bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)
Authors: Wang Tong , Chen Xue , Hui Shuang , Ni Jingbo , Yin Ying , Cao Wei , Zhang Yan , Wang Xinyu , Ma Xiaoli , Cao Panxiang , Liu Mingyue , Chen Kylan N. , wang Fang , Zhang Yang , Nie Daijing , Yuan Lili , Liu Hongxing 
Published: January 2020

Abstract
Chromosome translocation t(12;22)(p13;q12)/MN1-ETV6 and MN1 overexpression confer a subset of adverse prognostic AML but so far lack in-depth research. We focused on the clinical course and comprehensive genetic analysis of eight cases with t(12;22)(p13;q12) and one with t(12;17;22) (p13;q21;q13) to elucidate their molecular etiology and outcomes of allogeneic hemopoietic stem cell transplantation (allo-HSCT). The total incidence of t(12;22)(p13;q12) and related translocations was 0.32% in myeloid neoplasms. These patients were confirmed to have dismal prognosis when treated only with chemotherapy, and we firstly provided evidence that they can significantly benefit from timely allo-HSCT. Five cases were MN1-ETV6 positive, and a novel MN1-STAT3 fusion was identified in the patient with triadic translocation. Significant MN1 overexpression was observed in all three MN1-fusion-negative cases. Genetic analysis highlighted the evidence of an ectopic super-enhancer associated orchestrated mechanism of MN1 overexpression and ETV6 haploinsufficiency in t(12;22)(p13;q12) myeloid neoplasms, rather than the conventional thought of MN1-ETV6 fusion formation. We also disclosed the high concomitance of trisomy 8 and 531 Kbps focal 8q duplication in t(12;22)(p13;q12) cases. The new perspective about this entity of disease will enlighten further research to define the mechanism of tumorigenesis and discover effective treatments for MN1-driven malignancies.
Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts
Authors: Steffen Fabio D. , Khier Mokrane , Kowerko Danny , Cunha Richard A. , Börner Richard , Sigel Roland K. O. 
Published: January 2020

AbstractThe fidelity of group II intron self-splicing and retrohoming relies on long-range tertiary interactions between the intron and its flanking exons. By single-molecule FRET, we explore the binding kinetics of the most important, structurally conserved contact, the exon and intron binding site 1 (EBS1/IBS1). A comparison of RNA-RNA and RNA-DNA hybrid contacts identifies transient metal ion binding as a major source of kinetic heterogeneity which typically appears in the form of degenerate FRET states. Molecular dynamics simulations suggest a structural link between heterogeneity and the sugar conformation at the exon-intron binding interface. While Mg2+ ions lock the exon in place and give rise to long dwell times in the exon bound FRET state, sugar puckering alleviates this structural rigidity and likely promotes exon release. The interplay of sugar puckering and metal ion coordination may be an important mechanism to balance binding affinities of RNA and DNA interactions in general.
Charge distribution guided by grain crystallographic orientations in polycrystalline battery materials
Authors: Xu Zhengrui , Jiang Zhisen , Kuai Chunguang , Xu Rong , Qin Changdong , Zhang Yan , Rahman Muhammad Mominur , Wei Chenxi , Nordlund Dennis , Sun Cheng-Jun , Xiao Xianghui , Du Xi-Wen , Zhao Kejie , Yan Pengfei , Liu Yijin , Lin Feng 
Published: January 2020

AbstractArchitecting grain crystallographic orientation can modulate charge distribution and chemomechanical properties for enhancing the performance of polycrystalline battery materials. However, probing the interplay between charge distribution, grain crystallographic orientation, and performance remains a daunting challenge. Herein, we elucidate the spatially resolved charge distribution in lithium layered oxides with different grain crystallographic arrangements and establish a model to quantify their charge distributions. While the holistic “surface-to-bulk” charge distribution prevails in polycrystalline particles, the crystallographic orientation-guided redox reaction governs the charge distribution in the local charged nanodomains. Compared to the randomly oriented grains, the radially aligned grains exhibit a lower cell polarization and higher capacity retention upon battery cycling. The radially aligned grains create less tortuous lithium ion pathways, thus improving the charge homogeneity as statistically quantified from over 20 million nanodomains in polycrystalline particles. This study provides an improved understanding of the charge distribution and chemomechanical properties of polycrystalline battery materials.
Chromatin fibers stabilize nucleosomes under torsional stress
Authors: Kaczmarczyk Artur , Meng He , Ordu Orkide , Noort John van , Dekker Nynke H. 
Published: January 2020

AbstractTorsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.
Two dominant boreal conifers use contrasting mechanisms to reactivate photosynthesis in the spring
Authors: Yang Qi , Blanco Nicolás E. , Hermida-Carrera Carmen , Lehotai Nóra , Hurry Vaughan , Strand Åsa 
Published: January 2020

AbstractBoreal forests are dominated by evergreen conifers that show strongly regulated seasonal photosynthetic activity. Understanding the mechanisms behind seasonal modulation of photosynthesis is crucial for predicting how these forests will respond to changes in seasonal patterns and how this will affect their role in the terrestrial carbon cycle. We demonstrate that the two co-occurring dominant boreal conifers, Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies), use contrasting mechanisms to reactivate photosynthesis in the spring. Scots pine downregulates its capacity for CO2 assimilation during winter and activates alternative electron sinks through accumulation of PGR5 and PGRL1 during early spring until the capacity for CO2 assimilation is recovered. In contrast, Norway spruce lacks this ability to actively switch between different electron sinks over the year and as a consequence suffers severe photooxidative damage during the critical spring period.
Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations
Authors: Xiang Tingting , Lehnert Erik , Jinkerson Robert E. , Clowez Sophie , Kim Rick G. , DeNofrio Jan C. , Pringle John R. , Grossman Arthur R. 
Published: January 2020

AbstractIn cnidarian-Symbiodiniaceae symbioses, algal endosymbiont population control within the host is needed to sustain a symbiotic relationship. However, the molecular mechanisms that underlie such population control are unclear. Here we show that a cnidarian host uses nitrogen limitation as a primary mechanism to control endosymbiont populations. Nitrogen acquisition and assimilation transcripts become elevated in symbiotic Breviolum minutum algae as they reach high-densities within the sea anemone host Exaiptasia pallida. These same transcripts increase in free-living algae deprived of nitrogen. Symbiotic algae also have an elevated carbon-to-nitrogen ratio and shift metabolism towards scavenging nitrogen from purines relative to free-living algae. Exaiptasia glutamine synthetase and glutamate synthase transcripts concomitantly increase with the algal endosymbiont population, suggesting an increased ability of the host to assimilate ammonium. These results suggest algal growth and replication in hospite is controlled by access to nitrogen, which becomes limiting for the algae as their population within the host increases.
Integrin-specific hydrogels modulate transplanted human bone marrow-derived mesenchymal stem cell survival, engraftment, and reparative activities
Authors: Clark Amy Y. , Martin Karen E. , García José R. , Johnson Christopher T. , Theriault Hannah S. , Han Woojin M. , Zhou Dennis W. , Botchwey Edward A. , García Andrés J. 
Published: January 2020

AbstractStem cell therapies are limited by poor cell survival and engraftment. A hurdle to the use of materials for cell delivery is the lack of understanding of material properties that govern transplanted stem cell functionality. Here, we show that synthetic hydrogels presenting integrin-specific peptides enhance the survival, persistence, and osteo-reparative functions of human bone marrow-derived mesenchymal stem cells (hMSCs) transplanted in murine bone defects. Integrin-specific hydrogels regulate hMSC adhesion, paracrine signaling, and osteoblastic differentiation in vitro. Hydrogels presenting GFOGER, a peptide targeting α2β1 integrin, prolong hMSC survival and engraftment in a segmental bone defect and result in improved bone repair compared to other peptides. Integrin-specific hydrogels have diverse pleiotropic effects on hMSC reparative activities, modulating in vitro cytokine secretion and in vivo gene expression for effectors associated with inflammation, vascularization, and bone formation. These results demonstrate that integrin-specific hydrogels improve tissue healing by directing hMSC survival, engraftment, and reparative activities.
zeo19: A thermodynamic database for assessing zeolite stability during the corrosion of nuclear waste immobilization glasses
Authors: Zhen-Wu Bi Yun , Prentice Dale P. , Ryan Joseph V. , Ellison Kirk , Bauchy Mathieu , Sant Gaurav 
Published: January 2020

