bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dosimetric comparison of linac-based stereotactic fractionated radiotherapy techniques for pituitary adenoma and craniopharyngioma
Authors: Varghese Sunitha S. , Goudar Giriyappa , Abraham Susen , Peace Timothy , Singh Rabi R. , Backianathan Sevamani 
Published: February 2018

AbstractAimTo compare the dosimetric outcomes of linear accelerator-based stereotactic radiotherapy (SRT) techniques—static conformal field (SCF), static conformal arc (SCA) and dynamic conformal arc (DCA), for treating pituitary adenoma and craniopharyngioma.Materials and methodsComputer image sets of 20 patients with pituitary adenoma or craniopharyngioma and treated with post-operative SRT were selected for this study. For each dataset, three SRT plans, with SCF, SCA and DCA techniques were generated using Brain LAB, iPlan RT V.4.5.3, TPS software. The conformity index (CI), homogeneity index (HI), quality of coverage of the target, dose–volume histograms for the target and organs at risk (OARs) and the time taken to deliver treatment was compared across three sets of plan.ResultsThere were 12 patients with pituitary adenoma and eight with craniopharyngioma. The CI and HI were comparable across three techniques. The quality of coverage was superior in DCA technique. OARs were better spared in SCF and DCA techniques. Time taken to deliver treatment was least in SCF technique.ConclusionsThe linac-based SRT techniques SCF, SCA and DCA are efficient in delivering highly conformal and homogenous dose to the target in pituitary adenoma and craniopharyngioma. Among these three techniques, SCF and DCA had acceptable quality of coverage. The dose received by OARs was least in the SCF technique.
hiPSC-derived neural stem cells from patients with schizophrenia induce an impaired angiogenesis
Authors: Casas Bárbara S. , Vitória Gabriela , do Costa Marcelo N. , Madeiro da Costa Rodrigo , Trindade Pablo , Maciel Renata , Navarrete Nelson , Rehen Stevens K. , Palma Verónica 
Published: February 2018

AbstractSchizophrenia is a neurodevelopmental disease characterized by cerebral connectivity impairment and loss of gray matter. It was described in adult schizophrenia patients (SZP) that concentration of VEGFA, a master angiogenic factor, is decreased. Recent evidence suggests cerebral hypoperfusion related to a dysfunctional Blood Brain Barrier (BBB) in SZP. Since neurogenesis and blood-vessel formation occur in a coincident and coordinated fashion, a defect in neurovascular development could result in increased vascular permeability and, therefore, in poor functionality of the SZP’s neurons. Here, we characterized the conditioned media (CM) of human induced Pluripotent Stem Cells (hiPSC)-derived Neural Stem Cells of SZP (SZP NSC) versus healthy subjects (Ctrl NSC), and its impact on angiogenesis. Our results reveal that SZP NSC have an imbalance in the secretion and expression of several angiogenic factors, among them non-canonical neuro-angiogenic guidance factors. SZP NSC migrated less and their CM was less effective in inducing migration and angiogenesis both in vitro and in vivo. Since SZP originates during embryonic brain development, our findings suggest a defective crosstalk between NSC and endothelial cells (EC) during the formation of the neuro-angiogenic niche.
The interactome and spatial redistribution feature of Ca2+ receptor protein calmodulin reveals a novel role in invadopodia-mediated invasion
Authors: Li Tao , Yi Li , Hai Long , Ma Haiwen , Tao Zhennan , Zhang Chen , Abeysekera Iruni Roshanie , Zhao Kai , Yang Yihan , Wang Wei , Liu Bo , Yu Shengping , Tong Luqing , Liu Peidong , Zhu Meng , Ren Bingcheng , Lin Yu , Zhang Kai , Cheng Cheng , Huang Yubao , Yang Xuejun 
Published: February 2018

