bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic deep learning-driven label-free image-guided patch clamp system
Authors: Koos Krisztian , Oláh Gáspár , Balassa Tamas , Mihut Norbert , Rózsa Márton , Ozsvár Attila , Tasnadi Ervin , Barzó Pál , Faragó Nóra , Puskás László , Molnár Gábor , Molnár József , Tamás Gábor , Horvath Peter
Published: February 2021

Patch clamp recording of neurons is a labor-intensive and time-consuming procedure. Here, we demonstrate a tool that fully automatically performs electrophysiological recordings in label-free tissue slices. The automation covers the detection of cells in label-free images, calibration of the micropipette movement, approach to the cell with the pipette, formation of the whole-cell configuration, and recording. The cell detection is based on deep learning. The model is trained on a new image database of neurons in unlabeled brain tissue slices. The pipette tip detection and approaching phase use image analysis techniques for precise movements. High-quality measurements are performed on hundreds of human and rodent neurons. We also demonstrate that further molecular and anatomical analysis can be performed on the recorded cells. The software has a diary module that automatically logs patch clamp events. Our tool can multiply the number of daily measurements to help brain research.
Long-ranged Cu-based order with $$d_{z^2}$$ orbital character at a YBa2Cu3O7/ manganite interface
Authors: Gaina Roxana , Nicholson Christopher W. , Rumo Maxime , Sarkar Subhrangsu , Khmaladze Jarji , Paris Eugenio , Tseng Yi , Zhang Wenliang , Asmara Teguh C. , McNally Daniel , Piamonteze Cinthia , Weschke Eugen , Schmitt Thorsten , Monney Claude , Bernhard Christian
Published: February 2021

The interplay of nearly degenerate orders in quantum materials can lead to a myriad of emergent phases. A prominent case is that of the high-Tc cuprates for which the relationship between superconductivity and a short-ranged, incommensurate charge density wave in the CuO2 planes involving the $$d_{x^2 - y^2}$$

d

x

2

−

y

2

orbitals (Cu-CDW) is a subject of great current interest. Strong modifications of the strength and coherence of this Cu-CDW have been achieved by applying large magnetic fields, uniaxial pressure, or via the interfacial coupling in cuprate/manganite multilayers. However, such modifications do not alter the dominant orbital character. Here we investigate cuprate/manganite multilayers with resonant inelastic X-ray scattering (RIXS) and show that a new kind of Cu-based density wave order can be induced that has not been previously observed in the cuprates. This order has an unusually small in-plane wave vector in the range of Q|| < 0.1 reciprocal lattice units (r.l.u.), a large correlation length of about 40 nm, and a predominant $$d_{z^2}$$

d

z

2

orbital character, instead of the typical $$d_{x^2 - y^2}$$

d

x

2

−

y

2

one. Its appearance is determined by the hole doping of the manganite which is a key parameter controlling the interfacial charge transfer and orbital reconstruction. We anticipate that the observation of a previously unknown type of density wave order at the YBCO interface will allow for fresh perspectives on the enigmatic relation between superconductivity and charge order (CO) in the cuprates.
Expansion and characterization of epithelial stem cells with potential for cyclical hair regeneration
Authors: Takeo Makoto , Asakawa Kyosuke , Toyoshima Koh-ei , Ogawa Miho , Tong JingJing , Irié Tarou , Yanagisawa Masayuki , Sato Akio , Tsuji Takashi
Published: February 2021

In mammals, organ induction occurs only during embryonic development except for hair follicles (HFs). However, HF-resident epithelial stem cells (HFSCs), which are responsible for repetitive HF regeneration, are not fully characterized. Here, we establish in vitro culture systems that are capable of controlling the ability of HFSCs to regenerate HFs. Based on a method that precisely controlled the number of HFs for regeneration, functional analysis revealed that CD34/CD49f/integrin β5 (Itgβ5)-triple-positive (CD34+/CD49f+/Itgβ5+) cells have multipotency and functional significance for continual hair regeneration. In native HFs, these cells reside in the uppermost area of the bulge region, which is surrounded by tenascin in mice and humans. This study unveils the subpopulation of HFSCs responsible for long-term hair cycling of HFs regenerated from bioengineered HF germ, suggesting the presence of functional heterogeneity among bulge HFSCs and the utility of our culture system to achieve HF regenerative therapy.
Landscape-induced spatial oscillations in population dynamics
Authors: Dornelas Vivian , Colombo Eduardo H. , López Cristóbal , Hernández-García Emilio , Anteneodo Celia
Published: February 2021

We study the effect that disturbances in the ecological landscape exert on the spatial distribution of a population that evolves according to the nonlocal FKPP equation. Using both numerical and analytical techniques, we characterize, as a function of the interaction kernel, the three types of stationary profiles that can develop near abrupt spatial variations in the environmental conditions vital for population growth: sustained oscillations, decaying oscillations and exponential relaxation towards a flat profile. Through the mapping between the features of the induced wrinkles and the shape of the interaction kernel, we discuss how heterogeneities can reveal information that would be hidden in a flat landscape.
Ensemble machine learning prediction and variable importance analysis of 5-year mortality after cardiac valve and CABG operations
Authors: Castela Forte José , Mungroop Hubert E. , de Geus Fred , van der Grinten Maureen L. , Bouma Hjalmar R. , Pettilä Ville , Scheeren Thomas W. L. , Nijsten Maarten W. N. , Mariani Massimo A. , van der Horst Iwan C. C. , Henning Robert H. , Wiering Marco A. , Epema Anne H.
Published: February 2021

