bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscopic and in-situ cross-sectional observations of Li-based conversion coating formation using liquid-phase TEM
Authors: Kosari A. , Tichelaar F. , Visser P. , Taheri P. , Zandbergen H. , Terryn H. , Mol J. M. C. 
Published: August 2021

AbstractLithium salts have been proposed as promising environmentally friendly alternatives to carcinogenic hexavalent chromium-based inhibitors for the corrosion protection of aerospace aluminium alloys (AAs). Incorporated into organic coatings, lithium salts are released at damaged locations to establish a conversion layer in which distinct sublayers have different barrier characteristics. Thus, detailed knowledge on the sequence of formation events from the early stages of nucleation towards the final multi-layered arrangement is essential for developing and optimising lithium-leaching technology for protective coatings. Here, liquid-phase-transmission electron microscopy (LP-TEM) is employed to observe nanoscopic morphological evolutions in situ during the lithium-based conversion process of AA2024-T3. Thanks to dedicated preparation of delicate sandwiched TEM specimens allowing us to explore the events cross-sectionally, we provide real-time direct mechanistic information on the conversion process from the initiation to an advanced growth stage. In parallel, we perform supplementary ex situ SEM and TEM investigations to support and validate the LP-TEM findings. The unprecedented experimental approach developed and executed in this study provides an inspiring base for studying also other complicated surface conversion processes in situ and at the nanoscopic scale.
High-performance quantum entanglement generation via cascaded second-order nonlinear processes
Authors: Zhang Zichang , Yuan Chenzhi , Shen Si , Yu Hao , Zhang Ruiming , Wang Heqing , Li Hao , Wang You , Deng Guangwei , Wang Zhiming , You Lixing , Wang Zhen , Song Haizhi , Guo Guangcan , Zhou Qiang 
Published: August 2021

AbstractIn this paper, we demonstrate the generation of high-performance entangled photon-pairs in different degrees of freedom from a single piece of fiber pigtailed periodically poled LiNbO3 (PPLN) waveguide. We utilize cascaded second-order nonlinear optical processes, i.e., second-harmonic generation (SHG) and spontaneous parametric downconversion (SPDC), to generate photon-pairs. Previously, the performance of the photon-pairs is contaminated by Raman noise photons. Here by fiber-integrating the PPLN waveguide with noise-rejecting filters, we obtain a coincidence-to-accidental ratio (CAR) higher than 52,600 with photon-pair generation and detection rate of 52.36 kHz and 3.51 kHz, respectively. Energy-time, frequency-bin, and time-bin entanglement is prepared by coherently superposing correlated two-photon states in these degrees of freedom, respectively. The energy-time entangled two-photon states achieve the maximum value of CHSH-Bell inequality of S = 2.71 ± 0.02 with two-photon interference visibility of 95.74 ± 0.86%. The frequency-bin entangled two-photon states achieve fidelity of 97.56 ± 1.79% with a spatial quantum beating visibility of 96.85 ± 2.46%. The time-bin entangled two-photon states achieve the maximum value of CHSH-Bell inequality of S = 2.60 ± 0.04 and quantum tomographic fidelity of 89.07 ± 4.35%. Our results provide a potential candidate for the quantum light source in quantum photonics.
ACO2 clinicobiological dataset with extensive phenotype ontology annotation
Authors: Guehlouz Khadidja , Foulonneau Thomas , Amati-Bonneau Patrizia , Charif Majida , Colin Estelle , Bris Céline , Desquiret-Dumas Valérie , Milea Dan , Gohier Philippe , Procaccio Vincent , Bonneau Dominique , den Dunnen Johan T. , Lenaers Guy , Reynier Pascal , Ferré Marc 
Published: August 2021