AbstractNumerous studies have shown that calmodulin (CaM) is a major regulator of calcium-dependent signaling, which regulates cell proliferation, programmed cell death, and autophagy in cancer. However, limited information is available on mechanisms underlying the effect of CaM on the invasive property of glioblastoma multiforme (GBM) cells, especially with respect to invadopodia formation. In this study, we find that CaM serves as a prognostic factor for GBM, and it is strongly associated with the invasive nature of this tumor. Results of preliminary experiments indicated that CaM concentration was significantly correlated with the invasive capacity of and invadopodia formation by different GBM cell lines. CaM inhibition via a small hairpin RNA or a pharmacological inhibitor significantly disrupted invadopodia formation and MMP activity and downregulated vimentin expression. Moreover, CaM knockdown exerted a strong anti-invasive effect on GBM in vivo. Interestingly, epidermal growth factor treatment promoted CaM redistribution from the nucleus to the cytoplasm, eventually activating invadopodia-associated proteins by binding to them via their cytosolic-binding sites. Moreover, CaM inhibition suppressed the activation of invadopodia-associated proteins. Thus, our findings provide a novel therapeutic strategy to impede GBM invasion by inhibiting invadopodia formation, and shed light on the spatial organization of CaM signals during GBM invasion.
Erythrocyte glutathione transferase in kidney transplantation: a probe for kidney detoxification efficiency
Authors: Bocedi Alessio , Noce Annalisa , Rovella Valentina , Marrone Giulia , Cattani Giada , Iappelli Massimo , De Paolis Paolo , Iaria Giuseppe , Sforza Daniele , Gallù Mariacarla , Tisone Giuseppe , Di Daniele Nicola , Ricci Giorgio 
Published: February 2018

AbstractErythrocyte glutathione transferase (e-GST) is overexpressed in case of increased blood toxicity and its level correlates with the kidney disease progression. Thus, it represents a probe of kidney efficiency against circulating toxins. We measured the activity of e-GST in patients with transplant kidney from living and cadaver donors, correlated its level to biochemical parameters of kidney function, and measured the level of oxidized albumin as a probe of oxidative stress using a new simple procedure. Interestingly, the activity of e-GST in transplant patients from cadaver donors (N = 153) is very high (11.7 U/gHb) compared to healthy subjects (N = 80) ( 5.6 U/gHb). Lower values were observed in transplant patients with kidney from living donors (N = 16) (9.8 U/gHb). Except for steroids, no correlation has been found with the immunosuppressive therapies and routine clinical and laboratory parameters. Also serum oxidized albumin, which reveals oxidative stress, is significantly higher in transplant patients from cadaver donors (53%) compared to that from living donors (36%). Overall, these data indicate that most of transplant kidneys from cadavers lost part of the detoxifying power against circulating toxins and suffer a relevant oxidative stress compared to those coming from living donors. A case report suggests that e-GST could represent a very early marker of incipient graft rejection. In conclusion, e-GST may be used to check the decline or maintenance of the kidney detoxification competence during post-transplantation course.
Calpain7 impairs embryo implantation by downregulating β3-integrin expression via degradation of HOXA10
Authors: Yan Qiang , Huang Chenyang , Jiang Yue , Shan Huizhi , Jiang Ruiwei , Wang Junxia , Liu Jingyu , Ding Lijun , Yan Guijun , Sun Haixiang 
Published: February 2018

AbstractEndometriosis (ENDO) is a common gynecological disease that causes infertility in many women. Previous studies noted that the dysregulation of Homeo box A10 (HOXA10) in the endometrium of women with ENDO was involved in the failure of embryo implantation. However, the mechanism by which HOXA10 expression is reduced in women with ENDO is still poorly understood. Here we found that a member of the calcium (Ca2+)-dependent cysteine protease family calpain7 (CAPN7), negatively correlated with HOXA10, was highly expressed in the endometrium of infertile women with ENDO and was significantly downregulated during the window of embryo implantation in mice. Overexpression of CAPN7 in Ishikawa cells or in the uterus of mice inhibited embryo implantation in vitro and in vivo. In the current study, we identified a sequence rich in proline, glutamic acid, serine, and threonine (PEST sequence) that enhanced the Ca2+-dependent degradation of HOXA10 by CAPN7. Furthermore, the interaction between HOXA10 and CAPN7 repressed the transcriptional activity and protein stability of HOXA10. In contrast, the administration of the calpain inhibitor ALLN reversed the CAPN7-induced HOXA10 degradation. Moreover, truncation of the PEST motif in HOXA10 abolished its CAPN7-dependent proteolysis. These studies reveal a novel pattern of HOXA10 regulation via PEST sequence-mediated calpain proteolysis that was demonstrated to be reversed by a calpain inhibitor. Thus, the inhibition of CAPN7-induced HOXA10 degradation may represent a novel potential therapeutic method to improve impaired embryo implantation in women with ENDO.
Common medium versus advanced IVF medium for cryopreserved oocytes in heterologous cycles
Authors: Poverini R. , Lisi R. , Lisi F. , Berlinghieri V. , Bielli W. , Carfagna P. , Costantino A. , Iacomino D. , Nicodemo G. 
Published: February 2018