Despite having a similar post-operative complication profile, cardiac valve operations are associated with a higher mortality rate compared to coronary artery bypass grafting (CABG) operations. For long-term mortality, few predictors are known. In this study, we applied an ensemble machine learning (ML) algorithm to 88 routinely collected peri-operative variables to predict 5-year mortality after different types of cardiac operations. The Super Learner algorithm was trained using prospectively collected peri-operative data from 8241 patients who underwent cardiac valve, CABG and combined operations. Model performance and calibration were determined for all models, and variable importance analysis was conducted for all peri-operative parameters. Results showed that the predictive accuracy was the highest for solitary mitral (0.846 [95% CI 0.812–0.880]) and solitary aortic (0.838 [0.813–0.864]) valve operations, confirming that ensemble ML using routine data collected perioperatively can predict 5-year mortality after cardiac operations with high accuracy. Additionally, post-operative urea was identified as a novel and strong predictor of mortality for several types of operation, having a seemingly additive effect to better known risk factors such as age and postoperative creatinine.
TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity
Authors: Mei Yang , Deng Zhong , Vladimirova Olga , Gulve Nitish , Johnson F. Brad , Drosopoulos William C. , Schildkraut Carl L. , Lieberman Paul M.
Published: February 2021

Telomere dysfunction causes chromosomal instability which is associated with many cancers and age-related diseases. The non-coding telomeric repeat-containing RNA (TERRA) forms a structural and regulatory component of the telomere that is implicated in telomere maintenance and chromosomal end protection. The basic N-terminal Gly/Arg-rich (GAR) domain of telomeric repeat-binding factor 2 (TRF2) can bind TERRA but the structural basis and significance of this interaction remains poorly understood. Here, we show that TRF2 GAR recognizes G-quadruplex features of TERRA. We show that small molecules that disrupt the TERRA-TRF2 GAR complex, such as N-methyl mesoporphyrin IX (NMM) or genetic deletion of TRF2 GAR domain, result in the loss of TERRA, and the induction of γH2AX-associated telomeric DNA damage associated with decreased telomere length, and increased telomere aberrations, including telomere fragility. Taken together, our data indicates that the G-quadruplex structure of TERRA is an important recognition element for TRF2 GAR domain and this interaction between TRF2 GAR and TERRA is essential to maintain telomere stability.
Separation of phenyl acetic acid and 6-aminopenicillanic acid applying aqueous two-phase systems based on copolymers and salts
Authors: Ahsaie Farzaneh Ghazizadeh , Pazuki Gholamreza
Published: February 2021

6-Aminopenicillanic acid (6-APA) is used for synthesis of semisynthetic antibiotics. Polymer-salt aqueous two-phase systems (ATPSs) were applied for separation of 6-APA and phenyl acetic acid (PAA), as the products of hydrolyzation reaction of Penicillin G/Penicillin V. The binodal curves of ATPS composed of a copolymer (reverse Pluronic 10R5, Pluronic L35 and PEG-ran-PPG) and a salt (Tri-sodium citrate, tri-potassium citrate, di-potassium phosphate, sodium sulphate and magnesium sulphate) were obtained. The results show that, at a fixed PPG/PEG ratio, block copolymers have larger two-phase region compared with random copolymer. After screening on the partition coefficient of PAA and 6-APA separately, Na2SO4 was selected for studying the effect of the copolymer structure and the composition of salt and copolymer on partitioning, considering higher selectivity of PAA and 6-APA. 10R5-Na2SO4 ATPS was selected as the most appropriate system for separation of 6-APA and PAA. This system was used for separation of mixture of 6-APA and PAA. The results show that selectivity was $$\approx$$
≈
53 and smaller in a system, containing a mixture of 6-APA and PAA. This observation can be justified by the interaction between 6-APA and PAA. Molecular interaction between these two molecules were investigated by the Flory–Huggins interaction parameter.
Eyewitness identification performance is not affected by time-of-day optimality
Authors: Yaremenko Sergii , Sauerland Melanie , Hope Lorraine
Published: February 2021

The circadian rhythm regulates arousal levels throughout the day and determines optimal periods for engaging in mental activities. Individuals differ in the time of day at which they reach their peak: Morning-type individuals are at their best in the morning and evening types perform better in the evening. Performance in recall and recognition of non-facial stimuli is generally superior at an individual’s circadian peak. In two studies (Ns = 103 and 324), we tested the effect of time-of-testing optimality on eyewitness identification performance. Morning- and evening-type participants viewed stimulus films depicting staged crimes and made identification decisions from target-present and target-absent lineups either at their optimal or non-optimal time-of-day. We expected that participants would make more accurate identification decisions and that the confidence-accuracy and decision time-accuracy relationships would be stronger at optimal compared to non-optimal time of day. In Experiment 1, identification accuracy was unexpectedly superior at non-optimal compared to optimal time of day in target-present lineups. In Experiment 2, identification accuracy did not differ between the optimal and non-optimal time of day. Contrary to our expectations, confidence-accuracy relationship was generally stronger at non-optimal compared to optimal time of day. In line with our predictions, non-optimal testing eliminated decision-time-accuracy relationship in Experiment 1.
Untargeted analysis of first trimester serum to reveal biomarkers of pregnancy complications: a case–control discovery phase study
Authors: Harville E. W. , Li Y.-Y. , Pan K. , McRitchie S. , Pathmasiri W. , Sumner S.
Published: February 2021