AbstractPathogenic variants of the aconitase 2 gene (ACO2) are responsible for a broad clinical spectrum involving optic nerve degeneration, ranging from isolated optic neuropathy with recessive or dominant inheritance, to complex neurodegenerative syndromes with recessive transmission. We created the first public locus-specific database (LSDB) dedicated to ACO2 within the “Global Variome shared LOVD” using exclusively the Human Phenotype Ontology (HPO), a standard vocabulary for describing phenotypic abnormalities. All the variants and clinical cases listed in the literature were incorporated into the database, from which we produced a dataset. We followed a rational and comprehensive approach based on the HPO thesaurus, demonstrating that ACO2 patients should not be classified separately between isolated and syndromic cases. Our data highlight that certain syndromic patients do not have optic neuropathy and provide support for the classification of the recurrent pathogenic variants c.220C>G and c.336C>G as likely pathogenic. Overall, our data records demonstrate that the clinical spectrum of ACO2 should be considered as a continuum of symptoms and refines the classification of some common variants.
Multi-modal magnetic resonance imaging in a mouse model of concussion
Authors: To Xuan Vinh , Nasrallah Fatima A. 
Published: August 2021

AbstractThis data collection contains Magnetic Resonance Imaging (MRI) data, including structural, diffusion, stimulus-evoked, and resting-state functional MRI and behavioural assessment results, including acute post-impact Loss-of-Righting Reflex time and acute, subacute, and longer-term Neural Severity Score, and Open Field Behaviour obtained from a mouse model of concussion. Four cohorts with 43 3–4 months old male mice in total were used: Sham (n = 14, n = 6 day 2, n = 3 day 7, n = 5 day 14), concussion day 2 (CON 2; n = 9), concussion day 7 (CON 7; n = 10), concussion day 14 (CON 14; n = 10). The data collection contains the aforementioned MRI data in compressed NIFTI format, data sheets on animal’s backgrounds and behavioural outcomes and is made publicly available from a data repository. The available data are intended to facility cross-study comparisons, meta-analysis, and science reproducibility.
An annotated T2-weighted magnetic resonance image collection of testicular germ and non-germ cell tumors
Authors: Feliciani Giacomo , Mellini Lorenzo , Loi Emiliano , Piccinini Filippo , Galeotti Roberto , Sarnelli Anna , Parenti Gian Carlo 
Published: August 2021

AbstractTesticular cancer is a rare tumor with a worldwide incidence that has increased over the last few decades. The majority of these tumors are testicular non-germ (TNGCTs) and germ cell tumors (TGCTs); the latter divided into two broad classes - seminomatous (SGCTs) and non-seminomatous germ cell tumors (NSGCTs). Although ultrasonography (US) maintains a primary role in the diagnostic workup of scrotal pathology, magnetic resonance imaging (MRI) has emerged as the imaging modality recommended for challenging cases, providing additional information to clarify inconclusive/equivocal US. In this work we describe and publicly share a collection of 44 images of annotated T2-weighted MRI lesions from 42 patients. Given that testicular cancer is a rare tumor, we are confident that this collection can be used to validate statistical models and to further investigate TNGCT and TGCT peculiarities using medical imaging features.
A dataset of distribution and diversity of blood-sucking mites in China
Authors: Meng Fan-Fei , Xu Qiang , Chen Jin-Jin , Ji Yang , Zhang Wen-Hui , Fan Zheng-Wei , Zhao Guo-Ping , Jiang Bao-Gui , Shi Tao-Xing , Fang Li-Qun , Liu Wei 
Published: August 2021

AbstractMite-borne diseases, such as scrub typhus and hemorrhagic fever with renal syndrome, present an increasing global public health concern. Most of the mite-borne diseases are caused by the blood-sucking mites. To present a comprehensive understanding of the distributions and diversity of blood-sucking mites in China, we derived information from peer-reviewed journal articles, thesis publications and books related to mites in both Chinese and English between 1978 and 2020. Geographic information of blood-sucking mites’ occurrence and mite species were extracted and georeferenced at the county level. Standard operating procedures were applied to remove duplicates and ensure accuracy of the data. This dataset contains 6,443 records of mite species occurrences at the county level in China. This geographical dataset provides an overview of the species diversity and wide distributions of blood-sucking mites, and can potentially be used in distribution prediction of mite species and risk assessment of mite-borne diseases in China.
Solubility of vitamin A in supercritical CO2: experimental study and thermodynamic modeling
Authors: Naikoo Gowhar Ahmad , Saeedi Zadegan Mohammad , Zamani Pedram Mona , Hassan Israr Ul , Ahmed Waqar , Yousefi Attar Golshan 
Published: August 2021

