical data. It enables processing of clinical, genomic and perturbation profiles of cancer samples through automated processing pipelines that are user-customizable. ORCESTRA creates integrated and fully documented data objects with persistent identifiers (DOI) and manages multiple dataset versions, which can be shared for future studies.
Phonon-induced disorder in dynamics of optically pumped metals from nonlinear electron-phonon coupling
Authors: Sous John , Kloss Benedikt , Kennes Dante M. , Reichman David R. , Millis Andrew J. 
Published: October 2021

AbstractThe non-equilibrium dynamics of matter excited by light may produce electronic phases, such as laser-induced high-transition-temperature superconductivity, that do not exist in equilibrium. Here we simulate the dynamics of a metal driven at initial time by a spatially uniform pump that excites dipole-active vibrational modes which couple nonlinearly to electrons. We provide evidence for rapid loss of spatial coherence, leading to emergent effective disorder in the dynamics, which arises in a system unitarily evolving under a translation-invariant Hamiltonian, and dominates the electronic behavior as the system evolves towards a correlated electron-phonon long-time state, possibly explaining why transient superconductivity is not observed. Our framework provides a basis within which to understand correlation dynamics in current pump-probe experiments of vibrationally coupled electrons, highlight the importance of the evolution of phase coherence, and demonstrate that pumped electron-phonon systems provide a means of realizing dynamically induced disorder in translation-invariant systems.
Urban mining by flash Joule heating
Authors: Deng Bing , Luong Duy Xuan , Wang Zhe , Kittrell Carter , McHugh Emily A. , Tour James M. 
Published: October 2021

AbstractPrecious metal recovery from electronic waste, termed urban mining, is important for a circular economy. Present methods for urban mining, mainly smelting and leaching, suffer from lengthy purification processes and negative environmental impacts. Here, a solvent-free and sustainable process by flash Joule heating is disclosed to recover precious metals and remove hazardous heavy metals in electronic waste within one second. The sample temperature ramps to ~3400 K in milliseconds by the ultrafast electrical thermal process. Such a high temperature enables the evaporative separation of precious metals from the supporting matrices, with the recovery yields >80% for Rh, Pd, Ag, and >60% for Au. The heavy metals in electronic waste, some of which are highly toxic including Cr, As, Cd, Hg, and Pb, are also removed, leaving a final waste with minimal metal content, acceptable even for agriculture soil levels. Urban mining by flash Joule heating would be 80× to 500× less energy consumptive than using traditional smelting furnaces for metal-component recovery and more environmentally friendly.
An energy-efficient pathway to turbulent drag reduction
Authors: Marusic Ivan , Chandran Dileep , Rouhi Amirreza , Fu Matt K. , Wine David , Holloway Brian , Chung Daniel , Smits Alexander J. 
Published: October 2021

AbstractSimulations and experiments at low Reynolds numbers have suggested that skin-friction drag generated by turbulent fluid flow over a surface can be decreased by oscillatory motion in the surface, with the amount of drag reduction predicted to decline with increasing Reynolds number. Here, we report direct measurements of substantial drag reduction achieved by using spanwise surface oscillations at high friction Reynolds numbers ($${{{\mathrm{Re}}}_{\tau }}$$

Re

τ

) up to 12,800. The drag reduction occurs via two distinct physical pathways. The first pathway, as studied previously, involves actuating the surface at frequencies comparable to those of the small-scale eddies that dominate turbulence near the surface. We show that this strategy leads to drag reduction levels up to 25% at $${{{{{{{{\mathrm{Re}}}}}}}}}_{\tau }$$

Re

τ

= 6,000, but with a power cost that exceeds any drag-reduction savings. The second pathway is new, and it involves actuation at frequencies comparable to those of the large-scale eddies farther from the surface. This alternate pathway produces drag reduction of 13% at $${{{{{{{{\mathrm{Re}}}}}}}}}_{\tau }$$

Re

τ

= 12,800. It requires significantly less power and the drag reduction grows with Reynolds number, thereby opening up potential new avenues for reducing fuel consumption by transport vehicles and increasing power generation by wind turbines.
Designing small organic non-fullerene acceptor molecules with diflorobenzene or quinoline core and dithiophene donor moiety through density functional theory
Authors: Bary Ghulam , Ghani Lubna , Jamil Muhammad Imran , Arslan Muhammad , Ahmed Waqar , Ahmad Anees , Sajid Muhammad , Ahmad Riaz , Huang Duohui 
Published: October 2021