Understanding of causal biology and predictive biomarkers are lacking for hypertensive disorders of pregnancy (HDP) and preterm birth (PTB). First-trimester serum specimens from 51 cases of HDP, including 18 cases of pre-eclampsia (PE) and 33 cases of gestational hypertension (GH); 53 cases of PTB; and 109 controls were obtained from the Global Alliance to Prevent Prematurity and Stillbirth repository. Metabotyping was conducted using liquid chromatography high resolution mass spectroscopy and nuclear magnetic resonance spectroscopy. Multivariable logistic regression was used to identify signals that differed between groups after controlling for confounders. Signals important to predicting HDP and PTB were matched to an in-house physical standards library and public databases. Pathway analysis was conducted using GeneGo MetaCore. Over 400 signals for endogenous and exogenous metabolites that differentiated cases and controls were identified or annotated, and models that included these signals produced substantial improvements in predictive power beyond models that only included known risk factors. Perturbations of the aminoacyl-tRNA biosynthesis, l-threonine, and renal secretion of organic electrolytes pathways were associated with both HDP and PTB, while pathways related to cholesterol transport and metabolism were associated with HDP. This untargeted metabolomics analysis identified signals and common pathways associated with pregnancy complications.
Predictive modeling of clinical trial terminations using feature engineering and embedding learning
Authors: Elkin Magdalyn E. , Zhu Xingquan
Published: February 2021

In this study, we propose to use machine learning to understand terminated clinical trials. Our goal is to answer two fundamental questions: (1) what are common factors/markers associated to terminated clinical trials? and (2) how to accurately predict whether a clinical trial may be terminated or not? The answer to the first question provides effective ways to understand characteristics of terminated trials for stakeholders to better plan their trials; and the answer to the second question can direct estimate the chance of success of a clinical trial in order to minimize costs. By using 311,260 trials to build a testbed with 68,999 samples, we use feature engineering to create 640 features, reflecting clinical trial administration, eligibility, study information, criteria etc. Using feature ranking, a handful of features, such as trial eligibility, trial inclusion/exclusion criteria, sponsor types etc., are found to be related to the clinical trial termination. By using sampling and ensemble learning, we achieve over 67% Balanced Accuracy and over 0.73 AUC (Area Under the Curve) scores to correctly predict clinical trial termination, indicating that machine learning can help achieve satisfactory prediction results for clinical trial study.
Pluripotency and immunomodulatory signatures of canine induced pluripotent stem cell-derived mesenchymal stromal cells are similar to harvested mesenchymal stromal cells
Authors: Shahsavari Arash , Weeratunga Prasanna , Ovchinnikov Dmitry A. , Whitworth Deanne J.
Published: February 2021

With a view towards harnessing the therapeutic potential of canine mesenchymal stromal cells (cMSCs) as modulators of inflammation and the immune response, and to avoid the issues of the variable quality and quantity of harvested cMSCs, we examined the immunomodulatory properties of cMSCs derived from canine induced pluripotent stem cells (ciMSCs), and compared them to cMSCs harvested from adipose tissue (cAT-MSC) and bone marrow (cBM-MSC). A combination of deep sequencing and quantitative RT-PCR of the ciMSC transcriptome confirmed that ciMSCs express more genes in common with cBM-MSCs and cAT-MSCs than with the ciPSCs from which they were derived. Both ciMSCs and harvested cMSCs express a range of pluripotency factors in common with the ciPSCs including NANOG, POU5F1 (OCT-4), SOX-2, KLF-4, LIN-28A, MYC, LIF, LIFR, and TERT. However, ESRRB and PRDM-14, both factors associated with naïve, rather than primed, pluripotency were expressed only in the ciPSCs. CXCR-4, which is essential for the homing of MSCs to sites of inflammation, is also detectable in ciMSCs, cAT- and cBM-MSCs, but not ciPSCs. ciMSCs constitutively express the immunomodulatory factors iNOS, GAL-9, TGF-β1, PTGER-2α and VEGF, and the pro-inflammatory mediators COX-2, IL-1β and IL-8. When stimulated with the canine pro-inflammatory cytokines tumor necrosis factor-α (cTNF-α), interferon-γ (cIFN-γ), or a combination of both, ciMSCs upregulated their expression of IDO, iNOS, GAL-9, HGF, TGF-β1, PTGER-2α, VEGF, COX-2, IL-1β and IL-8. When co-cultured with mitogen-stimulated lymphocytes, ciMSCs downregulated their expression of iNOS, HGF, TGF-β1 and PTGER-2α, while increasing their expression of COX-2, IDO and IL-1β. Taken together, these findings suggest that ciMSCs possess similar immunomodulatory capabilities as harvested cMSCs and support further investigation into their potential use for the management of canine immune-mediated and inflammatory disorders.
A non-invasive method to generate induced pluripotent stem cells from primate urine
Authors: Geuder Johanna , Wange Lucas E. , Janjic Aleksandar , Radmer Jessica , Janssen Philipp , Bagnoli Johannes W. , Müller Stefan , Kaul Artur , Ohnuki Mari , Enard Wolfgang
Published: February 2021

Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that suspension- Sendai Virus transduction of reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to non-invasively generate iPSCs from primate urine. This will extend the zoo of species available for a comparative approach to molecular and cellular phenotypes.
Coherent amplification and inversion less lasing of surface plasmon polaritons in a negative index metamaterial with a resonant atomic medium
Authors: Asgarnezhad-Zorgabad Saeid
Published: February 2021

Surface plasmon polaritons (SPPs) lasing requires population inversion, it is inefficient and possesses poor spectral properties. We develop an inversion-less concept for a quantum plasmonic waveguide that exploits unidirectional superradiant SPP (SSPP) emission of radiation to produce intense coherent surface plasmon beams. Our scheme includes a resonantly driven cold atomic medium in a lossless dielectric situated above an ultra-low loss negative index metamaterial (NIMM) layer. We propose generating unidirectional superradiant radiation of the plasmonic field within an atomic medium and a NIMM layer interface and achieve amplified SPPs by introducing phase-match between the superradiant SPP wave and coupled laser fields. We also establish a parametric resonance between the weak modulated plasmonic field and the collective oscillations of the atomic ensemble, thereby suppressing decoherence of the stably amplified directional polaritonic mode. Our method incorporates the quantum gain of the atomic medium to obtain sufficient conditions for coherent amplification of superradiant SPP waves, and we explore this method to quantum dynamics of the atomic medium being coupled with the weak polaritonic waves. Our waveguide configuration acts as a surface plasmon laser and quantum plasmonic transistor and opens prospects for designing controllable nano-scale lasers for quantum and nano-photonic applications.
A pilot study on biaxial mechanical, collagen microstructural, and morphological characterizations of a resected human intracranial aneurysm tissue
Authors: Laurence Devin W. , Homburg Hannah , Yan Feng , Tang Qinggong , Fung Kar-Ming , Bohnstedt Bradley N. , Holzapfel Gerhard A. , Lee Chung-Hao
Published: February 2021

Intracranial aneurysms (ICAs) are focal dilatations that imply a weakening of the brain artery. Incidental rupture of an ICA is increasingly responsible for significant mortality and morbidity in the American’s aging population. Previous studies have quantified the pressure-volume characteristics, uniaxial mechanical properties, and morphological features of human aneurysms. In this pilot study, for the first time, we comprehensively quantified the mechanical, collagen fiber microstructural, and morphological properties of one resected human posterior inferior cerebellar artery aneurysm. The tissue from the dome of a right posterior inferior cerebral aneurysm was first mechanically characterized using biaxial tension and stress relaxation tests. Then, the load-dependent collagen fiber architecture of the aneurysm tissue was quantified using an in-house polarized spatial frequency domain imaging system. Finally, optical coherence tomography and histological procedures were used to quantify the tissue’s microstructural morphology. Mechanically, the tissue was shown to exhibit hysteresis, a nonlinear stress-strain response, and material anisotropy. Moreover, the unloaded collagen fiber architecture of the tissue was predominantly aligned with the testing Y-direction and rotated towards the X-direction under increasing equibiaxial loading. Furthermore, our histological analysis showed a considerable damage to the morphological integrity of the tissue, including lack of elastin, intimal thickening, and calcium deposition. This new unified characterization framework can be extended to better understand the mechanics-microstructure interrelationship of aneurysm tissues at different time points of the formation or growth. Such specimen-specific information is anticipated to provide valuable insight that may improve our current understanding of aneurysm growth and rupture potential.
Rapid seroconversion and persistent functional IgG antibodies in severe COVID-19 patients correlates with an IL-12p70 and IL-33 signature
Authors: Munitz Ariel , Edry-Botzer L. , Itan M. , Tur-Kaspa R. , Dicker D. , Marcoviciu D. , Goren M. G. , Mor M. , Lev S. , Gottesman T. , Muhsen K. , Cohen D. , Stein M. , Qimron U. , Freund N. T. , Wine Y. , Gerlic Motti
Published: February 2021

Despite ongoing efforts to characterize the host response toward SARS-CoV-2, a major gap in our knowledge still exists regarding the magnitude and duration of the humoral response. Analysis of the antibody response in mild versus moderate/severe patients, using our new developed quantitative electrochemiluminescent assay for detecting IgM/IgA/IgG antibodies toward SARS-CoV-2 antigens, revealed a rapid onset of IgG/IgA antibodies, specifically in moderate/severe patients. IgM antibodies against the viral receptor binding domain, but not against nucleocapsid protein, were detected at early stages of the disease. Furthermore, we observed a marked reduction in IgM/IgA antibodies over-time. Adapting our assay for ACE2 binding-competition, demonstrated that the presence of potentially neutralizing antibodies is corelated with IgG/IgA. Finally, analysis of the cytokine profile in COVID-19 patients revealed unique correlation of an IL-12p70/IL33 and IgG seroconversion, which correlated with disease severity. In summary, our comprehensive analysis has major implications on the understanding and monitoring of SARS-CoV-2 infections.
The potential role of MR based radiomic biomarkers in the characterization of focal testicular lesions
Authors: Feliciani Giacomo , Mellini Lorenzo , Carnevale Aldo , Sarnelli Anna , Menghi Enrico , Piccinini Filippo , Scarpi Emanuela , Loi Emiliano , Galeotti Roberto , Giganti Melchiore , Parenti Gian Carlo
Published: February 2021