AbstractGranulocyte-macrophage colony-stimulation factor plays different crucial roles during embryo implantation and subsequent development. Here we aimed to evaluate the effects of embryo cell culture medium, with the inclusion of granulocyte-macrophage colony-stimulation factor (GM-CSF), on embryo development and pregnancy rate. To this end, we took advantage of our retrospective observational study to correlate the outcomes from two different culture media. We included in this study 25 unselected patient from our IVF Center that underwent heterologous IVF cycle with crypreserved oocytes. We analyze the fertilization rate, pregnancy rate, and embryo quality at different day of transfer obtained from two different media composition. Our results show that the rate of fertilization and the pregnancy rate were increased using medium added with this particular type of cytokines (GM-CSF).
Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation
Authors: Stephenson William , Donlin Laura T. , Butler Andrew , Rozo Cristina , Bracken Bernadette , Rashidfarrokhi Ali , Goodman Susan M. , Ivashkiv Lionel B. , Bykerk Vivian P. , Orange Dana E. , Darnell Robert B. , Swerdlow Harold P. , Satija Rahul 
Published: February 2018

AbstractDroplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While this approach offers the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we developed a 3D-printed, low-cost droplet microfluidic control instrument and deploy it in a clinical environment to perform single-cell transcriptome profiling of disaggregated synovial tissue from five rheumatoid arthritis patients. We sequence 20,387 single cells revealing 13 transcriptomically distinct clusters. These encompass an unsupervised draft atlas of the autoimmune infiltrate that contribute to disease biology. Additionally, we identify previously uncharacterized fibroblast subpopulations and discern their spatial location within the synovium. We envision that this instrument will have broad utility in both research and clinical settings, enabling low-cost and routine application of microfluidic techniques.
Quantum and electrochemical interplays in hydrogenated graphene
Authors: Jiang Lin , Fu Wangyang , Birdja Yuvraj Y. , Koper Marc T. M. , Schneider Grégory F. 
Published: February 2018

AbstractThe design of electrochemically gated graphene field-effect transistors for detecting charged species in real time, greatly depends on our ability to understand and maintain a low level of electrochemical current. Here, we exploit the interplay between the electrical in-plane transport and the electrochemical activity of graphene. We found that the addition of one H-sp3 defect per hundred thousand carbon atoms reduces the electron transfer rate of the graphene basal plane by more than five times while preserving its excellent carrier mobility. Remarkably, the quantum capacitance provides insight into the changes of the electronic structure of graphene upon hydrogenation, which predicts well the suppression of the electrochemical activity based on the non-adiabatic theory of electron transfer. Thus, our work unravels the interplay between the quantum transport and electrochemical kinetics of graphene and suggests hydrogenated graphene as a potent material for sensing applications with performances going beyond previously reported graphene transistor-based sensors.
Retrosynthesis of multi-component metal−organic frameworks
Authors: Yuan Shuai , Qin Jun-Sheng , Li Jialuo , Huang Lan , Feng Liang , Fang Yu , Lollar Christina , Pang Jiandong , Zhang Liangliang , Sun Di , Alsalme Ali , Cagin Tahir , Zhou Hong-Cai 
Published: February 2018

