bluuebunny/crossref_metadata_2025_split huggingface dataset:
CXCR4/CXCL12 axis counteracts hematopoietic stem cell exhaustion through selective protection against oxidative stress
Authors: Zhang Yanyan , Dépond Mallorie , He Liang , Foudi Adlen , Kwarteng Edward Owusu , Lauret Evelyne , Plo Isabelle , Desterke Christophe , Dessen Philippe , Fujii Nobutaka , Opolon Paule , Herault Olivier , Solary Eric , Vainchenker William , Joulin Virginie , Louache Fawzia , Wittner Monika 
Published: November 2016

AbstractHematopoietic stem cells (HSCs) undergo self-renewal to maintain hematopoietic homeostasis for lifetime, which is regulated by the bone marrow (BM) microenvironment. The chemokine receptor CXCR4 and its ligand CXCL12 are critical factors supporting quiescence and BM retention of HSCs. Here, we report an unknown function of CXCR4/CXCL12 axis in the protection of HSCs against oxidative stress. Disruption of CXCR4 receptor in mice leads to increased endogenous production of reactive oxygen species (ROS), resulting in p38 MAPK activation, increased DNA double-strand breaks and apoptosis leading to marked reduction in HSC repopulating potential. Increased ROS levels are directly responsible for exhaustion of the HSC pool and are not linked to loss of quiescence of CXCR4-deficient HSCs. Furthermore, we report that CXCL12 has a direct rescue effect on oxidative stress-induced HSC damage at the mitochondrial level. These data highlight the importance of CXCR4/CXCL12 axis in the regulation of lifespan of HSCs by limiting ROS generation and genotoxic stress.
Conspecific Leaf Litter-Mediated Effect of Conspecific Adult Neighborhood on Early-Stage Seedling Survival in A Subtropical Forest
Authors: Liu Heming , Shen Guochun , Ma Zunping , Yang Qingsong , Xia Jianyang , Fang Xiaofeng , Wang Xihua 
Published: November 2016

AbstractConspecific adults have strong negative effect on the survival of nearby early-stage seedlings and thus can promote species coexistence by providing space for the regeneration of heterospecifics. The leaf litter fall from the conspecific adults, and it could mediate this conspecific negative adult effect. However, field evidence for such effect of conspecific leaf litter remains absent. In this study, we used generalized linear mixed models to assess the effects of conspecific leaf litter on the early-stage seedling survival of four dominant species (Machilus leptophylla, Litsea elongate, Acer pubinerve and Distylium myricoides) in early-stage seedlings in a subtropical evergreen broad-leaved forest in eastern China. Our results consistently showed that the conspecific leaf litter of three species negatively affected the seedling survival. Meanwhile, the traditional conspecific adult neighborhood indices failed to detect this negative conspecific adult effect. Our study revealed that the accumulation of conspecific leaf litter around adults can largely reduce the survival rate of nearby seedlings. Ignoring it could result in underestimation of the importance of negative density dependence and negative species interactions in the natural forest communities.
Sigma-1 Receptor Agonism Promotes Mechanical Allodynia After Priming the Nociceptive System with Capsaicin
Authors: Entrena J. M. , Sánchez-Fernández C. , Nieto F. R. , González-Cano R. , Yeste S. , Cobos E. J. , Baeyens J. M. 
Published: November 2016

AbstractSigma-1 receptor antagonists promote antinociception in several models of pain, but the effects of sigma-1 agonists on nociception (particularly when the nociceptive system is primed) are not so well characterized; therefore we evaluated the effects of sigma-1 agonists on pain under different experimental conditions. The systemic administration of the selective sigma-1 agonists (+)-pentazocine and PRE-084, as well as the nonselective sigma-1 agonist carbetapentane (used clinically as an antitussive drug), did not alter sensitivity to mechanical stimulation under baseline conditions. However, they greatly promoted secondary mechanical allodynia after priming the nociceptive system with capsaicin. These effects of sigma-1 agonists were consistent in terms potency with the affinities of these drugs for sigma-1 receptors, were reversed by sigma-1 antagonists, and were not observed in sigma-1 knockout mice, indicating that they are sigma-1-mediated. Repeated systemic treatment with PRE-084 induced proallodynic effects even 24 h after treatment completion, but only after the nociceptive system was primed. However, neither the presence of this drug in the organism nor changes in sigma-1 receptor expression in areas involved in pain processing explains its long-term effects, suggesting that sustained sigma-1 agonism induces plastic changes in the nociceptive system that promote nociception.
A holistic approach to dissecting SPARC family protein complexity reveals FSTL-1 as an inhibitor of pancreatic cancer cell growth
Authors: Viloria Katrina , Munasinghe Amanda , Asher Sharan , Bogyere Roberto , Jones Lucy , Hill Natasha J. 
Published: November 2016