How to differentiate with MRI-based techniques testicular germ (TGCTs) and testicular non-germ cell tumors (TNGCTs) is still under debate and Radiomics may be the turning key. Our purpose is to investigate the performance of MRI-based Radiomics signatures for the preoperative prediction of testicular neoplasm histology. The aim is twofold: (i), differentiating TGCTs and TNGCTs status and (ii) differentiating seminomas (SGCTs) from non-seminomatous (NSGCTs). Forty-two patients with pathology-proven testicular neoplasms and referred for pre-treatment MRI, were retrospectively enrolled. Thirty-two out of 44 lesions were TGCTs. Twelve out of 44 were TNGCTs or other histologies. Two radiologists segmented the volume of interest on T2-weighted images. Approximately 500 imaging features were extracted. Least Absolute Shrinkage and Selection Operator (LASSO) was applied as method for variable selection. A linear model and a linear support vector machine (SVM) were trained with selected features to assess discrimination scores for the two endpoints. LASSO identified 3 features that were employed to build fivefold validated linear discriminant and linear SVM classifiers for the TGCT-TNGCT endpoint giving an overall accuracy of 89%. Four features were employed to build another SVM for the SGCT-SNGCT endpoint with an overall accuracy of 86%. The data obtained proved that T2-weighted-based Radiomics is a promising tool in the diagnostic workup of testicular neoplasms by discriminating germ cell from non-gem cell tumors, and seminomas from non-seminomas.
Practicable assessment of cochlear size and shape from clinical CT images
Authors: Gee Andrew H. , Zhao Yufeng , Treece Graham M. , Bance Manohar L.
Published: February 2021

There is considerable interpersonal variation in the size and shape of the human cochlea, with evident consequences for cochlear implantation. The ability to characterize a specific cochlea, from preoperative computed tomography (CT) images, would allow the clinician to personalize the choice of electrode, surgical approach and postoperative programming. In this study, we present a fast, practicable and freely available method for estimating cochlear size and shape from clinical CT. The approach taken is to fit a template surface to the CT data, using either a statistical shape model or a locally affine deformation (LAD). After fitting, we measure cochlear size, duct length and a novel measure of basal turn non-planarity, which we suggest might correlate with the risk of insertion trauma. Gold-standard measurements from a convenience sample of 18 micro-CT scans are compared with the same quantities estimated from low-resolution, noisy, pseudo-clinical data synthesized from the same micro-CT scans. The best results were obtained using the LAD method, with an expected error of 8–17% of the gold-standard sample range for non-planarity, cochlear size and duct length.
Respiratory syncytial virus B sequence analysis reveals a novel early genotype
Authors: Muñoz-Escalante Juan C. , Comas-García Andreu , Bernal-Silva Sofía , Noyola Daniel E.
Published: February 2021

Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.
Integrative analysis identifies bHLH transcription factors as contributors to Parkinson’s disease risk mechanisms
Authors: Berge-Seidl Victoria , Pihlstrøm Lasse , Toft Mathias
Published: February 2021

Genome-wide association studies (GWAS) have identified multiple genetic risk signals for Parkinson’s disease (PD), however translation into underlying biological mechanisms remains scarce. Genomic functional annotations of neurons provide new resources that may be integrated into analyses of GWAS findings. Altered transcription factor binding plays an important role in human diseases. Insight into transcriptional networks involved in PD risk mechanisms may thus improve our understanding of pathogenesis. We analysed overlap between genome-wide association signals in PD and open chromatin in neurons across multiple brain regions, finding a significant enrichment in the superior temporal cortex. The involvement of transcriptional networks was explored in neurons of the superior temporal cortex based on the location of candidate transcription factor motifs identified by two de novo motif discovery methods. Analyses were performed in parallel, both finding that PD risk variants significantly overlap with open chromatin regions harboring motifs of basic Helix-Loop-Helix (bHLH) transcription factors. Our findings show that cortical neurons are likely mediators of genetic risk for PD. The concentration of PD risk variants at sites of open chromatin targeted by members of the bHLH transcription factor family points to an involvement of these transcriptional networks in PD risk mechanisms.
A dynamic lesion model for differentiation of malignant and benign pathologies
Authors: Cao Weiguo , Liang Zhengrong , Gao Yongfeng , Pomeroy Marc J. , Han Fangfang , Abbasi Almas , Pickhardt Perry J.
Published: February 2021

Malignant lesions have a high tendency to invade their surrounding environment compared to benign ones. This paper proposes a dynamic lesion model and explores the 2nd order derivatives at each image voxel, which reflect the rate of change of image intensity, as a quantitative measure of the tendency. The 2nd order derivatives at each image voxel are usually represented by the Hessian matrix, but it is difficult to quantify a matrix field (or image) through the lesion space as a measure of the tendency. We conjecture that the three eigenvalues contain important information of the Hessian matrix and are chosen as the surrogate representation of the Hessian matrix. By treating the three eigenvalues as a vector, called Hessian vector, which is defined in a local coordinate formed by three orthogonal Hessian eigenvectors and further adapting the gray level occurrence computing method to extract the vector texture descriptors (or measures) from the Hessian vector, a quantitative presentation for the dynamic lesion model is completed. The vector texture descriptors were applied to differentiate malignant from benign lesions from two pathologically proven datasets: colon polyps and lung nodules. The classification results not only outperform four state-of-the-art methods but also three radiologist experts.
Retrieving the structure of probabilistic sequences of auditory stimuli from EEG data
Authors: Hernández Noslen , Duarte Aline , Ost Guilherme , Fraiman Ricardo , Galves Antonio , Vargas Claudia D.
Published: February 2021