AbstractStable, durable immobilization of radioactive wastes requires robust understanding of the sub-surface geochemical processes that occur in repository environments. For example, the accelerated dissolution (corrosion) of nuclear waste immobilization glasses (i.e., the so-called “Stage III” corrosion) following the precipitation of zeolitic phases is a significant issue that could result in radionuclide release. However, current uncertainties in establishing the tendency for the persistence of zeolites results in difficulties in estimating the chemical environments and state variables that favor zeolite precipitation. To assess the tendency for Stage III corrosion, we compiled a unified, internally-consistent thermodynamic database to estimate zeolite stability under conditions relevant to nuclear waste repositories (namely, p = 1 bar and T < 95 °C), i.e., for compounds including: analcime, clinoptilolite, mordenite, erionite, thomsonite, bikitaite, brewsterite, dachiardite, epistilbite, ferrierite, gonnardite, harmotome, leonhardite, paranatrolite, tetranatrolite, yugawaralite zeolite X, and zeolite P(Ca). The database, which features both existing and/or newly-derived thermodynamic properties, is integrated with a Gibbs (free) energy minimization (GEM) solver to estimate stable zeolite phase equilibria and their partitioning at equilibrium. The database offers favorable predictions of the solubility of the zeolite phases as a function of temperature. The validity of the database is ascertained by comparing newly-constructed equilibrium activity diagrams with experimental observations of zeolite formation during glass dissolution across conditions encompassing diverse solution chemistries, pH’s, and temperatures.
Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes
Authors: Satoh Yasunari , Asakawa Jun-ichi , Nishimura Mayumi , Kuo Tony , Shinkai Norio , Cullings Harry M. , Minakuchi Yohei , Sese Jun , Toyoda Atsushi , Shimada Yoshiya , Nakamura Nori , Uchimura Arikuni 
Published: January 2020

AbstractThe exposure of germ cells to radiation introduces mutations in the genomes of offspring, and a previous whole-genome sequencing study indicated that the irradiation of mouse sperm induces insertions/deletions (indels) and multisite mutations (clustered single nucleotide variants and indels). However, the current knowledge on the mutation spectra is limited, and the effects of radiation exposure on germ cells at stages other than the sperm stage remain unknown. Here, we performed whole-genome sequencing experiments to investigate the exposure of spermatogonia and mature oocytes. We comparedde novomutations in a total of 24 F1 mice conceived before and after the irradiation of their parents. The results indicated that radiation exposure, 4 Gy of gamma rays, induced 9.6 indels and 2.5 multisite mutations in spermatogonia and 4.7 indels and 3.1 multisite mutations in mature oocytes in the autosomal regions of each F1 individual. Notably, we found two types of deletions, namely, small deletions (mainly 1~12 nucleotides) in non-repeat sequences, many of which showed microhomology at the breakpoint junction, and single-nucleotide deletions in mononucleotide repeat sequences. The results suggest that these deletions and multisite mutations could be a typical signature of mutations induced by parental irradiation in mammals.
GPU acceleration of a model-based iterative method for Digital Breast Tomosynthesis
Authors: Cavicchioli R. , Hu J. Cheng , Loli Piccolomini E. , Morotti E. , Zanni L. 
Published: January 2020

AbstractDigital Breast Tomosynthesis (DBT) is a modern 3D Computed Tomography X-ray technique for the early detection of breast tumors, which is receiving growing interest in the medical and scientific community. Since DBT performs incomplete sampling of data, the image reconstruction approaches based on iterative methods are preferable to the classical analytic techniques, such as the Filtered Back Projection algorithm, providing fewer artifacts. In this work, we consider a Model-Based Iterative Reconstruction (MBIR) method well suited to describe the DBT data acquisition process and to include prior information on the reconstructed image. We propose a gradient-based solver named Scaled Gradient Projection (SGP) for the solution of the constrained optimization problem arising in the considered MBIR method. Even if the SGP algorithm exhibits fast convergence, the time required on a serial computer for the reconstruction of a real DBT data set is too long for the clinical needs. In this paper we propose a parallel SGP version designed to perform the most expensive computations of each iteration on Graphics Processing Unit (GPU). We apply the proposed parallel approach on three different GPU boards, with computational performance comparable with that of the boards usually installed in commercial DBT systems. The numerical results show that the proposed GPU-based MBIR method provides accurate reconstructions in a time suitable for clinical trials.
Identification of quantitative trait loci (QTL) controlling resistance to pea weevil (Bruchus pisorum) in a high-density integrated DArTseq SNP-based genetic map of pea
Authors: Aznar-Fernández Thais , Barilli Eleonora , Cobos María J. , Kilian Andrzej , Carling Jason , Rubiales Diego 
Published: January 2020

