bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic modification of primary human B cells to model high-grade lymphoma
Authors: Caeser Rebecca , Di Re Miriam , Krupka Joanna A. , Gao Jie , Lara-Chica Maribel , Dias João M. L. , Cooke Susanna L. , Fenner Rachel , Usheva Zelvera , Runge Hendrik F. P. , Beer Philip A. , Eldaly Hesham , Pak Hyo-Kyung , Park Chan-Sik , Vassiliou George S. , Huntly Brian J. P. , Mupo Annalisa , Bashford-Rogers Rachael J. M. , Hodson Daniel J.
Published: October 2019

Sequencing studies of diffuse large B cell lymphoma (DLBCL) have identified hundreds of recurrently altered genes. However, it remains largely unknown whether and how these mutations may contribute to lymphomagenesis, either individually or in combination. Existing strategies to address this problem predominantly utilize cell lines, which are limited by their initial characteristics and subsequent adaptions to prolonged in vitro culture. Here, we describe a co-culture system that enables the ex vivo expansion and viral transduction of primary human germinal center B cells. Incorporation of CRISPR/Cas9 technology enables high-throughput functional interrogation of genes recurrently mutated in DLBCL. Using a backbone ofBCL2with eitherBCL6orMYC, we identify co-operating genetic alterations that promote growth or even full transformation into synthetically engineered DLBCL models. The resulting tumors can be expanded and sequentially transplanted in vivo, providing a scalable platform to test putative cancer genes and to create mutation-directed, bespoke lymphoma models.
Interleukin 22 disrupts pancreatic function in newborn mice expressing IL-23
Authors: Chen Lili , Strohmeier Valentina , He Zhengxiang , Deshpande Madhura , Catalan-Dibene Jovani , Durum Scott K. , Moran Thomas M. , Kraus Thomas , Xiong Huabao , Faith Jeremiah J. , Sodhi Chhinder P. , Hackam David J. , Lira Sergio A. , Furtado Glaucia C.
Published: October 2019

Neonatal inflammatory diseases are associated with severe morbidity, but the inflammatory factors underlying them and their potential effector mechanisms are poorly defined. Here we show that necrotizing enterocolitis in neonate mice is accompanied by elevation of IL-23 and IL-22 and decreased production of pancreatic enzymes. These phenotypes are mirrored in neonate mice overexpressing IL-23 in CX3CR1+ myeloid cells or in keratinocytes. The mice fail to grow and die prematurely, displaying systemic inflammation, nutrient malabsorption and decreased expression of intestinal and pancreatic genes mediating digestion and absorption of carbohydrates, proteins, and lipids. Germ-free environment improves, and genetic ablation of IL-22 restores normal growth in mice overexpressing IL-23. Mechanistically, IL-22 acts directly at the level of pancreatic acinar cells to decrease expression of the pancreas associated transcription factor 1a (PTF1a). These results show that augmented production of IL-23 and IL-22 in early life has a negative impact on pancreatic enzyme secretion and food absorption.
Strong phonon localization in PbTe with dislocations and large deviation to Matthiessen’s rule
Authors: Sun Yandong , Zhou Yanguang , Han Jian , Liu Wei , Nan Cewen , Lin Yuanhua , Hu Ming , Xu Ben
Published: October 2019

Dislocations can greatly enhance the figure of merit of thermoelectric materials by prominently reducing thermal conductivity. However, the evolution of phonon modes with different energies when they propagate through a single dislocation is unknown. Here we perform non-equilibrium molecular dynamics simulation to study phonon transport in PbTe crystal with dislocations by excluding boundary scattering and strain coupling effect. The frequency-dependent heat flux, phonon mode analysis, and frequency-dependent phonon mean free paths (MFPs) are presented. The thermal conductivity of PbTe with dislocation density on the order of 1015 m−2 is decreased by 62%. We provide solid evidence of strong localization of phonon modes in dislocation sample. Moreover, by comparing the frequency-dependent phonon MFPs between atomistic modeling and traditional theory, it is found that the conventional theories are inadequate to describe the phonon behavior throughout the full phonon spectrum, and large deviation to the well-known semi-classical Matthiessen’s rule is observed. These results provide insightful guidance for the development of PbTe based thermoelectrics and shed light on new routes for enhancing the performance of existing thermoelectrics by incorporating dislocations.
The study of magnetic topological semimetals by first principles calculations
Authors: Zou Jinyu , He Zhuoran , Xu Gang
Published: October 2019

Magnetic topological semimetals (TSMs) are topological quantum materials with broken time-reversal symmetry (TRS) and isolated nodal points or lines near the Fermi level. Their topological properties would typically reveal from the bulk-edge correspondence principle as nontrivial surface states such as Fermi arcs or drumhead states, etc. Depending on the degeneracies and distribution of the nodes in the crystal momentum space, TSMs are usually classified into Weyl semimetals (WSMs), Dirac semimetals (DSMs), nodal-line semimetals (NLSMs), triple-point semimetals (TPSMs), etc. In this review article, we present the recent advances of magnetic TSMs from a computational perspective. We first review the early predicted magnetic WSMs such as pyrochlore iridates and HgCr2Se4, as well as the recently proposed Heusler, Kagome layers, and honeycomb lattice WSMs. Then we discuss the recent developments of magnetic DSMs, especially CuMnAs in Type-III and EuCd2As2in Type-IV magnetic space groups (MSGs). Then we introduce some magnetic NLSMs that are robust against spin–orbit coupling (SOC), namely Fe3GeTe2and LaCl (LaBr). Finally, we discuss the prospects of magnetic TSMs and the interesting directions for future research.
Generalizable control for quantum parameter estimation through reinforcement learning
Authors: Xu Han , Li Junning , Liu Liqiang , Wang Yu , Yuan Haidong , Wang Xin
Published: October 2019