Using a new probabilistic approach we model the relationship between sequences of auditory stimuli generated by stochastic chains and the electroencephalographic (EEG) data acquired while 19 participants were exposed to those stimuli. The structure of the chains generating the stimuli are characterized by rooted and labeled trees whose leaves, henceforth called contexts, represent the sequences of past stimuli governing the choice of the next stimulus. A classical conjecture claims that the brain assigns probabilistic models to samples of stimuli. If this is true, then the context tree generating the sequence of stimuli should be encoded in the brain activity. Using an innovative statistical procedure we show that this context tree can effectively be extracted from the EEG data, thus giving support to the classical conjecture.
Temporal and vertical variations of polycyclic aromatic hydrocarbon at low elevations in an industrial city of southern Taiwan
Authors: Chen Wei-Hsiang , Hsieh Ming-Tsuen , You Jie-Yu , Quadir Adnan , Lee Chon-Lin
Published: February 2021

Considered that human activities mostly occur below building heights, the objective of this study was to investigate the temporal variations of fine particular matter (PM2.5)-associated polycyclic aromatic hydrocarbons (PAHs) and benzo[a]pyrene-equivalent (BaPeq) concentrations at four different elevations (6.1, 12.4, 18.4, and 27.1 m) in Kaohsiung City, the largest industrial city of southern Taiwan. Temperature variation was critical for the PM2.5-associated PAH concentrations, which were dominated by benzo[g,h,i]perylene (0.27 ± 0.04 ng m−3 and 24.43% of the total concentration) and other high molecular weight (HMW) species. The PM2.5-associated BaPeq was dominated by 5-ring PAH (36.09%). The PM2.5-associated PAH and BaPeq concentrations at all elevations were significantly increased in winter. In the night, the correlations between the PM2.5-associated PAH concentrations and atmospheric temperatures became negatively stronger, notably at lower elevations (r = − 0.73 ~ − 0.86), whereas the BaPeq during daytime and nighttime were not changed significantly in most months. The PAHs analysis with different PM sizes demonstrated the importance of smaller particles such as PM2.5. The meteorological variation was more important than elevation to influence the low-elevation PM2.5-associated PAH and BaPeq concentrations in an urban area like Kaohsiung City, as the two concentrations were dominated by the PAHs with HMWs and those 5-ring species, respectively.
PHAIR: a biosensor for pH measurement in air–liquid interface cell culture
Authors: Dabaghi Mohammadhossein , Saraei Neda , Xu Gang , Chandiramohan Abiram , Yeung Jonas , Nguyen Jenny P. , Vukmirovic Milica , Selvaganapathy Ponnambalam Ravi , Hirota Jeremy A.
Published: February 2021

In many biological systems, pH can be used as a parameter to understand and study cell dynamics. However, measuring pH in live cell culture is limited by the sensor ion specificity, proximity to the cell surface, and scalability. Commercially available pH sensors are difficult to integrate into a small-scale cell culture system due to their size and are not cost-effective for disposable use. We made PHAIR—a new pH sensor that uses a micro-wire format to measure pH in vitro human airway cell culture. Tungsten micro-wires were used as the working electrodes, and silver micro-wires with a silver/silver chloride coating were used as a pseudo reference electrode. pH sensitivity, in a wide and narrow range, and stability of these sensors were tested in common standard buffer solutions as well as in culture media of human airway epithelial cells grown at the air–liquid interface in a 24 well cell culture plate. When measuring the pH of cells grown under basal and challenge conditions using PHAIR, cell viability and cytokine responses were not affected. Our results confirm that micro-wire-based sensors have the capacity for miniaturization and detection of diverse ions while maintaining sensitivity. This suggests the broad application of PHAIR in various biological experimental settings.
Two-dimensional iodine-monofluoride epitaxy on WSe2
Authors: Lin Yung-Chang , Lee Sungwoo , Yang Yueh-Chiang , Chiu Po-Wen , Lee Gun-Do , Suenaga Kazu
Published: February 2021

Interhalogen compounds (IHCs) are extremely reactive molecules used for halogenation, catalyst, selective etchant, and surface modification. Most of the IHCs are unstable at room temperature especially for the iodine-monofluoride (IF) whose structure is still unknown. Here we demonstrate an unambiguous observation of two-dimensional (2D) IF bilayer grown on the surface of WSe2 by using scanning transmission electron microscopy and electron energy loss spectroscopy. The bilayer IF shows a clear hexagonal lattice and robust epitaxial relationship with the WSe2 substrate. Despite the IF is known to sublimate at −14 °C and has never found as a solid form in the ambient condition, but surprisingly it is found stabilized on a suitable substrate and the stabilized structure is supported by a density functional theory. This 2D form of IHC is actually a byproduct during a chemical vapor deposition growth of WSe2 in the presence of alkali metal halides as a growth promoter and requires immediate surface passivation to sustain. This work points out a great possibility to produce 2D structures that are unexpected to be crystallized or cannot be obtained by a simple exfoliation but can be grown only on a certain substrate.
Direct observation of long-lived cyanide anions in superexcited states
Authors: Gao Xiao-Fei , Xie Jing-Chen , Li Hao , Meng Xin , Wu Yong , Tian Shan Xi
Published: February 2021