AbstractPea weevil (Bruchus pisorum) is a damaging insect pest affecting pea (Pisum sativum) production worldwide. No resistant cultivars are available, although some levels of incomplete resistance have been identified inPisumgermplasm. To decipher the genetic control underlying the resistance previously identify inP. sativumssp.syriacum, a recombinant inbred line (RIL F8:9) population was developed. The RIL was genotyped through Diversity Arrays Technology PL’s DArTseq platform and screened under field conditions for weevil seed infestation and larval development along 5 environments. A newly integrated genetic linkage map was generated with a subset of 6,540 markers, assembled into seven linkage groups, equivalent to the number of haploid pea chromosomes. An accumulated distance of 2,503 cM was covered with an average density of 2.61 markers cM−1. The linkage map allowed the identification of three QTLs associated to reduced seed infestation along LGs I, II and IV. In addition, a QTL for reduced larval development was also identified in LGIV. Expression of these QTLs varied with the environment, being particularly interesting QTLBpSI.IIIthat was detected in most of the environments studied. This high-saturated pea genetic map has also allowed the identification of seven potential candidate genes co-located with QTLs for marker-assisted selection, providing an opportunity for breeders to generate effective and sustainable strategies for weevil control.
Structural analysis of retinal blood vessels in patients with COPD during a pulmonary rehabilitation program
Authors: Vaes Anouk W. , Spruit Martijn A. , Van Keer Karel , Barbosa-Breda João , Wouters Emiel F. M. , Franssen Frits M. E. , Theunis Jan , De Boever Patrick 
Published: January 2020

AbstractCardiovascular diseases are frequently present in chronic obstructive pulmonary disease (COPD). Population-based studies found associations between retinal vessel diameters and cardiovascular health, but it is unknown whether this also applies to COPD patients. Therefore, we measured retinal vessel diameters in COPD patients and aimed to determine the association with cardiovascular risk factors, lung function, and functional outcomes. In addition, we investigated whether an exercise-based pulmonary rehabilitation (PR) program would change retinal vessel diameters, as a proxy for improved microvascular health. Demographics and clinical characteristics, including pulmonary function, exercise capacity, blood pressure, blood measurements and level of systemic inflammation were obtained from 246 patients during routine assessment before and after PR. Retinal vessel diameters were measured from digital retinal images. Older age and higher systolic blood pressure were associated with narrower retinal arterioles (β: −0.224; p = 0.042 and β: −0.136; p < 0.001, respectively). Older age, higher systolic blood pressure and lower level of systemic inflammation were associated with narrower retinal venules (β: −0.654; −0.229; and −13.767, respectively; p < 0.05). No associations were found between retinal vessel diameters and lung function parameters or functional outcomes. After PR, no significant changes in retinal venular or arteriolar diameter were found. To conclude, retinal vessel diameters of COPD patients were significantly associated with systolic blood pressure and systemic inflammation, whilst there was no evidence for an association with lung function parameters, functional outcomes or other cardiovascular risk factors. Furthermore, an exercise-based PR program did not affect retinal vessel diameter.
Comparative study of stenting and ostium packing in Endoscopic Dacryocystorhinostomy for Primary Acquired Nasolacrimal Duct Obstruction
Authors: Chin Joyce , Lam Vincent , Chan Regine , Li C. L. , Yeung Luke , Law Antony , Young Alvin , Yuen Hunter , Ali Mohammad Javed , Chong Kelvin K. L. 
Published: January 2020