Measurement and estimation of parameters are essential for science and engineering, where one of the main quests is to find systematic schemes that can achieve high precision. While conventional schemes for quantum parameter estimation focus on the optimization of the probe states and measurements, it has been recently realized that control during the evolution can significantly improve the precision. The identification of optimal controls, however, is often computationally demanding, as typically the optimal controls depend on the value of the parameter which then needs to be re-calculated after the update of the estimation in each iteration. Here we show that reinforcement learning provides an efficient way to identify the controls that can be employed to improve the precision. We also demonstrate that reinforcement learning is highly generalizable, namely the neural network trained under one particular value of the parameter can work for different values within a broad range. These desired features make reinforcement learning an efficient alternative to conventional optimal quantum control methods.
Detecting multipartite entanglement structure with minimal resources
Authors: Zhou You , Zhao Qi , Yuan Xiao , Ma Xiongfeng
Published: October 2019

Recently, there are tremendous developments on the number of controllable qubits in several quantum computing systems. For these implementations, it is crucial to determine the entanglement structure of the prepared multipartite quantum state as a basis for further information processing tasks. In reality, evaluation of a multipartite state is in general a very challenging task owing to the exponential increase of the Hilbert space with respect to the number of system components. In this work, we propose a systematic method using very few local measurements to detect multipartite entanglement structures based on the graph state—one of the most important classes of quantum states for quantum information processing. Thanks to the close connection between the Schmidt coefficient and quantum entropy in graph states, we develop a family of efficient witness operators to detect the entanglement between subsystems under any partitions and hence the entanglement intactness. We show that the number of local measurements equals to the chromatic number of the underlying graph, which is a constant number, independent of the number of qubits. In reality, the optimization problem involved in the witnesses can be challenging with large system size. For several widely used graph states, such as 1-D and 2-D cluster states and the Greenberger–Horne–Zeilinger state, by taking advantage of the area law of entanglement entropy, we derive analytical solutions for the witnesses, which only employ two local measurements. Our method offers a standard tool for entanglement-structure detection to benchmark multipartite quantum systems.
Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives
Authors: Long Keren , Feng Siyuan , Ma Jideng , Zhang Jinwei , Jin Long , Tang Qianzi , Wang Xun , Mai Miaomiao , Xiao Weihang , Liu Lingyan , Li Xuewei , Li Mingzhou
Published: October 2019

Animals that lived at high altitudes have evolved distinctive physiological traits that allow them to tolerate extreme high-altitude environment, including higher hemoglobin concentration, increased oxygen saturation of blood and a high energy metabolism. Although previous investigations performed plenty of comparison between high- and low-altitude mammals at the level of morphology, physiology and genomics, mechanism underlying high-altitude adaptation remains largely unknown. Few studies provided comparative analyses in high-altitude adaptation, such as parallel analysis in multiple species. In this study, we generated high-quality small RNA sequencing data for six tissues (heart, liver, spleen, lung, kidney and muscle) from low- and high-altitude populations of four typical livestock animals, and identified comparable numbers of miRNAs in each species. This dataset will provide valuable information for understanding the molecular mechanism of high-altitude adaptation in vertebrates.
Anaerobic reduction of europium by a Clostridium strain as a strategy for rare earth biorecovery
Authors: Maleke Maleke , Valverde Angel , Gomez-Arias Alba , Cason Errol D. , Vermeulen Jan-G , Coetsee-Hugo Liza , Swart Hendrik , van Heerden Esta , Castillo Julio
Published: October 2019

The biorecovery of europium (Eu) from primary (mineral deposits) and secondary (mining wastes) resources is of interest due to its remarkable luminescence properties, important for modern technological applications. In this study, we explored the tolerance levels, reduction and intracellular bioaccumulation of Eu by a site-specific bacterium,Clostridiumsp. 2611 isolated from Phalaborwa carbonatite complex.Clostridiumsp. 2611 was able to grow in minimal medium containing 0.5 mM Eu3+. SEM-EDX analysis confirmed an association between Eu precipitates and the bacterium, while TEM-EDX analysis indicated intracellular accumulation of Eu. According to the HR-XPS analysis, the bacterium was able to reduce Eu3+to Eu2+under growth and non-growth conditions. Preliminary protein characterization seems to indicate that a cytoplasmic pyruvate oxidoreductase is responsible for Eu bioreduction. These findings suggest the bioreduction of Eu3+byClostridiumsp. as a resistance mechanism, can be exploited for the biorecovery of this metal.
Differential Modulation of Human Innate Lymphoid Cell (ILC) Subsets by IL-10 and TGF-β
Authors: Bonne-Année Sandra , Bush Mabel C. , Nutman Thomas B.
Published: October 2019

Using multiparameter flow cytometry human innate lymphoid cell (ILC) subsets can be detected in the circulation, in relatively low frequencies. Despite the low frequency of ILCs in circulation, ex vivo experiments have demonstrated that these ILCs release extremely large per cell quantities of signature ILC cytokines following activation. To determine how activated ILC cytokine production is regulated, ILC subsets were activated in the presence or absence of the immunoregulatory cytokines IL-10 and TGF-β. An examination of circulating ILC subsets revealed surface expression of IL-10Rα and mRNA expression of both IL-10Rα and TGF-βR1 for all ILC subsets. Stimulated ILC1 production of IFN-γ was decreased by TGF-β and not IL-10. Interestingly, ILC2s stimulated in the presence of IL-10 had a marked reduction in cytokine production of IL-5 and IL-13 while TGF-β had no effect on ILC2 cytokine production. Ex vivo activated ILC1 and ILC2 subsets were also found to be a source of the immunoregulatory cytokine IL-10, raising the potential for ILC-mediated regulation of immune cells. These findings demonstrate the differential effects of immunoregulatory cytokines IL-10 and TGF-β on activated ILC1 and ILC2 populations ex vivo.
Resveratrol affects Zika virus replication in vitro
Authors: Mohd Azirah , Zainal Nurhafiza , Tan Kim-Kee , AbuBakar Sazaly
Published: October 2019