The cyanide anion (CN−) has been identified in cometary coma, interstellar medium, planetary atmosphere and circumstellar envelopes, but its origin and abundance are still disputed. An isolated CN− is stabilized in the vibrational states up to ν = 17 of the electronic ground-state 1Σ+, but it is not thought to survive in the electronic or vibrational states above the electron autodetachment threshold, namely, in superexcited states. Here we report the direct observation of long-lived CN− yields of the dissociative electron attachment to cyanogen bromide (BrCN), and confirm that some of the CN− yields are distributed in the superexcited vibrational states ν ≥ 18 (1Σ+) or the superexcited electronic states 3Σ+ and 3Π. The triplet state can be accessed directly in the impulsive dissociation of BrCN− or by an intersystem transition from the superexcited vibrational states of CN−. The exceptional stability of CN− in the superexcited states profoundly influences its abundance and is potentially related to the production of other compounds in interstellar space.
Quantum capacity analysis of multi-level amplitude damping channels
Authors: Chessa Stefano , Giovannetti Vittorio
Published: February 2021

Evaluating capacities of quantum channels is the first purpose of quantum Shannon theory, but in most cases the task proves to be very hard. Here, we introduce the set of Multi-level Amplitude Damping quantum channels as a generalization of the standard qubit Amplitude Damping Channel to quantum systems of finite dimension d. In the special case of d = 3, by exploiting degradability, data-processing inequalities, and channel isomorphism, we compute the associated quantum and private classical capacities for a rather wide class of maps, extending the set of models whose capacity can be computed known so far. We proceed then to the evaluation of the entanglement assisted quantum and classical capacities.
Fluorescence resonance energy transfer using DNA-templated copper nanoparticles for ratiometric detection of microRNAs
Authors: Kim Seokjoon , Park Ki Soo
Published: February 2021

DNA-templated copper nanoparticles function as a probe for fluorescence resonance energy transfer, allowing for the ratiometric detection of miRNAs.
Regulating metal–organic frameworks as stationary phases and absorbents for analytical separations
Authors: Meng Sha-Sha , Xu Ming , Han Ting , Gu Yu-Hao , Gu Zhi-Yuan
Published: February 2021

Metal–organic frameworks (MOFs) are highly ordered framework systems composed of metal centers and organic linkers formed through coordination bonds.
Recent advancements in cardiovascular bioprinting and bioprinted cardiac constructs
Authors: Budharaju Harshavardhan , Subramanian Anuradha , Sethuraman Swaminathan
Published: February 2021

Three-dimensionally bioprinted cardiac constructs with biomimetic bioink helps to create native-equivalent cardiac tissues to treat patients with myocardial infarction.
Understanding of TEMPO-electrocatalyzed acceptorless dehydrogenation of tetrahydroquinoline by in situ extractive electrospray ionization mass spectrometry
Authors: Li Weixiang , Sun Jianghui , Wang Yan , Qiao Jinping , He Lixin , Ouyang Jin , Na Na
Published: February 2021

The TEMPO-electrocatalyzed acceptorless dehydrogenation of tetrahydroquinoline was investigated by coupling an electrocatalytic system to in situ extraction electrospray ionization mass spectrometry.
Transition anionic complex in trihexyl(tetradecyl)phosphonium-bis(oxalato)borate ionic liquid – revisited
Authors: Shimpi Manishkumar R. , Rohlmann Patrick , Shah Faiz Ullah , Glavatskih Sergei , Antzutkin Oleg N.
Published: February 2021

A Transition Anionic Complex (TAC) was formed and passed into [P6,6,6,14][BOB] when Li[BOB] (but not Na[BOB]) was used in the synthesis, significantly altering ILs' properties. The TAC transformed into [BOB]− in the IL upon heating at 413 K for 1 h.
Observation of ordered arrays of endotaxially grown nanostructures from size-selected Cu-nanoclusters deposited on patterned substrates of Si
Authors: Mondal Shyamal , Chowdhury Debasree , Das Pabitra , Satpati Biswarup , Ghose Debabrata , Bhattacharyya Satya Ranjan
Published: February 2021

We report the observation of endotaxial growth during thermal treatment of size-selected nanoclusters on a patterned substrate, when we fabricate highly ordered and partially embedded 3D crystalline Cu nanostructure arrays of controlled size in Si-substrates.
Macrocyclic squaramides as ion pair receptors and fluorescent sensors selective towards sulfates
Authors: Zaleskaya Marta , Jagleniec Damian , Romański Jan
Published: February 2021

A library of macrocyclic ion pair receptors was obtained utilizing the high dilution technique. Incorporation of a fluorescent signaling unit in proximity to the amide function gave an optical sensor selective towards sulfates.
Rhamnetin decelerates the elimination and enhances the antitumor effect of the molecular-targeting agent sorafenib in hepatocellular carcinoma cells via the miR-148a/PXR axis
Authors: Li Boan , Feng Fan , Jia Hui , Jiang Qiyu , Cao Shuang , Wei Ling , Zhang Yingshi , Lu Jincai
Published: February 2021