AbstractThe non-fullerene acceptors A1–A5 with diflourobenzene or quinoline core (bridge) unit, donor cyclopenta[1,2-b:3,4-b′]dithiophene unit and 2-(2-methylene-3-oxo-2,3-dihydro-1H-inden-1-ylidene)malononitrile as acceptor unit with additional phenyl, fulvene or thieno[3,2-d]pyrimidinyl 5-oxide groups have been designed through DFT calculations. The optimization of molecular geometries were performed with density functional theory (DFT) at B3LYP 6-31G (d,p) level of theory. The frontier molecular orbital (FMO) energies, band gap energies and dipole moments (ground and excited state) have been calculated to probe the photovoltaic properties. The band gap (1.42–2.01 eV) and dipole moment values (5.5–18. Debye) showed that these designed acceptors are good candidates for organic solar cells. Time-Dependent Density Functional Theory (TD-DFT) results showed λmax (wave length at maximum absorption) value (611–837 nm), oscillator strength (f) and excitation energies (1.50–2.02 eV) in gas phase and in CHCl3 solvent (1.48–1.89 eV) using integral equation formalism variant (IEFPCM) model. The λmax in CHCl3 showed marginal red shift for all designed acceptors compared with gas phase absorption. The partial density of states (PDOS) has been plotted by using multiwfn which showed that all the designed molecules have more electronic distribution at the donor moiety and lowest at the central bridge. The reorganization energies of electron (λe) (0.0007 eV to 0.017 eV), and the hole reorganization energy values (0.0003 eV to − 0.0403 eV) were smaller which suggested that higher charged motilities. The blends of acceptors A1–A5 with donor polymer D1 provided open circuit voltage (Voc) and ∆HOMO off-set of the HOMO of donor and acceptors. These blends showed 1.04 to 1.5 eV values of Voc and 0 to 0.38 eV ∆HOMO off set values of the donor–acceptor bends which indicate improved performance of the cell. Finally, the blend of D1–A4 was used for the study of distribution of HOMO and LUMO. The HOMO were found distributed on the donor polymer (D1) while the A4 acceptor was found with LUMO distribution. Based on λmax values, and band gap energies (Eg), excitation energies (Ex), reorganization energies; the A3 and A4 will prove good acceptor molecules for the development of organic solar cells.
Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites
Authors: Ikebe Jinzen , Suzuki Munenori , Komori Aya , Kobayashi Kaito , Kameda Tomoshi 
Published: October 2021

AbstractEnzymes with low regioselectivity of substrate reaction sites may produce multiple products from a single substrate. When a target product is produced industrially using these enzymes, the production of non-target products (byproducts) causes adverse effects such as increased processing costs for purification and the amount of raw material. Thus it is required the development of modified enzymes to reduce the amount of byproducts’ production. In this paper, we report a method called mutation site prediction for enhancing the regioselectivity of substrate reaction sites (MSPER). MSPER takes conformational data for docking poses of an enzyme and a substrate as input and automatically generates a ranked list of mutation sites to destabilize docking poses for byproducts while maintaining those for target products in silico. We applied MSPER to the enzyme cytochrome P450 CYP102A1 (BM3) and the two substrates to enhance the regioselectivity for four target products with different reaction sites. The 13 of the total 14 top-ranked mutation sites predicted by MSPER for the four target products succeeded in selectively enhancing the regioselectivity up to 6.4-fold. The results indicate that MSPER can distinguish differences of substrate structures and the reaction sites, and can accurately predict mutation sites to enhance regioselectivity without selection by directed evolution screening.
Sensory integration abilities for balance in glaucoma, a preliminary study
Authors: O’Connell Caitlin , Redfern Mark , Chan Kevin C. , Wollstein Gadi , Conner Ian P. , Cham Rakié 
Published: October 2021

AbstractThe goal of this study was to quantify the association between sensory integration abilities relevant for standing balance and disease stage in glaucoma. The disease stage was assessed using both functional (visual field deficit) and structural (retinal nerve fiber layer thickness) deficits in the better and worse eye. Balance was assessed using an adapted version of the well-established Sensory Organization Test (SOT). Eleven subjects diagnosed with mild to moderate glaucoma stood for 3 min in 6 sensory challenging postural conditions. Balance was assessed using sway magnitude and sway speed computed based on center-of-pressure data. Mixed linear regression analyses were used to investigate the associations between glaucoma severity and balance measures. Findings revealed that the visual field deficit severity in the better eye was associated with increased standing sway speed. This finding was confirmed in eyes open and closed conditions. Balance was not affected by the extent of the visual field deficit in the worse eye. Similarly, structural damage in either eye was not associated with the balance measures. In summary, this study found that postural control performance was associated with visual field deficit severity. The fact that this was found during eyes closed as well suggests that reduced postural control in glaucoma is not entirely attributed to impaired peripheral visual inputs. A larger study is needed to further investigate potential interactions between visual changes and central processing changes contributing to reduced balance function and increased incidence of falls in adults with glaucoma.
Spotlight onto surfactant–steam–bitumen interfacial behavior via molecular dynamics simulation
Authors: Ahmadi Mohammadali , Chen Zhangxin 
Published: October 2021