Zika virus (ZIKV) infection is a serious public health concern. ZIKV infection has been associated with increased occurrences of microcephaly among newborns and incidences of Guillain-Barré syndrome among adults. No specific therapeutics or vaccines are currently available to treat and protect against ZIKV infection. Here, a plant-secreted phytoalexin, resveratrol (RES), was investigated for its ability to inhibit ZIKV replication in vitro. Several RES treatment regimens were used. The ZIKV titers of mock- and RES-treated infected cell cultures were determined using the focus-forming assay and the Zika mRNA copy number as determined using qRT-PCR. Our results suggested that RES treatment reduced ZIKV titers in a dose-dependent manner. A reduction of >90% of virus titer and ZIKV mRNA copy number was achieved when infected cells were treated with 80 µM of RES post-infection. Pre-incubation of the virus with 80 µM RES showed >30% reduction in ZIKV titers and ZIKV mRNA copy number, implying potential direct virucidal effects of RES against the virus. The RES treatment reduced >70% virus titer in the anti-adsorption assay, suggesting the possibility that RES also interferes with ZIKV binding. However, there was no significant decrease in ZIKV titer when a short-period of RES treatment was applied to cells before ZIKV infection (pre-infection) and after the virus bound to the cells (virus internalization inhibition), implying that RES acts through its continuous presence in the cell cultures after virus infection. Overall, our results suggested that RES exhibited direct virucidal activity against ZIKV and possessed anti-ZIKV replication properties, highlighting the need for further exploration of RES as a potential antiviral molecule against ZIKV infection.
Evidence from 3-month-old infants shows that a combination of postnatal feeding and exposures in utero shape lipid metabolism
Authors: Furse Samuel , Snowden Stuart G. , Olga Laurentya , Prentice Philippa , Ong Ken K. , Hughes Ieuan A. , Acerini Carlo L. , Dunger David B. , Koulman Albert
Published: October 2019

We tested the hypothesis that both postnatal feeding and conditions in utero affect lipid metabolism in infants. Infants who experienced restrictive growth conditions in utero and others exposed to maternal hyperglycaemia were compared to a control group with respect to feeding mode. Dried blood spots were collected from a pilot subset of infant participants of the Cambridge Baby Growth Study at 3mo. Groups: (a) a normal gestation (control, n = 40), (b) small for gestational age (SGA, n = 34) and (c) whose mothers developed hyperglycaemia (n = 59). These groups were further stratified by feeding mode; breastfed, formula-fed or received a mixed intake. Their phospholipid, glyceride and sterol fractions were profiled using direct infusion mass spectrometry. Statistical tests were used to identify molecular species that indicated differences in lipid metabolism. The abundance of several phospholipids identified by multivariate analysis, PC(34:1), PC(34:2) and PC-O(34:1), was 30–100% higher across all experimental groups. SM(39:1) was around half as abundant in in utero groups among breastfed infants only. The evidence from this pilot study shows that phospholipid metabolism is modulated by both conditions in utero and postnatal feeding in a cohort of 133 Caucasian infants, three months post partum.
Association between genetic polymorphisms of NRF2, KEAP1, MAFF, MAFK and anti-tuberculosis drug-induced liver injury: a nested case-control study
Authors: Chen Shixian , Pan Hongqiu , Chen Yongzhong , Lu Lihuan , He Xiaomin , Chen Hongbo , Chen Ru , Zhan Siyan , Tang Shaowen
Published: October 2019

Reactive metabolites of anti-tuberculosis (anti-TB) drugs can result in excessive reactive oxygen species (ROS), which are responsible for drug-induced liver injury. The nuclear factor erythroid 2-related factor 2 (Nrf2) - antioxidant response elements (ARE) (Nrf2-ARE) signaling pathway plays a crucial role in protecting liver cells from ROS, inducing enzymes such as phase II metabolizing enzymes and antioxidant enzymes. Based on a Chinese anti-TB treatment cohort, a nested case-control study was performed to explore the association between 13 tag single-nucleotide polymorphisms (tagSNPs) in the NRF2, KEAP1, MAFF, MAFK genes in Nrf2-ARE signaling pathway and the risk of anti-TB drug-induced liver injury (ATLI) in 314 cases and 628 controls. Conditional logistic regression models were used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) after adjusting weight and usage of hepatoprotectant. Patients carrying the TC genotype at rs4243387 or haplotype C-C (rs2001350-rs6726395) in NRF2 were at an increased risk of ATLI (adjusted OR = 1.362, 95% CI: 1.017–1.824, P = 0.038; adjusted OR = 2.503, 95% CI: 1.273–4.921, P = 0.008, respectively), whereas patients carrying TC genotype at rs2267373 or haplotype C-G-C (rs2267373-rs4444637-rs4821767) in MAFF were at a reduced risk of ATLI (adjusted OR = 0.712, 95% CI: 0.532–0.953, P = 0.022; adjusted OR = 0.753, 95% CI: 0.587–0.965, P = 0.025, respectively). Subgroup analysis also detected a significant association between multiple tagSNPs (rs4821767 and rs4444637 in MAFF, rs4720833 in MAFK) and specific clinical patterns of liver injury under different genetic models. This study shows that genetic polymorphisms of NRF2, MAFF and MAFK may contribute to the susceptibility to ATLI in the Chinese anti-TB treatment population.
Ex vivo evaluation of an atherosclerotic human coronary artery via histology and high-resolution hard X-ray tomography
Authors: Buscema Marzia , Hieber Simone E. , Schulz Georg , Deyhle Hans , Hipp Alexander , Beckmann Felix , Lobrinus Johannes A. , Saxer Till , Müller Bert
Published: October 2019