AbstractSPARC is a matricellular protein that is involved in both pancreatic cancer and diabetes. It belongs to a wider family of proteins that share structural and functional similarities. Relatively little is known about this extended family, but evidence of regulatory interactions suggests the importance of a holistic approach to their study. We show that Hevin, SPOCKs, and SMOCs are strongly expressed within islets, ducts, and blood vessels, suggesting important roles for these proteins in the normal pancreas, while FSTL-1 expression is localised to the stromal compartment reminiscent of SPARC. In direct contrast to SPARC, however, FSTL-1 expression is reduced in pancreatic cancer. Consistent with this, FSTL-1 inhibited pancreatic cancer cell proliferation. The complexity of SPARC family proteins is further revealed by the detection of multiple cell-type specific isoforms that arise due to a combination of post-translational modification and alternative splicing. Identification of splice variants lacking a signal peptide suggests the existence of novel intracellular isoforms. This study underlines the importance of addressing the complexity of the SPARC family and provides a new framework to explain their controversial and contradictory effects. We also demonstrate for the first time that FSTL-1 suppresses pancreatic cancer cell growth.
Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa
Authors: Zhong Zilin , Yan Min , Sun Wan , Wu Zehua , Han Liyun , Zhou Zheng , Zheng Fang , Chen Jianjun 
Published: November 2016

AbstractRetinitis pigmentosa (RP) is a heterogeneous set of hereditary eye diseases, characterized by selective death of photoreceptor cells in the retina, resulting in progressive visual impairment. Approximately 20–40% of RP cases are autosomal dominant RP (ADRP). In this study, a Chinese ADRP family previously localized to the region between D1S2819 and D1S2635 was sequenced via whole-exome sequencing and a variant c.1345C > G (p.R449G) was identified in PRPF3. The Sanger sequencing was performed in probands of additional 95 Chinese ADRP families to investigate the contribution of PRPF3 to ADRP in Chinese population and another variant c.1532A > C (p.H511P) was detected in one family. These two variants, co-segregate with RP in two families respectively and both variants are predicted to be pathological. This is the first report about the spectrum of PRPF3 mutations in Chinese population, leading to the identification of two novel PRPF3 mutations. Only three clustered mutations in PRPF3 have been identified so far in several populations and all are in exon 11. Our study expands the spectrum of PRPF3 mutations in RP. We also demonstrate that PRPF3 mutations are responsible for 2.08% of ADRP families in this cohort indicating that PRPF3 mutations might be relatively rare in Chinese ADRP patients.
Neil3 induced neurogenesis protects against prion disease during the clinical phase
Authors: Jalland Clara M. O. , Scheffler Katja , Benestad Sylvie L. , Moldal Torfinn , Ersdal Cecilie , Gunnes Gjermund , Suganthan Rajikala , Bjørås Magnar , Tranulis Michael A. 
Published: November 2016

AbstractBase excision repair (BER) is the major pathway for repair of oxidative DNA damage. Mice with genetic knockout of the BER enzyme Neil3 display compromised neurogenesis in the sub-ventricular zone of the lateral ventricle and sub-granular layer of the dentate gyrus of the hippocampus. To elucidate the impact of oxidative DNA damage-induced neurogenesis on prion disease we applied the experimental prion disease model on Neil3-deficient mice. The incubation period for the disease was similar in both wild type and Neil3−/− mice and the overall neuropathology appeared unaffected by Neil3 function. However, disease in the Neil3−/− mice was of shorter clinical duration. We observed a mildly reduced astrogliosis in the hippocampus and striatum in the Neil3-deficient mice. Brain expression levels of neuronal progenitor markers, nestin (Nestin), sex determining region Box 2 (Sox2), Class III beta-tubulin (Tuj1) decreased towards end-stage prion disease whereas doublecortin (Dcx) levels were less affected. Neuronal nuclei (NeuN), a marker for mature neurons declined during prion disease and more pronounced in the Neil3−/− group. Microglial activation was prominent and appeared unaffected by loss of Neil3. Our data suggest that neurogenesis induced by Neil3 repair of oxidative DNA damage protects against prion disease during the clinical phase.
Slowing down light using a dendritic cell cluster metasurface waveguide
Authors: Fang Z. H. , Chen H. , Yang F. S. , Luo C. R. , Zhao X. P. 
Published: November 2016