AbstractIn this retrospective study, we compared the efficacy and safety of mechanical adjuvants in mucosal-sparing, mechanical endoscopic dacryocystorhinostomy (MMED) for primary acquired nasolacrimal duct obstruction (PANDO). 116 adult patients (90 female) aged 61 ± 11 received one of the following after MMED without topical mitomycin: no stenting or packing (group 1, n = 25), 1-week ostium packing by ribbon gauze (group 2, n = 29) or non-medicated absorbable gelatin sponge (group 3, n = 25), 8-week bicanalicular stenting (group 4, n = 28). 104 patients(92%) provided 12-month outcomes. Number of patients, age, gender, surgeon, and osteotomy size were comparable among groups (p = 0.4–0.9). Marginal significance was found in anatomical (group 1:80%, group 2:96.6%, group 3:96%, group 4:96.4%, p = 0.05) but not functional success (group 1:85%, group 2:85.7%, group 3:83.3%, group 4:88.9%, p = 0.75) at postoperative 12-month. Patients receiving any packing or stenting achieved better anatomical (96% versus 80%, p = 0.015) but not functional success (85% versus 86%, p = 0.90) compared to those receiving none. More patients receiving stenting developed postoperative granuloma than those who did not (87% versus 63%, p = 0.04). 1-week ostium packing was found to be as effective as 8-week bicanalicular intubation in improving anatomical outcome after MMED for PANDO. Functional outcome, however, did not differ among patients receiving mechanical adjuvant or not.
Perceived stress and non-alcoholic fatty liver disease in apparently healthy men and women
Authors: Kang Danbee , Zhao Di , Ryu Seungho , Guallar Eliseo , Cho Juhee , Lazo Mariana , Shin Hocheol , Chang Yoosoo , Sung Eunju 
Published: January 2020

AbstractPsychological stress may have adverse metabolic effects and induce unhealthy behaviors, but the role of stress in the development of non-alcoholic fatty liver disease (NAFLD) is largely unexplored. We investigated the association between perceived stress and the prevalence of NAFLD in a large sample of apparently healthy men and women. We performed a cross-sectional study of 171,321 adults who underwent health screening examination between 2011 and 2013 in one health screening center. Perceived stress was assessed using the short version of the Perceived Stress Inventory (PSI). NAFLD was assessed using ultrasonography in the absence of excessive alcohol use or any other identifiable cause of liver disease. The prevalence of NAFLD was 27.8%. In fully-adjusted multivariable models, the odds ratio (95% confidence intervals) for NAFLD comparing participants in the 5th quintile of PSI score (≥23) with those in the lowest quintile (<12) was 1.17 (1.11, 1.22), with a moderately increased prevalence of NALFD across quintiles of PSI score. The positive association between PSI score and NAFLD was observed in all subgroups analyzed, although the association was stronger in men compared to women (p interaction <0.001), and in obese compared to non-obese (p interaction 0.005). In this large study of apparently healthy men and women, higher perceived stress was independently associated with an increased prevalence of NAFLD, supporting a possible relationship between perceived stress and NAFLD. Prospective study is needed to elucidate mediating mechanisms to warrant stress management to reduce NAFLD.
A method to disentangle and quantify host anabolic turnover in photosymbiotic holobionts with subcellular resolution
Authors: Gibbin Emma , Banc-Prandi Guilhem , Fine Maoz , Comment Arnaud , Meibom Anders 
Published: January 2020

AbstractA wide range of organisms host photosynthesizing symbionts. In these animals the metabolic exchange between host and symbionts has prevented in situ host anabolic turnover to be studied without the confounding effect of translocated photosynthates. Using the symbiotic coral Stylophora pistillata as a model organism and [1-13C]-pyruvate and [2,3-13C]-pyruvate in different incubation conditions (light, light + DCMU, and darkness), we employed NanoSIMS isotopic imaging to quantify host anabolism, with and without translocated metabolites from their photosynthesizing dinoflagellate symbionts. Under our experimental conditions, host de novo lipid synthesis accounted for ~40% of the total holobiont lipid reserve, and dinoflagellate recycling of metabolic 13CO2 enhanced host tissue 13C-enrichment by 13–22% in the epidermis, 40–58% in the gastrodermis, and 135–169% in host lipid bodies. Furthermore, we show that host anabolic turnover in different tissue structures differs, in a manner consistent with the localisation, function and cellular composition of these structures.