Atherosclerotic arteries exhibit characteristic constrictions and substantial deviations from cylindrical shape. Therefore, determining the artery’s cross-section along the centerline is challenging, although high-resolution isotropic three-dimensional data are available. Herein, we apply high-resolution computed tomography in absorption and phase to a plaque-containing human artery post-mortem, through the course of the preparation stages for histology. We identify the impact of paraffin embedding and decalcification on the artery lumen. For automatic extraction of lumen’s cross-section along centerline we present a dedicated pipeline. Comparing fixated tissue before and after paraffin embedding gives rise to shape changes with lumen reduction to 50–80%. The histological slicing induces further deformations with respect to tomography. Data acquired after decalcification show debris unintentionally distributed within the vessel preventing the reliable automatic lumen segmentation. Comparing tomography of laboratory- and synchrotron-radiation-based X rays by means of joint histogram analysis leads us to conclude that advanced desktop tomography is capable of quantifying the artery’s lumen as an essential input for blood flow simulations. The results indicate that the most reliable lumen quantification is achieved by imaging the non-decalcified specimen fixed in formalin, using phase contrast modality and a dedicated processing pipeline. This study focusses on a methodology to quantitatively evaluate diseased artery segments post-mortem and provides unique structural parameters on the treatment-induced local shrinkage, which will be the basis of future studies on the flow in vessels affected by constrictions.
Damages at the nanoscale on red blood cells promoted by fire corals
Authors: Díaz-Marrero Ana R. , Rodríguez González Miriam C. , Hernández Creus Alberto , Rodríguez Hernández Adriana , Fernández José J.
Published: October 2019

The hydrocoral Millepora alcicornis, known as fire coral, biosynthesize protein toxins with phospholipase A2 (PLA2) activity as a main defense mechanism; proteins that rapidly catalyse the hydrolysis at the sn-2 position of phosphatidylcholine-type phospholipids of cellular membranes. This hydrolysis mechanism triggers a structural damage in the outer leaflet of the red blood cells (RBC) membrane, by generating pores in the lipid bilayer that leads to a depletion of the cellular content of the damaged cell. A secondary mechanism, tentatively caused by pore-forming proteins toxins (PFTs), has been observed. The use of atomic force microscopy (AFM) has allowed to visualize the evolution of damages produced on the surface of the cells at the nanoscale level along the time.
Mesencephalic Astrocyte-Derived Neurotrophic Factor Is Upregulated with Therapeutic Fasting in Humans and Diet Fat Withdrawal in Obese Mice
Authors: Galli Emilia , Rossi Jari , Neumann Thomas , Andressoo Jaan-Olle , Drinda Stefan , Lindholm Päivi
Published: October 2019

Dietary restriction induces beneficial metabolic changes and prevents age-related deterioration. Mesencephalic astrocyte-derived neurotrophic factor (MANF) shows protective effects on cells in various models of degenerative diseases. Here we studied whether circulating concentrations of MANF are associated with fasting-induced positive effects. We quantified the levels of circulating MANF from 40 human subjects before and after therapeutic fasting. As measured by an enzyme-linked immunosorbent assay (ELISA), the mean concentration of plasma MANF increased after an average fasting of 15 days. Plasma MANF levels correlated inversely with adiponectin, a hormone that regulates metabolism, thus suggesting that MANF levels are related to metabolic homeostasis. To study the effects of dietary intervention on MANF concentrations in mice, we developed an ELISA for mouse MANF and verified its specificity using MANF knock-out (KO) tissue. A switch from high-fat to normal diet increased MANF levels and downregulated the expression of unfolded protein response (UPR) genes in the liver, indicating decreased endoplasmic reticulum (ER) stress. Liver MANF and serum adiponectin concentrations correlated inversely in mice. Our findings demonstrate that MANF expression and secretion increases with dietary intervention. The MANF correlation to adiponectin and its possible involvement in metabolic regulation and overall health warrants further studies.
Galewone, an Anti-Fibrotic Polyketide from Daldinia eschscholzii with an Undescribed Carbon Skeleton
Authors: Zhang Ai Hua , Jiang Nan , Wang Xing Qi , Tan Ren Xiang
Published: October 2019

A novel polyphenolic natural product, galewone, with undescribed carbon skeleton, was isolated as a racemate from the culture of Daldinia eschscholzii IFB-TL01, a fungus obtained from the mantis (Tenodera aridifolia) gut. The galewone structure was elucidated by a combination of MS and NMR spectra, and substantiated by X-ray crystallographic diffraction. The absolute stereochemistry of each galewone enantiomers was determined by the CD spectrum. In compliance of the structural similarities, galewone might be the shunt products of the dalesconol biosynthetic pathway. Both (−)- and ( + )-galewones were evaluated to be anti-fibrotic against activated hepatic stellate cell line, CFSC-8B, with the IC50 values being 3.73 ± 0.21 and 10.10 ± 0.41 μM, respectively. Thus, galewone may serve as a starting molecule for the discovery of new anti-fibrotic drug.
Genotyping-by-sequencing based QTL mapping for rice grain yield under reproductive stage drought stress tolerance
Authors: Yadav Shailesh , Sandhu Nitika , Singh Vikas Kumar , Catolos Margaret , Kumar Arvind
Published: October 2019