AbstractSlowing down or even stopping light is the first task to realising optical information transmission and storage. Theoretical studies have revealed that metamaterials can slow down or even stop light; however, the difficulty of preparing metamaterials that operate in visible light hinders progress in the research of slowing or stopping light. Metasurfaces provide a new opportunity to make progress in such research. In this paper, we propose a dendritic cell cluster metasurface consisting of dendritic structures. The simulation results show that dendritic structure can realise abnormal reflection and refraction effects. Single- and double-layer dendritic metasurfaces that respond in visible light were prepared by electrochemical deposition. Abnormal Goos-Hänchen (GH) shifts were experimentally obtained. The rainbow trapping effect was observed in a waveguide constructed using the dendritic metasurface sample. The incident white light was separated into seven colours ranging from blue to red light. The measured transmission energy in the waveguide showed that the energy escaping from the waveguide was zero at the resonant frequency of the sample under a certain amount of incident light. The proposed metasurface has a simple preparation process, functions in visible light, and can be readily extended to the infrared band and communication wavelengths.
A Retrospective Analysis on Two-week Short-course Pre-operative Radiotherapy in Elderly Patients with Resectable Locally Advanced Rectal Cancer
Authors: Shi Chen , Zhou Hao , Li Xiaofan , Cai Yong 
Published: November 2016

AbstractTo validate that a two-week short-course pre-operative radiotherapy regimen is feasible, safe, and effective for the management of elderly patients with locally advanced rectal cancer (LARC), we retrospectively analyzed 99 radiotherapy-naive patients ≥70 years of age with LARC. Patients received pelvic radiation therapy (3D-CRT 30Gy/10f/2w) followed by TME surgery; some patients received adjuvant chemotherapy. The primary endpoint was OS, while the secondary endpoints were DFS, safety and response rate. The median follow-up time was 5.1 years. The 5-year OS and DFS rates were 58.3% and 51.2%, respectively. The completion rate of radiotherapy (RT) was 99.0% (98 of 99). Grade 3 acute adverse events, which resulted from RT, occurred in only 1 patient (1.0%). In addition, no grade 4 acute adverse events induced by RT were observed. All 99 patients (100%) were able to undergo R0 surgical resection, and 68.6% of the patients received sphincter-sparing surgery. The rate of occurrence of clinically relevant post-operative complications was 12.1%. Three patients (3.0%) achieved pathologic complete responses, and forty-three patients (43.4%) achieved pathologic partial responses. The rates of T-downsizing and N-downstaging were 30.3% and 55.7%, respectively. Therefore, we believe that a two-week short-course pre-operative radiotherapy is feasible in elderly patients with resectable LARC.
Circulating periostin in relation to insulin resistance and nonalcoholic fatty liver disease among overweight and obese subjects
Authors: Yang Zhen , Zhang Hongmei , Niu Yixin , Zhang Weiwei , Zhu Lingfei , Li Xiaoyong , Lu Shuai , Fan Jiangao , Li Xiaoying , Ning Guang , Qin Li , Su Qing 
Published: November 2016

AbstractRecent study showed periostin play a pivotal role in abnormal liver triglyceride (TG) accumulation and in the development of obesity-related liver fat accumulation. However, little is known regarding whether periostin plays a key role in the heightened prevalence of NAFLD and other metabolic phenotypes among large-scale populations. A cross-sectional sample of 8850 subjects aged 40 yr or older from China were evaluated in this study. Serum periostin was measured by ELISA methods. The diagnosis of NAFLD by liver ultrasonic examination. Among overweight and obese subjects, NAFLD subjects had higher serum periostin levels than those without NAFLD (126.75 ng/ml vs. 75.96 ng/ml, p < 0.001). Periostin was associated with a higher risk for NAFLD (OR 1.75 for each SD increase in periostin, 95% CI 1.04–3.37, p < 0.001) among overweight and obese subjects after confounder adjustment. Furthermore, periostin levels among overweight and obese subjects were correlated with aspartate aminotransferase (r = 0.102, p = 0.004), alanine aminotransferase (r = 0.108, p = 0.003), waist circumference (r = 0.111, p = 0.002), homeostasis model assessment index-insulin resistance (r = 0.154, p < 0.001) and fasting plasma insulin (r = 0.098, p = 0.006), TG (r = 0.117, p = 0.001). Elevated circulating periostin level was associated with an increased risk of having NAFLD and insulin resistance among overweight and obese individuals.
From Quasi-Planar B56 to Penta-Ring Tubular Ca©B56: Prediction of Metal-Stabilized Ca©B56 as the Embryo of Metal-Doped Boron α-Nanotubes
Authors: Tian Wen-Juan , Chen Qiang , Tian Xin-Xin , Mu Yue-Wen , Lu Hai-Gang , Li Si-Dian 
Published: November 2016