AbstractHeavy oil and bitumen play a vital role in the global energy supply, and to unlock such resources, thermal methods, e.g., steam injection, are applied. To improve the performance of these methods, different additives, such as air, solvents, and chemicals, can be used. As a subset of chemicals, surfactants are one of the potential additives for steam-based bitumen recovery methods. Molecular interactions between surfactant/steam/bitumen have not been addressed in the literature. This paper investigates molecular interactions between anionic surfactants, steam, and bitumen in high-temperature and high-pressure conditions. For this purpose, a real Athabasca oil sand composition is employed to assess the phase behavior of surfactant/steam/bitumen under in-situ steam-based bitumen recovery. Two different asphaltene architectures, archipelago and Island, are used to examine the effect of asphaltene type on bitumen's interfacial behavior. The influence of having sulfur heteroatoms in a resin structure and a benzene ring's effect in an anionic surfactant structure on surfactant–steam–bitumen interactions are investigated systematically. The outputs are supported by different analyses, including radial distribution functions (RDFs), mean squared displacement (MSD), radius of gyration, self-diffusion coefficient, solvent accessible surface area (SASA), interfacial thickness, and interaction energies. According to MD outputs, adding surfactant molecules to the steam phase improved the interaction energy between steam and bitumen. Moreover, surfactants can significantly improve steam emulsification capability by decreasing the interfacial tension (IFT) between bitumen and the steam phase. Asphaltene architecture has a considerable effect on the interfacial behavior in such systems. This study provides a better and more in-depth understanding of surfactant–steam–bitumen systems and spotlights the interactions between bitumen fractions and surfactant molecules under thermal recovery conditions.
NBS1 I171V variant underlies individual differences in chromosomal radiosensitivity within human populations
Authors: Tomioka Keita , Miyamoto Tatsuo , Akutsu Silvia Natsuko , Yanagihara Hiromi , Fujita Kazumasa , Royba Ekaterina , Tauchi Hiroshi , Yamamoto Takashi , Koh Iemasa , Hirata Eiji , Kudo Yoshiki , Kobayashi Masao , Okada Satoshi , Matsuura Shinya 
Published: October 2021

AbstractGenetic information is protected against a variety of genotoxins including ionizing radiation (IR) through the DNA double-strand break (DSB) repair machinery. Genome-wide association studies and clinical sequencing of cancer patients have suggested that a number of variants in the DNA DSB repair genes might underlie individual differences in chromosomal radiosensitivity within human populations. However, the number of established variants that directly affect radiosensitivity is still limited. In this study, we performed whole-exome sequencing of 29 Japanese ovarian cancer patients and detected the NBS1 I171V variant, which is estimated to exist at a rate of approximately 0.15% in healthy human populations, in one patient. To clarify whether this variant indeed contributes to chromosomal radiosensitivity, we generated NBS1 I171V variant homozygous knock-in HCT116 cells and mice using the CRISPR/Cas9 system. Radiation-induced micronucleus formation and chromosomal aberration frequency were significantly increased in both HCT116 cells and mouse embryonic fibroblasts (MEFs) with knock-in of the NBS1 I171V variant compared with the levels in wild-type cells. These results suggested that the NBS1 I171V variant might be a genetic factor underlying individual differences in chromosomal radiosensitivity.
Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic
Authors: Melekhina E. N. , Belykh E. S. , Markarova M. Yu. , Taskaeva A. A. , Rasova E. E. , Baturina O. A. , Kabilov M. R. , Velegzhaninov I. O. 
Published: October 2021

AbstractThe present comprehensive study aimed to estimate the aftermath of oil contamination and the efficacy of removing the upper level of polluted soil under the conditions of the extreme northern taiga of northeastern European Russia. Soil samples from three sites were studied. Two sites were contaminated with the contents of a nearby sludge collector five years prior to sampling. The highly contaminated upper soil level was removed from one of them. The other was left for self-restoration. A chemical analysis of the soils was conducted, and changes in the composition of the soil zoocoenosis and bacterial and fungal microbiota were investigated. At both contaminated sites, a decrease in the abundance and taxonomic diversity of indicator groups of soil fauna, oribatid mites and collembolans compared to the background site were found. The pioneer eurytopic species Oppiella nova, Proisotoma minima and Xenyllodes armatus formed the basis of the microarthropod populations in the contaminated soil. A complete change in the composition of dominant taxonomic units was observed in the microbiota, both the bacterial and fungal communities. There was an increase in the proportion of representatives of Proteobacteria and Actinobacteria in polluted soils compared to the background community. Hydrocarbon-degrading bacteria—Alcanivorax, Rhodanobacter ginsengisoli, Acidobacterium capsulatum, and Acidocella—and fungi—Amorphotheca resinae abundances greatly increased in oil-contaminated soil. Moreover, among both bacteria and fungi, a sharp increase in the abundance of uncultivated organisms that deserve additional attention as potential oil degraders or organisms with a high resistance to oil contamination were observed. The removal of the upper soil level was partly effective in terms of decreasing the oil product concentration (from approximately 21 to 2.6 g/kg of soil) and preventing a decrease in taxonomic richness but did not prevent alterations in the composition of the microbiota or zoocoenosis.