QTLs for rice grain yield under reproductive stage drought stress (qDTY) identified earlier with low density markers have shown linkage drag and need to be fine mapped before their utilization in breeding programs. In this study, genotyping-by-sequencing (GBS) based high-density linkage map of rice was developed using two BC1F3 mapping populations namely Swarna*2/Dular (3929 SNPs covering 1454.68 cM) and IR11N121*2/Aus196 (1191 SNPs covering 1399.68 cM) with average marker density of 0.37 cM to 1.18 cM respectively. In total, six qDTY QTLs including three consistent effect QTLs were identified in Swarna*2/Dular while eight qDTY QTLs including two consistent effect QTLs were identified in IR11N121*2/Aus 196 mapping population. Comparative analysis revealed four stable and novel QTLs (qDTY2.4, qDTY3.3, qDTY6.3, and qDTY11.2) which explained 8.62 to 14.92% PVE. However, one of the identified stable grain yield QTL qDTY1.1 in both the populations was located nearly at the same physical position of an earlier mapped major qDTY QTL. Further, the effect of the identified qDTY1.1 was validated in a subset of lines derived from five mapping populations confirming robustness of qDTY1.1 across various genetic backgrounds/seasons. The study successfully identified stable grain yield QTLs free from undesirable linkages of tall plant height/early maturity utilizing high density linkage maps.
Bioinspired DNA Origami Quasi-Yagi Helical Antenna with Beam Direction and Beamwidth Switching Capability
Authors: Shah Syed Imran Hussain , Lim Sungjoon
Published: October 2019

We propose a bioinspired origami quasi-Yagi helical antenna with beam direction and beamwidth switching capability based on transformable DNA origami structure. Each DNA molecule consists of a double helical chain, and its length can be transformed by folding and unfolding. When three transformable origami DNA structures are applied to the quasi-Yagi helical antenna, beam direction and beamwidth can be controlled by folding and unfolding the origami DNA. The transformable DNA structures act as driven, director and reflector elements. The proposed DNA origami antenna provides four beam direction switching states (three states with narrow beamwidth and one state with wide beamwidth) at fixed frequency of 1.9 GHz. For example, the main beam direction of the proposed antenna can be steered to −30°, 0°, +30° and −40° for states 1, 2, 3 and 4, respectively. State 4 provides a 3-dB wider beamwidth of 104°, whereas the beamwidth of other states is narrower than 64°. The proposed concept is numerically and experimentally demonstrated.
A machine learning based delta-radiomics process for early prediction of treatment response of pancreatic cancer
Authors: Nasief Haidy , Zheng Cheng , Schott Diane , Hall William , Tsai Susan , Erickson Beth , Allen Li X.
Published: October 2019

Changes of radiomic features over time in longitudinal images, delta radiomics, can potentially be used as a biomarker to predict treatment response. This study aims to develop a delta-radiomic process based on machine learning by (1) acquiring and registering longitudinal images, (2) segmenting and populating regions of interest (ROIs), (3) extracting radiomic features and calculating their changes (delta-radiomic features, DRFs), (4) reducing feature space and determining candidate DRFs showing treatment-induced changes, and (5) creating outcome prediction models using machine learning. This process was demonstrated by retrospectively analyzing daily non-contrast CTs acquired during routine CT-guided-chemoradiation therapy for 90 pancreatic cancer patients. A total of 2520 CT sets (28-daily-fractions-per-patient) along with their pathological response were analyzed. Over 1300 radiomic features were extracted from the segmented ROIs. Highly correlated DRFs were ruled out using Spearman correlations. Correlation between the selected DRFs and pathological response was established using linear-regression-models. T test and linear-mixed-effects-models were used to determine which DRFs changed significantly compared with first fraction. A Bayesian-regularization-neural-network was used to build a response prediction model. The model was trained using 50 patients and leave-one-out-cross-validation. Performance was judged using the area-under-ROC-curve. External independent validation was done using data from the remaining 40 patients. The results show that 13 DRFs passed the tests and demonstrated significant changes following 2–4 weeks of treatment. The best performing combination differentiating good versus bad responders (CV-AUC = 0.94) was obtained using normalized-entropy-to-standard-deviation-difference-(NESTD), kurtosis, and coarseness. With further studies using larger data sets, delta radiomics may develop into a biomarker for early prediction of treatment response.
On the use of CdSe scintillating nanoplatelets as time taggers for high-energy gamma detection
Authors: Turtos R. M. , Gundacker S. , Omelkov S. , Mahler B. , Khan A. H. , Saaring J. , Meng Z. , Vasil’ev A. , Dujardin C. , Kirm M. , Moreels I. , Auffray E. , Lecoq P.
Published: October 2019

The technological challenge imposed by the time resolution essential to achieve real-time molecular imaging calls for a new generation of ultrafast detectors. In this contribution, we demonstrate that CdSe-based semiconductor nanoplatelets can be combined with standard scintillator technology to achieve 80 ps coincidence time resolution on a hybrid functional pixel. This result contrasts with the fact that the overall detector light output is considerably affected by the loss of index-light-guiding. Here, we exploit the principle of 511 keV energy sharing between a high-Z, high stopping power bulk scintillator, and a nano-scintillator with sub-1 ns radiative recombination times, aiming at a breakthrough in the combined energy and time resolution performance. This proof-of-concept test opens the way to the design and study of larger size sensors using thin nanocomposite layers able to perform as efficient time taggers in a sampling detector geometry of new generation.
3D mapping reveals network-specific amyloid progression and subcortical susceptibility in mice
Authors: Gail Canter Rebecca , Huang Wen-Chin , Choi Heejin , Wang Jun , Ashley Watson Lauren , Yao Christine G. , Abdurrob Fatema , Bousleiman Stephanie M. , Young Jennie Z. , Bennett David A. , Delalle Ivana , Chung Kwanghun , Tsai Li-Huei
Published: October 2019