AbstractCrystal engineering of metal−organic frameworks (MOFs) has allowed the construction of complex structures at atomic precision, but has yet to reach the same level of sophistication as organic synthesis. The synthesis of complex MOFs with multiple organic and/or inorganic components is ultimately limited by the lack of control over framework assembly in one-pot reactions. Herein, we demonstrate that multi-component MOFs with unprecedented complexity can be constructed in a predictable and stepwise manner under simple kinetic guidance, which conceptually mimics the retrosynthetic approach utilized to construct complicated organic molecules. Four multi-component MOFs were synthesized by the subsequent incorporation of organic linkers and inorganic clusters into the cavity of a mesoporous MOF, each composed of up to three different metals and two different linkers. Furthermore, we demonstrated the utility of such a retrosynthetic design through the construction of a cooperative bimetallic catalytic system with two collaborative metal sites for three-component Strecker reactions.
A family of unconventional deubiquitinases with modular chain specificity determinants
Authors: Hermanns Thomas , Pichlo Christian , Woiwode Ilka , Klopffleisch Karsten , Witting Katharina F. , Ovaa Huib , Baumann Ulrich , Hofmann Kay 
Published: February 2018

AbstractDeubiquitinating enzymes (DUBs) regulate ubiquitin signaling by trimming ubiquitin chains or removing ubiquitin from modified substrates. Similar activities exist for ubiquitin-related modifiers, although the enzymes involved are usually not related. Here, we report human ZUFSP (also known as ZUP1 and C6orf113) and fission yeast Mug105 as founding members of a DUB family different from the six known DUB classes. The crystal structure of human ZUFSP in covalent complex with propargylated ubiquitin shows that the DUB family shares a fold with UFM1- and Atg8-specific proteases, but uses a different active site more similar to canonical DUB enzymes. ZUFSP family members differ widely in linkage specificity through differential use of modular ubiquitin-binding domains (UBDs). While the minimalistic Mug105 prefers K48 chains, ZUFSP uses multiple UBDs for its K63-specific endo-DUB activity. K63 specificity, localization, and protein interaction network suggest a role for ZUFSP in DNA damage response.
MEMS-tunable dielectric metasurface lens
Authors: Arbabi Ehsan , Arbabi Amir , Kamali Seyedeh Mahsa , Horie Yu , Faraji-Dana MohammadSadegh , Faraon Andrei 
Published: February 2018

AbstractVarifocal lenses, conventionally implemented by changing the axial distance between multiple optical elements, have a wide range of applications in imaging and optical beam scanning. The use of conventional bulky refractive elements makes these varifocal lenses large, slow, and limits their tunability. Metasurfaces, a new category of lithographically defined diffractive devices, enable thin and lightweight optical elements with precisely engineered phase profiles. Here we demonstrate tunable metasurface doublets, based on microelectromechanical systems (MEMS), with more than 60 diopters (about 4%) change in the optical power upon a 1-μm movement of one metasurface, and a scanning frequency that can potentially reach a few kHz. They can also be integrated with a third metasurface to make compact microscopes (~1 mm thick) with a large corrected field of view (~500 μm or 40 degrees) and fast axial scanning for 3D imaging. This paves the way towards MEMS-integrated metasurfaces as a platform for tunable and reconfigurable optics.
Experimental evidence of quantum radiation reaction in aligned crystals
Authors: Wistisen Tobias N. , Di Piazza Antonino , Knudsen Helge V. , Uggerhøj Ulrik I. 
Published: February 2018

AbstractQuantum radiation reaction is the influence of multiple photon emissions from a charged particle on the particle's dynamics, characterized by a significant energy-momentum loss per emission. Here we report experimental radiation emission spectra from ultrarelativistic positrons in silicon in a regime where quantum radiation reaction effects dominate the positron's dynamics. Our analysis shows that while the widely used quantum approach is overall the best model, it does not completely describe all the data in this regime. Thus, these experimental findings may prompt seeking more generally valid methods to describe quantum radiation reaction. This experiment is a fundamental test of quantum electrodynamics in a regime where the dynamics of charged particles is strongly influenced not only by the external electromagnetic fields but also by the radiation field generated by the charges themselves and where each photon emission may significantly reduce the energy of the charge.
Development differentially sculpts receptive fields across early and high-level human visual cortex
Authors: Gomez Jesse , Natu Vaidehi , Jeska Brianna , Barnett Michael , Grill-Spector Kalanit 
Published: February 2018

