bluuebunny/crossref_metadata_2025_split 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

AbstractSequencing 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

AbstractNeonatal 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

AbstractDislocations 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

AbstractMagnetic 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

AbstractMeasurement 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

AbstractRecently, 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

AbstractAnimals 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

AbstractThe 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

AbstractUsing 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

AbstractZika 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

AbstractWe 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

AbstractReactive 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

AbstractAtherosclerotic 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

AbstractThe 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

AbstractDietary 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.