Alzheimer’s disease (AD) is a progressive, neurodegenerative dementia with no cure. Prominent hypotheses suggest accumulation of beta-amyloid (Aβ) contributes to neurodegeneration and memory loss, however identifying brain regions with early susceptibility to Aβ remains elusive. Using SWITCH to immunolabel intact brain, we created a spatiotemporal map of Aβ deposition in the 5XFAD mouse. We report that subcortical memory structures show primary susceptibility to Aβ and that aggregates develop in increasingly complex networks with age. The densest early Aβ occurs in the mammillary body, septum, and subiculum- core regions of the Papez memory circuit. Previously, early mammillary body dysfunction in AD had not been established. We also show that Aβ in the mammillary body correlates with neuronal hyper-excitability and that modulation using a pharmacogenetic approach reduces Aβ deposition. Our data demonstrate large-tissue volume processing techniques can enhance biological discovery and suggest that subcortical susceptibility may underlie early brain alterations in AD.
Digital phenotyping by consumer wearables identifies sleep-associated markers of cardiovascular disease risk and biological aging
Authors: Teo Jing Xian , Davila Sonia , Yang Chengxi , Hii An An , Pua Chee Jian , Yap Jonathan , Tan Swee Yaw , Sahlén Anders , Chin Calvin Woon-Loong , Teh Bin Tean , Rozen Steven G. , Cook Stuart Alexander , Yeo Khung Keong , Tan Patrick , Lim Weng Khong
Published: October 2019

Sleep is associated with various health outcomes. Despite their growing adoption, the potential for consumer wearables to contribute sleep metrics to sleep-related biomedical research remains largely uncharacterized. Here we analyzed sleep tracking data, along with questionnaire responses and multi-modal phenotypic data generated from 482 normal volunteers. First, we compared wearable-derived and self-reported sleep metrics, particularly total sleep time (TST) and sleep efficiency (SE). We then identified demographic, socioeconomic and lifestyle factors associated with wearable-derived TST; they included age, gender, occupation and alcohol consumption. Multi-modal phenotypic data analysis showed that wearable-derived TST and SE were associated with cardiovascular disease risk markers such as body mass index and waist circumference, whereas self-reported measures were not. Using wearable-derived TST, we showed that insufficient sleep was associated with premature telomere attrition. Our study highlights the potential for sleep metrics from consumer wearables to provide novel insights into data generated from population cohort studies.
Quantum spacetime on a quantum simulator
Authors: Li Keren , Li Youning , Han Muxin , Lu Sirui , Zhou Jie , Ruan Dong , Long Guilu , Wan Yidun , Lu Dawei , Zeng Bei , Laflamme Raymond
Published: October 2019

Quantum simulation has shown its irreplaceable role in many fields, where it is difficult for classical computers to do much. On a four-qubit Nuclear Magnetic Resonance (NMR) quantum simulator, we experimentally simulate the spin-network states by simulating quantum spacetime tetrahedra. The fidelities of our experimentally prepared quantum tetrahedra are all above 95%. We then use the quantum tetradedra prepared by the Nuclear Magnetic Resonance to simulate a spinfoam vertex amplitude, which displays the local dynamics of quantum spacetime. By measuring the geometric properties on the corresponding quantum tetrahedra and simulating their interaction, our experiment serves as a basic module that represents the Feynman diagram vertex in the spinfoam formulation of Loop Quantum Gravity(LQG). This is an initial attempt to study LQG by quantum information processing.
Reconfigurable flows and defect landscape of confined active nematics
Authors: Hardoüin Jérôme , Hughes Rian , Doostmohammadi Amin , Laurent Justine , Lopez-Leon Teresa , Yeomans Julia M. , Ignés-Mullol Jordi , Sagués Francesc
Published: October 2019

The physics of active liquid crystals is mostly governed by the interplay between elastic forces that align their constituents, and active stresses that destabilize the order with constant nucleation of topological defects and chaotic flows. The average distance between defects, also called active length scale, depends on the competition between these forces. Here, in experiments with the microtubule/kinesin active nematic system, we show that the intrinsic active length scale loses its relevance under strong lateral confinement. Transitions are observed from chaotic to vortex lattices and defect-free unidirectional flows. Defects, which determine the active flow behaviour, are created and annihilated on the channel walls rather than in the bulk, and acquire a strong orientational order in narrow channels. Their nucleation is governed by an instability whose wavelength is effectively screened by the channel width. These results are recovered in simulations, and the comparison highlights the role of boundary conditions.
Topology-assisted, photo-strengthened DNA/siRNA delivery mediated by branched poly(β-amino ester)s via synchronized intracellular kinetics
Authors: Duan Shanzhou , Cao Desheng , Li Xudong , Zhu Huifang , Lan Min , Tan Zhengzhong , Song Ziyuan , Zhu Rongying , Yin Lichen , Chen Yongbing
Published: October 2019

Photo-degradable, branched poly(β-amino ester)s (BPAE-NB) were developed to mediate topology-assisted trans-membrane gene delivery as well as photo-strengthened intracellular gene release.
Etchable SERS nanosensor for accurate pH and hydrogen peroxide sensing in living cells
Authors: Bai Lu , Wang Xiaojie , Zhang Kaifu , Tan Xiaoyue , Zhang Yuying , Xie Wei
Published: October 2019

“Turning off” extracellular SERS signals for accurate pH and hydrogen peroxide sensing in living cells.
A robust photocatalyst of Au25@ZIF-8@TiO2-ReP with dual photoreductive sites to promote photoelectron utilization in H2O splitting to H2 and CO2 reduction to CO
Authors: Tian Linyuan , Luo Yucheng , Chu Kunlin , Wu Dongjun , Shi Jianying , Liang Zhenxing
Published: October 2019

Heterogenization of double redox active sites Au25 NCs and a Re(i) complex via composition engineering with improvement of activity and stability.
Multi-stimuli responsive properties switch by intra- and inter-molecular charge transfer constructed from triphenylamine derivative
Authors: Hu Wangqin , Yang Wen , Gong Tingfeng , Zhou Weiqun , Zhang Yuhan
Published: October 2019