AbstractOne of the best methods of extracting Vitamin A, as a helper of the immune body system and vision, was measured in supercritical carbon dioxide (SC-CO2); Mole fractions were gained at practical conditions in which the temperature was in the range of 303–323 K and the pressure range was 90–235 bar, respectively. Moreover, four Equation of States [Soave–Redlich–Kwong, Peng–Robinson, Stryjek–Vera and Dashtizadeh–Pazuki–Taghikhani–Ghotbi (DPTG)] were compared with the experimental data. Also, the mixing rules of Van der Waals (vdW1 and vdW2) selected to correlate the solubility data of vitamin A. The outcomes indicate that each of EOSs coupled with vdW2, as a method of estimating the physicochemical and critical properties, were correlated with the solubility data of vitamin A in SC-CO2 with more accuracy, in comparison with vdW1. Among the cubic EOSs, the DPTG model with vdW2 generated the most suitable correlation with the percentage average absolute relative deviation (Average Absolute Relative Deviation%) of 6.
Mycoremediation and toxicity assessment of textile effluent pertaining to its possible correlation with COD
Authors: Rajhans Geetanjali , Barik Adyasa , Sen Sudip Kumar , Masanta Amrita , Sahoo Naresh Kumar , Raut Sangeeta 
Published: August 2021

AbstractGlobally, textile industries are one of the major sectors releasing dye pollutants. This is the first report on the positive correlation between toxicity and chemical oxygen demand (COD) of textile effluent along with the proposed pathway for enzymatic degradation of acid orange 10 using Geotrichum candidum within a very short stretch of time (18 h). Removal efficiency of this mycoremedial approach after 18 h in terms of chemical oxygen demand, biological oxygen demand, total suspended solids, salinity, color and dye concentration in the treated effluent reached to 98.5%, 56.3%,73.2%, 64%, 89% and 87% respectively. Also there was a decrease in pH of the treated effluent. FTIR analysis of the treated effluent confirmed biodegradation. The LCMS analysis showed the degradation of acid orange 10, which was confirmed by the formation of two biodegradation products, 7-oxo-8-iminonapthalene-1,3-disulfonate and nitrosobenzene, which subsequently undergoes stepwise hydrogenation and dehydration to form aniline via phenyl hydroxyl amine as intermediate. The X-ray diffraction studies showed that heavy metal content in the treated effluent has reduced along with decrease in % crystallinity, indicating biodegradation. The connection between toxicity and COD was also inveterated using Pearson’s correlation coefficient. Further the toxicological studies indicated the toxicity of raw textile effluent and relatively lower toxic nature of metabolites generated after biodegradation by G. candidum.
Conformational dynamics of androgen receptors bound to agonists and antagonists
Authors: Gim Hyo Jin , Park Jiyong , Jung Michael E. , Houk K. N. 
Published: August 2021

AbstractThe androgen receptor (AR) is critical in the progression of prostate cancer (PCa). Small molecule antagonists that bind to the ligand binding domain (LBD) of the AR have been successful in treating PCa. However, the structural basis by which the AR antagonists manifest their therapeutic efficacy remains unclear, due to the lack of detailed structural information of the AR bound to the antagonists. We have performed accelerated molecular dynamics (aMD) simulations of LBDs bound to a set of ligands including a natural substrate (dihydrotestosterone), an agonist (RU59063) and three antagonists (bicalutamide, enzalutamide and apalutamide) as well as in the absence of ligand (apo). We show that the binding of AR antagonists at the substrate binding pocket alter the dynamic fluctuations of H12, thereby disrupting the structural integrity of the agonistic conformation of AR. Two antagonists, enzalutamide and apalutamide, induce considerable structural changes to the agonist conformation of LBD, when bound close to H12 of AR LBD. When the antagonists bind to the pocket with different orientations having close contact with H11, no significant conformational changes were observed, suggesting the AR remains in the functionally activated (agonistic) state. The simulations on a drug resistance mutant F876L bound to enzalutamide demonstrated that the mutation stabilizes the agonistic conformation of AR LBD, which compromises the efficacy of the antagonists. Principal component analysis (PCA) of the structural fluctuations shows that the binding of enzalutamide and apalutamide induce conformational fluctuations in the AR, which are markedly different from those caused by the agonist as well as another antagonist, bicalutamide. These fluctuations could only be observed with the use of aMD.
Unique transition of yielding mechanism and unexpected activation of deformation twinning in ultrafine grained Fe-31Mn-3Al-3Si alloy
Authors: Bai Yu , Kitamura Hiroki , Gao Si , Tian Yanzhong , Park Nokeun , Park Myeong-heom , Adachi Hiroki , Shibata Akinobu , Sato Masugu , Murayama Mitsuhiro , Tsuji Nobuhiro 
Published: August 2021