AbstractMotifs of planar metalloborophenes, cage-like metalloborospherenes, and metal-centered double-ring tubular boron species have been reported. Based on extensive first-principles theory calculations, we present herein the possibility of doping the quasi-planar C2v B56 (A-1) with an alkaline-earth metal to produce the penta-ring tubular Ca©B56 (B-1) which is the most stable isomer of the system obtained and can be viewed as the embryo of metal-doped (4,0) boron α-nanotube Ca©BNT(4,0) (C-1). Ca©BNT(4,0) (C-1) can be constructed by rolling up the most stable boron α-sheet and is predicted to be metallic in nature. Detailed bonding analyses show that the highly stable planar C2v B56 (A-1) is the boron analog of circumbiphenyl (C38H16) in π-bonding, while the 3D aromatic C4v Ca©B56 (B-1) possesses a perfect delocalized π system over the σ-skeleton on the tube surface. The IR and Raman spectra of C4v Ca©B56 (B-1) and photoelectron spectrum of its monoanion C4v Ca©B56− are computationally simulated to facilitate their spectroscopic characterizations.
Structure of Herbig AeBe disks at the milliarcsecond scale
Authors: Lazareff B. , Berger J.-P. , Kluska J. , Le Bouquin J.-B. , Benisty M. , Malbet F. , Koen C. , Pinte C. , Thi W.-F. , Absil O. , Baron F. , Delboulbé A. , Duvert G. , Isella A. , Jocou L. , Juhasz A. , Kraus S. , Lachaume R. , Ménard F. , Millan-Gabet R. , Monnier J. D. , Moulin T. , Perraut K. , Rochat S. , Soulez F. , Tallon M. , Thiébaut E. , Traub W. , Zins G. 
Published: November 2016

Context. It is now generally accepted that the near-infrared excess of Herbig AeBe stars originates in the dust of a circumstellar disk.
Aims. The aims of this article are to infer the radial and vertical structure of these disks at scales of order 1 au, and the properties of the dust grains.
Methods. The program objects (51 in total) were observed with the H-band (1.6 μm) PIONIER/VLTI interferometer. The largest baselines allowed us to resolve (at least partially) structures of a few tenths of an au at typical distances of a few hundred parsecs. Dedicated UBVRIJHK photometric measurements were also obtained. Spectral and 2D geometrical parameters are extracted via fits of a few simple models: ellipsoids and broadened rings with azimuthal modulation. Model bias is mitigated by parallel fits of physical disk models. Sample statistics were evaluated against similar statistics for the physical disk models to infer properties of the sample objects as a group.
Results. We find that dust at the inner rim of the disk has a sublimation temperature Tsub ≈ 1800 K. A ring morphology is confirmed for approximately half the resolved objects; these rings are wide δr/r ≥ 0.5. A wide ring favors a rim that, on the star-facing side, looks more like a knife edge than a doughnut. The data are also compatible with the combination of a narrow ring and an inner disk of unspecified nature inside the dust sublimation radius. The disk inner part has a thickness z/r ≈ 0.2, flaring to z/r ≈ 0.5 in the outer part. We confirm the known luminosity-radius relation; a simple physical model is consistent with both the mean luminosity-radius relation and the ring relative width; however, a significant spread around the mean relation is present. In some of the objects we find a halo component, fully resolved at the shortest interferometer spacing, that is related to the HAeBe class.
Microbial innovations in the world of food†
Authors: Kawasaki Hisashi , Ueda Kenji 
Published: November 2016