The compound TPA-BI exhibited multi-responsive fluorescence behaviors caused by inter-molecular charge transfer (CT) and intra-molecular CT formation.
Catalyst-free growth of zinc nanocrystals with various morphologies on ionic liquid surfaces
Authors: Bao Zhilong , Li Lu , Shen Jiawei , Ye Xunheng , Tao Xiangming , Yang Bo , Ye Gaoxiang
Published: October 2019

We report a catalyst-free growth of zinc nanocrystals with various morphologies on ionic liquid surfaces at room temperature.
Survival and confinement under quenched disorder
Authors: Aquino Tomás , Lapeyre G. John , Dentz Marco
Published: October 2019

We study the survival and confinement of random walkers under quenched disorder characterized by spatially-varying waiting times and decay rates.
2,4-Substituted bispidines as rigid hosts for versatile applications: from κ-opioid receptor to metal coordination
Authors: Nonat Aline M. , Roux Amandine , Sy Maryame , Charbonnière Loïc J.
Published: October 2019

Bispidines and their applications in medicine, catalysis, magnetism and medical imaging: what do we know about the influence of substituents?
Acetylenedicarboxylate-based cerium(iv) metal–organic framework with fcu topology: a potential material for air cleaning from toxic halogen vapors
Authors: Matemb Ma Ntep Tobie J. , Reinsch Helge , Liang Jun , Janiak Christoph
Published: October 2019

The most contracted Ce(iv)–metal–organic framework (MOF) with fcu topology incorporating an alkyne-based linker, namely acetylenedicarboxylate (ADC), was synthesized under green conditions in water at room temperature and thoroughly characterized.
A streamlined workflow to study direct photodegradation kinetic and transformation products for persistence assessment of a fragrance ingredient in natural waters
Authors: Lin Jianming , Apell Jennifer N. , McNeill Kristopher , Emberger Matthew , Ciraulo Valerie , Gimeno Sylvia
Published: October 2019

A streamlined workflow was developed to generate relevant, reliable and transparent data on direct photodegradation kinetic and transformation products for environmental persistence assessment of fragrance chemicals for regulatory compliance.
Characteristics of laser-induced aluminum plasma plumes after increasing sample temperature and spatial confinement
Authors: Xu Wanpeng , Chen Anmin , Wang Qiuyun , Zhang Dan , Li Suyu , Jiang Yuanfei , Gao Xun , Jin Mingxing
Published: October 2019

This paper exhibits the characteristics of laser-induced aluminum plasma plumes after increasing sample temperature and spatial confinement.
Correction: Preparation and characterization of primary magnesium mixtures for the ab initio calibration of absolute magnesium isotope ratio measurements
Authors: Brandt Björn , Vogl Jochen , Noordmann Janine , Kaltenbach Angela , Rienitz Olaf
Published: October 2019

Correction for ‘Preparation and characterization of primary magnesium mixtures for the ab initio calibration of absolute magnesium isotope ratio measurements’ by Björn Brandt et al., J. Anal. At. Spectrom., 2016, 31, 179–196.
Deep, sub-wavelength acoustic patterning of complex and non-periodic shapes on soft membranes supported by air cavities
Authors: Tung Kuan-Wen , Chung Pei-Shan , Wu Cong , Man Tianxing , Tiwari Sidhant , Wu Ben , Chou Yuan-Fang , Yang Fu-ling , Chiou Pei-Yu
Published: October 2019

This manuscript demonstrates a near-field acoustic platform to synthesize high resolution, complex and non-periodic energy potential wells for patterning micro-objects.
Ultrafine Pt cluster and RuO2 heterojunction anode catalysts designed for ultra-low Pt-loading anion exchange membrane fuel cells
Authors: Wang Rongyue , Li Dongguo , Maurya Sandip , Kim Yu Seung , Wu Yimin , Liu Yuzi , Strmcnik Dusan , Markovic Nenad M. , Stamenkovic Vojislav R.
Published: October 2019

Pt–RuO2 heterojunction catalysts with a unique morphology show excellent alkaline membrane fuel cell performance at an ultra-low loading Pt anode.
Tracking mitochondrial viscosity in living systems based on a two-photon and near red probe
Authors: Peng Min , Yin Junling , Lin Weiying
Published: October 2019

A two-photon fluorescence probe, Mito-V, with near-red emission to measure the viscosity changes of mitochondria in living cells and in vivo.
Synthesis and optimization of nanocomposite membranes based on SPEEK and perovskite nanoparticles for polymer electrolyte membrane fuel cells
Authors: Hosseinabadi Parisa , Hooshyari Khadijeh , Javanbakht Mehran , Enhessari Morteza
Published: October 2019

The addition of BaZr0.9Y0.1O3−δ (BZY10) nanoparticles as a perovskite material with a proton conductor oxide structure to enhance the performance of sulfonated poly(ether ether ketone) (SPEEK) in proton exchange membrane fuel cells (PEMFCs) has been investigated in this work.
Efficient removal of low-concentration Cr(vi) from aqueous solution by 4A/HACC particles
Authors: Guan Qingqing , Gao Kexuan , Ning Ping , Miao Rongrong , He Liang
Published: October 2019

A new cationic surface-modified 4A zeolite for adsorbing trace chromium in aqueous solution was successfully synthesized.
The development of mechanoluminescence from organic compounds: breakthrough and deep insight
Authors: Xie Yujun , Li Zhen
Published: October 2019