AbstractTensile mechanical properties of fully recrystallized TWIP steel specimens having various grain sizes (d) ranging from 0.79 μm to 85.6 μm were investigated. It was confirmed that the UFG specimens having the mean grain sizes of 1.5 μm or smaller abnormally showed discontinuous yielding characterized by a clear yield-drop while the specimens having grain sizes larger than 2.4 μm showed normal continuous yielding. In-situ synchrotron radiation XRD showed dislocation density around yield-drop in the UFG specimen quickly increased. ECCI observations revealed the nucleation of deformation twins and stacking faults from grain boundaries in the UFG specimen around yielding. Although it had been conventionally reported that the grain refinement suppresses deformation twinning in FCC metals and alloys, the number density of deformation twins in the 0.79 μm grain-sized specimen was much higher than that in the specimens with grain sizes of 4.5 μm and 15.4 μm. The unusual change of yielding behavior from continuous to discontinuous manner by grain refinement could be understood on the basis of limited number of free dislocations in each ultrafine grain. The results indicated that the scarcity of free dislocations in the recrystallized UFG specimens changed the deformation and twinning mechanisms in the TWIP steel.
Fast and accurate exhaustive higher-order epistasis search with BitEpi
Authors: Bayat Arash , Hosking Brendan , Jain Yatish , Hosking Cameron , Kodikara Milindi , Reti Daniel , Twine Natalie A. , Bauer Denis C. 
Published: August 2021

AbstractComplex genetic diseases may be modulated by a large number of epistatic interactions affecting a polygenic phenotype. Identifying these interactions is difficult due to computational complexity, especially in the case of higher-order interactions where more than two genomic variants are involved. In this paper, we present BitEpi, a fast and accurate method to test all possible combinations of up to four bi-allelic variants (i.e. Single Nucleotide Variant or SNV for short). BitEpi introduces a novel bitwise algorithm that is 1.7 and 56 times faster for 3-SNV and 4-SNV search, than established software. The novel entropy statistic used in BitEpi is 44% more accurate to identify interactive SNVs, incorporating a p-value-based significance testing. We demonstrate BitEpi on real world data of 4900 samples and 87,000 SNPs. We also present EpiExplorer to visualize the potentially large number of individual and interacting SNVs in an interactive Cytoscape graph. EpiExplorer uses various visual elements to facilitate the discovery of true biological events in a complex polygenic environment.
The effect of genetic polymorphisms on treatment duration following premolar extraction
Authors: Yu Jiyon , Choi Yoon Jeong , Choi Sung-Hwan , Jung Han-Sung , Lee Ji Hyun , Cha Jung-Yul 
Published: August 2021

AbstractTo elucidate genetic factors affecting orthodontic treatment duration, we employed targeted next-generation sequencing on DNA from the saliva of 117 patients undergoing orthodontic treatment after premolar extraction. The clinical characteristics of patients are summarized, and the association of clinical variables with treatment duration was assessed. Patients whose treatment duration deviated from the average were classified into an extreme long group or an extreme short group. We identified nine single nucleotide polymorphisms (SNPs) of six genes that significantly differed in the two groups via targeted sequencing. The frequency of the CC genotypes of WNT3A, SPP1 (rs4754, rs9138), and TNFSF11, TT genotype of SPP1 (rs1126616), and GG genotype of SFRP2 was significantly higher in the extreme long group than in the short group. In the extreme short group, the TC genotype of SPP1, AA genotype of P2RX7, CT genotype of TNFSF11, and AG genotype of TNFRSF11A tended to exhibit higher frequency than in the long group. Taken together, we identified genetic polymorphisms related to treatment duration in Korean orthodontic patients undergoing premolar extraction. Our findings could lead to further studies predicting the prolongation of the orthodontic treatment duration, and will be of great aid to patients as well as orthodontists.
Neural burst codes disguised as rate codes
Authors: Williams Ezekiel , Payeur Alexandre , Gidon Albert , Naud Richard 
Published: August 2021