The pregnane X receptor (PXR) mediates the resistance of sorafenib in hepatocellular carcinoma (HCC) by promoting the clearance or elimination of sorafenib via the drug resistance-related downstream genes of the PXR. Rhamnetin drepresses the activation of PXR via miR-148a.
Are lignin-derived monomers and polymers truly sustainable? An in-depth green metrics calculations approach
Authors: Fadlallah Sami , Sinha Roy Pallabi , Garnier Gil , Saito Kei , Allais Florent
Published: February 2021

The green aspects of the lignin-derived monomers and polymers have been analysed. A different viewpoint has been provided to encourage researchers to use simple and yet effective green metrics calculations in the development of sustainable syntheses.
On the development of chrome-free tanning agents: an advanced Trojan horse strategy using ‘Al–Zr-oligosaccharides’ produced by the depolymerization and oxidation of biomass
Authors: Jiang Zhicheng , Gao Mi , Remón Javier , Ding Wei , Hu Changwei , Shi Bi
Published: February 2021

Hemicellulose in corncob was simultaneously degraded and oxidized into oligosaccharides, which served as a masking agent for leather tanning.
Development of a sample preparation method for accurate analysis of 24 elemental impurities in oral drug products by ICP-MS according to USP/ICH guidelines
Authors: Gu Xiao , Zhu Siqi , Yan Linqi , Cheng Lei , Zhu Peixi , Zheng Jinqi
Published: February 2021

A novel sample preparation strategy was developed for accurate analysis of all 24 USP/ICH target elements in oral drug products.
High performance as-cast P3HT:PCBM devices: understanding the role of molecular weight in high regioregularity P3HT
Authors: Chandrasekaran Naresh , Kumar Anil , Thomsen Lars , Kabra Dinesh , McNeill Christopher R.
Published: February 2021

Four batches of P3HT with varied molecular weight (MW) but constant regioregularity (RR) are investigated. When RR is fixed at 100%, solar cell efficiency is less sensitive to MW with high efficiencies achieved for as-cast devices.
Synthesis and defect engineering of molybdenum oxides and their SERS applications
Authors: Gu Chenjie , Li Delong , Zeng Shuwen , Jiang Tao , Shen Xiang , Zhang Han
Published: February 2021

Review on crystal structures, material synthesis methods, defect engineering strategies for molybdenum oxides' SERS mechanism and application investigation.
Plasmonic nano-optical trap stiffness measurements and design optimization
Authors: Jiang Quanbo , Claude Jean-Benoît , Wenger Jérôme
Published: February 2021

A method is reported to experimentally measure the trap stiffness in double nanohole apertures and optimize the design parameters to maximize the plasmonic trapping performance.
Molecular self-assembly of a tyroservatide-derived octapeptide and hydroxycamptothecin for enhanced therapeutic efficacy
Authors: Liu Jing , Wu Can , Dai Guoru , Feng Feng , Chi Yuquan , Xu Keming , Zhong Wenying
Published: February 2021

A pure l-amino acid-based molecular hydrogel was designed through conjugation of an anticancer tripeptide tyroservatide (YSV) with a self-assembling moiety, which enhanced therapeutic efficacy of both YSV and hydroxycamptothecin in vitro and in vivo.
Emergent quasiparticles in Euclidean tilings
Authors: Crasto de Lima F. , Fazzio A.
Published: February 2021

In this article, we characterize 1255 lattices composed of k-uniform tiling of the Euclidean plane and unveil their intrinsic properties.
Bayberry tannin directed assembly of a bifunctional graphene aerogel for simultaneous solar steam generation and marine uranium extraction
Authors: Wu Fangwu , Liu Dan , Li Guangyong , Li Liqiang , Yan Lifeng , Hong Guo , Zhang Xuetong
Published: February 2021

A bayberry tannin (BT) directed assembly of a bifunctional graphene aerogel (BGA) has been successfully fabricated, which can simultaneously achieve high performance solar steam generation and uranium adsorption capacity.
Tunable branching and living character in ethylene polymerization using “polyethylene glycol sandwich” α-diimine nickel catalysts
Authors: Ma Xin , Zhang Yixin , Jian Zhongbao
Published: February 2021

The key effects of polyethylene glycol units as a unique secondary coordination sphere in α-diimine Ni(ii)-mediated ethylene polymerization are comprehensively disclosed.
Metabolomic profiling, biological evaluation of Aspergillus awamori, the river Nile-derived fungus using epigenetic and OSMAC approaches
Authors: Lotfy Momen M. , Sayed Ahmed M. , AboulMagd Asmaa M. , Hassan Hossam M. , El Amir Dalia , Abouzid Sameh F. , El-Gendy Ahmed O. , Rateb Mostafa E. , Abdelmohsen Usama R. , Alhadrami Hani , Mohammed Rabab
Published: February 2021

LC-HRMS-based metabolomics approach was applied to the river Nile-derived fungus Aspergillus awamori after its fermentation on four different media and using four epigenetic modifiers as elicitors.
TiO2-Based photocatalyst modified with a covalent triazine-based framework organocatalyst for carbamazepine photodegradation
Authors: Chao Xiaofang , Xu Yaqian , Chen Hui , Feng Diejing , Hu Jinxing , Yu Yan
Published: February 2021

A novel fluorine-doped TiO2 (TiO2−XFX) heterojunction semiconductor photocatalyst was synthesised using covalent triazine-based frameworks (CTFs) at different weight ratios.