The organic mechanoluminescence (ML) happens at the crack surface under force, and the ML composition is becoming more complicated, extending from the normal fluorescence to phosphorescence, persistent room temperature phosphorescence and the photo-sensitive ML.
A comparative study of different electrodeposited NiCo2O4 microspheres anchored on a reduced graphene oxide platform: electrochemical sensor for anti-depressant drug venlafaxine
Authors: Ali Marwa F. B. , El-Zahry Marwa R.
Published: October 2019

Different electrodeposited NiCo2O4 microspheres supported on a reduced graphene oxide platform for electrochemical sensing of venlafaxine.
Theoretical investigation of the ORR on boron–silicon nanotubes (B–SiNTs) as acceptable catalysts in fuel cells
Authors: Razavi Razieh , Najafi Meysam
Published: October 2019

Here, the potential of boron doped silicon nanotubes (7, 0) as ORR catalysts is examined.
Inhibitor-conjugated harmonic nanoparticles targeting fibroblast activation protein
Authors: De Matos Raphaël , Vuilleumier Jérémy , Mas Christophe , Constant Samuel , Staedler Davide , Gerber-Lemaire Sandrine
Published: October 2019

Harmonic nanoparticles, functionalized with a selective inhibitor of FAP, provide imaging probes targeting the fibroblastic element of the tumor stroma.
In situ self-assembly of Ni3S2/MnS/CuS/reduced graphene composite on nickel foam for high power supercapacitors
Authors: Li Wenbo , Song Weiming , Wang Haihua , Kang Yong-Mook
Published: October 2019

Transition metal sulfides (TMS), as promising electroactive materials for asymmetric supercapacitors, have been limited due to their relatively poor conductivity and cycle stability.
Adsorption performance of antimony by modified iron powder
Authors: Zhang Chun , Jiang Haiyan , Deng Yumei , Wang Aihe
Published: October 2019

Modified iron powders were obtained by ball-milling and acid modification and the adsorption behavior and mechanism for Sb(iii) and Sb(v) analyzed. The improved adsorption capacity and low cost show the application potential of the modified material.
Improvements in sticking, hygroscopicity, and compactibility of effervescent systems by fluid-bed coating
Authors: Zheng Xiao , Wu Fei , Hong YanLong , Shen Lan , Lin Xiao , Feng Yi
Published: October 2019

Recently, effervescent tablets (ETs) have become increasingly popular with patients in clinics due to their fast disintegration by acid–alkali reactions in water.
O-Methylation steps during strobilurin and bolineol biosynthesis
Authors: Lebe Karen E. , Cox Russell J.
Published: October 2019

Two methyltransferase genes involving in the biosynthesis of the antifungal agent strobilurin A were investigated. The antifungal activity of pathway intermediates increses with methylation.
Curing kinetics of phenolphthalein based polyphosphazene towards thermal stability and flame retardancy of polybenzoxazine
Authors: Zhao Ling , Zhao Chunxia , Wu Min , Li Yuntao , Li Hui , Xiang Dong , Guo Cuicui
Published: October 2019

Phenolphthalein type polyphosphazene (PZPT) microspheres were synthesized by an ultrasound assisted precipitation polymerization method, and their structures were confirmed by scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy.
Inhibition of osimertinib-resistant epidermal growth factor receptor EGFR-T790M/C797S
Authors: Lategahn Jonas , Keul Marina , Klövekorn Philip , Tumbrink Hannah L. , Niggenaber Janina , Müller Matthias P. , Hodson Luke , Flaßhoff Maren , Hardick Julia , Grabe Tobias , Engel Julian , Schultz-Fademrecht Carsten , Baumann Matthias , Ketzer Julia , Mühlenberg Thomas , Hiller Wolf , Günther Georgia , Unger Anke , Müller Heiko , Heimsoeth Alena , Golz Christopher , Blank-Landeshammer Bernhard , Kollipara Laxmikanth , Zahedi René P. , Strohmann Carsten , Hengstler Jan G. , van Otterlo Willem A. L. , Bauer Sebastian , Rauh Daniel
Published: October 2019

We present inhibitors of drug resistant mutants of EGFR including T790M and C797S. In addition, we present the first X-ray crystal structures of covalent inhibitors in complex with C797S-mutated EGFR to gain insight into their binding mode.
Programming permanent and transient molecular protection via mechanical stoppering
Authors: Soto Miguel A. , Lelj Francesco , MacLachlan Mark J.
Published: October 2019

A macrocycle (permanently or transiently) protects a viologen from heterogenous reduction, all thanks to bespoke mechanical stoppering.
Binary nickel iron phosphide composites with oxidized surface groups as efficient electrocatalysts for the oxygen evolution reaction
Authors: Liu Chen , Zhu Han , Zhang Zhili , Hao Jican , Wu Yudong , Guan Jibiao , Lu Shuanglong , Duan Fang , Zhang Ming , Du Mingliang
Published: October 2019

We have synthesized the binary NiFeOH, NiFeO and NiFeP two-dimensional (2D) nanosheets on carbon cloth (CC) via a facile hydrothermal method combined with phosphorization and oxidation treatment.
Formation of highly porous CuCo2O4 nanosheet assemblies for high-rate and long-term lithium storage
Authors: Li Jia , Zhang Yongxing , Li Li , Cheng Lixun , Dai Song , Wang Fei , Wang Yanming , Yu Xin-Yao
Published: October 2019

Mixed transition metal oxides with high theoretical capacity show great potential to replace carbonaceous anode materials in lithium-ion batteries.
Co-assembled supramolecular hydrogels of cell adhesive peptide and alginate for rapid hemostasis and efficacious wound healing
Authors: Zhai Ziran , Xu Keming , Mei Leixia , Wu Can , Liu Jing , Liu Ziqi , Wan Lanxin , Zhong Wenying
Published: October 2019

Co-assembly of a cell adhesive peptide conjugate and alginate affords multifunctional composite hydrogels for rapid hemostasis and efficacious wound healing.