AbstractThe burst coding hypothesis posits that the occurrence of sudden high-frequency patterns of action potentials constitutes a salient syllable of the neural code. Many neurons, however, do not produce clearly demarcated bursts, an observation invoked to rule out the pervasiveness of this coding scheme across brain areas and cell types. Here we ask how detrimental ambiguous spike patterns, those that are neither clearly bursts nor isolated spikes, are for neuronal information transfer. We addressed this question using information theory and computational simulations. By quantifying how information transmission depends on firing statistics, we found that the information transmitted is not strongly influenced by the presence of clearly demarcated modes in the interspike interval distribution, a feature often used to identify the presence of burst coding. Instead, we found that neurons having unimodal interval distributions were still able to ascribe different meanings to bursts and isolated spikes. In this regime, information transmission depends on dynamical properties of the synapses as well as the length and relative frequency of bursts. Furthermore, we found that common metrics used to quantify burstiness were unable to predict the degree with which bursts could be used to carry information. Our results provide guiding principles for the implementation of coding strategies based on spike-timing patterns, and show that even unimodal firing statistics can be consistent with a bivariate neural code.
Verification of the electromagnetic deep-penetration effect in the real world
Authors: Baccarelli Paolo , Calcaterra Alessandro , Frezza Fabrizio , Mangini Fabio , Ricciardella Nicholas , Simeoni Patrizio , Tedeschi Nicola 
Published: August 2021

AbstractThe deep penetration of electromagnetic waves into lossy media can be obtained by properly generating inhomogeneous waves. In this work, for the very first time, we demonstrate the physical implementation and the practical relevance of this phenomenon. A thorough numerical investigation of the deep-penetration effects has been performed by designing and comparing three distinct practical radiators, emitting either homogeneous or inhomogeneous waves. As concerns the latter kind, a typical Menzel microstrip antenna is first used to radiate improper leaky waves. Then, a completely new approach based on an optimized 3-D horn TEM antenna applied to a lossy prism is described, which may find applications even at optical frequencies. The effectiveness of the proposed radiators is measured using different algorithms to consider distinct aspects of the propagation in lossy media. We finally demonstrate that the deep penetration is possible, by extending the ideal and theoretical evidence to practical relevance, and discuss both achievements and limits obtained through numerical simulations on the designed antennas.
White matter tracts characteristics in habitual decision-making circuit underlie ritual behaviors in anorexia nervosa
Authors: Tadayonnejad Reza , Pizzagalli Fabrizio , Murray Stuart B. , Pauli Wolfgang M. , Conde Geena , Bari Ausaf A. , Strober Michael , O’Doherty John P. , Feusner Jamie D. 
Published: August 2021

AbstractAnorexia nervosa (AN) is a difficult to treat, pernicious psychiatric disorder that has been linked to decision-making abnormalities. We examined the structural characteristics of habitual and goal-directed decision-making circuits and their connecting white matter tracts in 32 AN and 43 healthy controls across two independent data sets of adults and adolescents as an explanatory sub-study. Total bilateral premotor/supplementary motor area-putamen tracts in the habit circuit had a significantly higher volume in adults with AN, relative to controls. Positive correlations were found between both the number of tracts and white matter volume (WMV) in the habit circuit, and the severity of ritualistic/compulsive behaviors in adults and adolescents with AN. Moreover, we found a significant influence of the habit circuit WMV on AN ritualistic/compulsive symptom severity, depending on the preoccupations symptom severity levels. These findings suggest that AN is associated with white matter plasticity alterations in the habit circuit. The association between characteristics of habit circuit white matter tracts and AN behavioral symptoms provides support for a circuit based neurobiological model of AN, and identifies the habit circuit as a focus for further investigation to aid in development of novel and more effective treatments based on brain-behavior relationships.