Abstract
Technological developments in Japan based on the results of microbial research were a major pillar supporting the postwar industrial revolution. The wellspring of these advancements was the sophisticated technology used in traditional brewing, a foundation of the characteristic Japanese food culture. In this manuscript, we will describe the fermentative production of amino acids and nucleic acids following the discovery of the umami component so distinct in Japanese cuisine, which finally revealed the true power of microbial production. Thereafter, we will describe acetic acid production stemming from brewed vinegar production and the fermentative production of some other organic acids. Finally, we will delve into the massive scale of innovations achieved by the discovery of valuable micro-organisms and how they have affected the field of food.
The path to producing pharmaceuticals from natural products uncovered by academia—from the perspective of a science coordinator†
Authors: Fujie Akihiko 
Published: November 2016

Abstract
To actualize the invention of all-Japanese medicines, the Department of Innovative Drug Discovery and Development (iD3) in the Japan Agency for Medical Research and Development (AMED) serves as the headquarters for the Drug Discovery Support Network. iD3 assists with creating research strategies for the seeds of medicines discovered by academia and provides technological support, intellectual property management, and aid for applying the seeds through industry-led efforts. In this review, from the perspective of a science coordinator, I will describe the current activities of the drug discovery support network and iD3 as well as the challenges and future developments of pharmaceutical research and development using the natural product drug discovery method.
A protease/peptidase from culture medium of Flammulina velutipes that acts on arabinogalactan-protein
Authors: Yoshimi Yoshihisa , Sugawara Yumi , Hori Chiaki , Igarashi Kiyohiko , Kaneko Satoshi , Tsumuraya Yoichi , Kotake Toshihisa 
Published: November 2016

Abstract
Arabinogalactan-proteins (AGPs) are highly diverse plant proteoglycans found on the plant cell surface. AGPs have large arabinogalactan (AG) moieties attached to a core-protein rich in hydroxyproline (Hyp). The AG undergoes hydrolysis by various glycoside hydrolases, most of which have been identified, whereas the core-proteins is presumably degraded by unknown proteases/peptidases secreted from fungi and bacteria in nature. Although several enzymes hydrolyzing other Hyp-rich proteins are known, the enzymes acting on the core-proteins of AGPs remain to be identified. The present study describes the detection of protease/peptidase activity toward AGP core-proteins in the culture medium of winter mushroom (Flammulina velutipes) and partial purification of the enzyme by several conventional chromatography steps. The enzyme showed higher activity toward Hyp residues than toward proline and alanine residues and acted on core-proteins prepared from gum arabic. Since the activity was inhibited in the presence of Pefabloc SC, the enzyme is probably a serine protease.
Aloe QDM complex enhances specific cytotoxic T lymphocyte killing in vivo in metabolic disease mice
Authors: Lee Youngjoo , Kim Jiyeon , An Jinho , Lee Heetae , Kong Hyunseok , Song Youngcheon , Shin Eunju , Do Seon-Gil , Lee Chong-Kil , Kim Kyungjae 
Published: November 2016

Abstract
We developed spontaneous diet-induced metabolic disease in mice by feeding them a high-fat diet for 23 weeks and administered Aloe QDM complex for 16 weeks to examine its restorative effect on immune disorders and metabolic syndrome. A series of immune functional assays indicated Aloe QDM complex enhanced lymphocyte proliferation and antigen-specific immunity as determined by the restored functions of cytotoxic T lymphocytes (CTL) and IgG production. The elevated serum TNF-α level was also regulated by Aloe QDM complex treatment, which suggested its complex therapeutic potential. As for metabolic phenotypes, oral administration of Aloe QDM complex significantly improved diabetic symptoms, including high fasting glucose levels and glucose tolerance, and distinctly alleviated lipid accumulation in adipose and hepatic tissue. The simultaneous restoration of Aloe QDM complex on metabolic syndrome and host immune dysfunction, especially on the specific CTL killing was first elucidated in our study.
RECKONER: read error corrector based on KMC
Authors: Długosz Maciej , Deorowicz Sebastian 
Published: November 2016

Abstract

Summary
Presence of sequencing errors in data produced by next-generation sequencers affects quality of downstream analyzes. Accuracy of them can be improved by performing error correction of sequencing reads. We introduce a new correction algorithm capable of processing eukaryotic close to 500 Mbp-genome-size, high error-rated data using less than 4 GB of RAM in about 35 min on 16-core computer.

Availability and Implementation
Program is freely available at http://sun.aei.polsl.pl/REFRESH/reckoner.

Supplementary information
Supplementary data are available at Bioinformatics online.