AbstractReceptive fields (RFs) processing information in restricted parts of the visual field are a key property of visual system neurons. However, how RFs develop in humans is unknown. Using fMRI and population receptive field (pRF) modeling in children and adults, we determine where and how pRFs develop across the ventral visual stream. Here we report that pRF properties in visual field maps, from the first visual area, V1, through the first ventro-occipital area, VO1, are adult-like by age 5. However, pRF properties in face-selective and character-selective regions develop into adulthood, increasing the foveal coverage bias for faces in the right hemisphere and words in the left hemisphere. Eye-tracking indicates that pRF changes are related to changing fixation patterns on words and faces across development. These findings suggest a link between face and word viewing behavior and the differential development of pRFs across visual cortex, potentially due to competition on foveal coverage.
Correlating chemical diversity with taxonomic distance for discovery of natural products in myxobacteria
Authors: Hoffmann Thomas , Krug Daniel , Bozkurt Nisa , Duddela Srikanth , Jansen Rolf , Garcia Ronald , Gerth Klaus , Steinmetz Heinrich , Müller Rolf 
Published: February 2018

AbstractSome bacterial clades are important sources of novel bioactive natural products. Estimating the magnitude of chemical diversity available from such a resource is complicated by issues including cultivability, isolation bias and limited analytical data sets. Here we perform a systematic metabolite survey of ~2300 bacterial strains of the order Myxococcales, a well-established source of natural products, using mass spectrometry. Our analysis encompasses both known and previously unidentified metabolites detected under laboratory cultivation conditions, thereby enabling large-scale comparison of production profiles in relation to myxobacterial taxonomy. We find a correlation between taxonomic distance and the production of distinct secondary metabolite families, further supporting the idea that the chances of discovering novel metabolites are greater by examining strains from new genera rather than additional representatives within the same genus. In addition, we report the discovery and structure elucidation of rowithocin, a myxobacterial secondary metabolite featuring an uncommon phosphorylated polyketide scaffold.
Bounding cross-shelf transport time and degradation in Siberian-Arctic land-ocean carbon transfer
Authors: Bröder Lisa , Tesi Tommaso , Andersson August , Semiletov Igor , Gustafsson Örjan 
Published: February 2018

AbstractThe burial of terrestrial organic carbon (terrOC) in marine sediments contributes to the regulation of atmospheric CO2 on geological timescales and may mitigate positive feedback to present-day climate warming. However, the fate of terrOC in marine settings is debated, with uncertainties regarding its degradation during transport. Here, we employ compound-specific radiocarbon analyses of terrestrial biomarkers to determine cross-shelf transport times. For the World’s largest marginal sea, the East Siberian Arctic shelf, transport requires 3600 ± 300 years for the 600 km from the Lena River to the Laptev Sea shelf edge. TerrOC was reduced by ~85% during transit resulting in a degradation rate constant of 2.4 ± 0.6 kyr−1. Hence, terrOC degradation during cross-shelf transport constitutes a carbon source to the atmosphere over millennial time. For the contemporary carbon cycle on the other hand, slow terrOC degradation brings considerable attenuation of the decadal-centennial permafrost carbon-climate feedback caused by global warming.
Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms
Authors: Pierce Brandon L. , Tong Lin , Argos Maria , Demanelis Kathryn , Jasmine Farzana , Rakibuz-Zaman Muhammad , Sarwar Golam , Islam Md. Tariqul , Shahriar Hasan , Islam Tariqul , Rahman Mahfuzar , Yunus Md. , Kibriya Muhammad G. , Chen Lin S. , Ahsan Habibul 
Published: February 2018

AbstractInherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i.e., shared mechanism) with many additional pairs we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite associations with expression and methylation, although many SNPs affect multiple CpGs in opposite directions. This work demonstrates the pervasiveness of co-regulated expression and methylation in the human genome. Applying this approach to other types of molecular QTLs can enhance our understanding of regulatory mechanisms.