bluuebunny/crossref_metadata_2025_split huggingface dataset:
The landscape of genomic alterations across childhood cancers
Authors:   ICGC PedBrain-Seq Project, Gröbner Susanne N. ,   ICGC MMML-Seq Project, Worst Barbara C. , Weischenfeldt Joachim , Buchhalter Ivo , Kleinheinz Kortine , Rudneva Vasilisa A. , Johann Pascal D. , Balasubramanian Gnana Prakash , Segura-Wang Maia , Brabetz Sebastian , Bender Sebastian , Hutter Barbara , Sturm Dominik , Pfaff Elke , Hübschmann Daniel , Zipprich Gideon , Heinold Michael , Eils Jürgen , Lawerenz Christian , Erkek Serap , Lambo Sander , Waszak Sebastian , Blattmann Claudia , Borkhardt Arndt , Kuhlen Michaela , Eggert Angelika , Fulda Simone , Gessler Manfred , Wegert Jenny , Kappler Roland , Baumhoer Daniel , Burdach Stefan , Kirschner-Schwabe Renate , Kontny Udo , Kulozik Andreas E. , Lohmann Dietmar , Hettmer Simone , Eckert Cornelia , Bielack Stefan , Nathrath Michaela , Niemeyer Charlotte , Richter Günther H. , Schulte Johannes , Siebert Reiner , Westermann Frank , Molenaar Jan J. , Vassal Gilles , Witt Hendrik , Burkhardt Birgit , Kratz Christian P. , Witt Olaf , van Tilburg Cornelis M. , Kramm Christof M. , Fleischhack Gudrun , Dirksen Uta , Rutkowski Stefan , Frühwald Michael , von Hoff Katja , Wolf Stephan , Klingebiel Thomas , Koscielniak Ewa , Landgraf Pablo , Koster Jan , Resnick Adam C. , Zhang Jinghui , Liu Yanling , Zhou Xin , Waanders Angela J. , Zwijnenburg Danny A. , Raman Pichai , Brors Benedikt , Weber Ursula D. , Northcott Paul A. , Pajtler Kristian W. , Kool Marcel , Piro Rosario M. , Korbel Jan O. , Schlesner Matthias , Eils Roland , Jones David T. W. , Lichter Peter , Chavez Lukas , Zapatka Marc , Pfister Stefan M. 
Published: February 2018

Abstract
Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7–8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
Influence of glass-based dental ceramic type and thickness with identical shade on the light transmittance and the degree of conversion of resin cement
Authors: Oh Soram , Shin Su-Mi , Kim Hyun-Jung , Paek Janghyun , Kim Sung-Joon , Yoon Tai Hyun , Kim Sun-Young 
Published: February 2018

AbstractThe purpose of this study was to assess the influence of the types and thicknesses of glass ceramic plates on light transmittance and compare the degrees of conversion (DC) of resin cement under the ceramic materials. Three ceramic plates with thicknesses of 0.5, 1.0, 2.0, and 4.0 mm were fabricated from each of five commercial ceramic blocks in shade A2: high-translucency and low-translucency IPS Empress CAD (Emp_HT and Emp_LT); high-translucency and low-translucency IPS e.max CAD (Emx_HT and Emx_LT); and Vita Mark II (Vita). The translucency parameter was obtained using a colorimeter. The light transmittance rate was measured using a photodetector attached to an optical power meter. The DC of a resin cement (Variolink N) underneath the ceramic plates was examined by Fourier transform infrared spectroscopy. The translucency parameter, light transmittance rate, and DC showed significant differences by ceramic type and thickness (P < 0.05). The Emp_HT specimens showed the highest light transmission and DCs, and the Emx_LT showed the least light transmission and the lowest DCs. The high-translucency Empress showed significantly higher DCs than the low-translucency types (P < 0.05), but there was no significant difference in e.max (P > 0.05). Both type and thickness of the glass ceramics significantly influenced the light transmittance and DC of the light-cured resin cement beneath the ceramic of the same shade.
Targeting glucocorticoid receptors prevents the effects of early life stress on amyloid pathology and cognitive performance in APP/PS1 mice
Authors: Lesuis Sylvie L , Weggen Sascha , Baches Sandra , Lucassen Paul J , Krugers Harm J 
Published: February 2018

AbstractExposure to chronic stress or elevated glucocorticoid hormone levels in adult life has been associated with cognitive deficits and an increased risk for Alzheimer’s disease (AD). Since exposure to stress during early life enhances stress-responsiveness and lastingly affects cognition in adult life, we here investigated; (i) whether chronic early life stress (ELS) affects AD pathology and cognition in middle-aged APPswe/PS1dE9 mice, and (ii) whether it is still possible to rescue these late effects by briefly blocking glucocorticoid receptors (GRs) at a translationally relevant, middle age. Transgenic APPswe/PS1dE9 mice were subjected to ELS by housing dams and pups with limited nesting and bedding material from postnatal days 2–9 only. In 6- and 12-month-old offspring, this resulted in enhanced hippocampal amyloid-β (Aβ)-40 and -42 levels, and in reduced cognitive flexibility, that correlated well with the Aβ42 levels. In parallel, CORT levels and BACE1 levels were significantly elevated. Surprisingly, blocking GRs for only 3 days at 12 months of age reduced CORT levels, reduced hippocampal Aβ40 and -42, and β-site APP-cleaving enzyme 1 (BACE1) levels, and notably rescued the cognitive deficits in 12-month-old APPswe/PS1dE9 mice. These mouse data demonstrate that exposure to stress during the sensitive period early in life influences later amyloid pathology and cognition in genetically predisposed, mutant mice, and as such, may increase AD vulnerability. The fact that a short treatment with a GR antagonist at middle age lastingly reduced Aβ levels and rescued the cognitive deficits after ELS, highlights the therapeutic potential of this drug for reducing amyloid pathology.
Mitochondria-associated membranes in aging and senescence: structure, function, and dynamics
Authors: Janikiewicz Justyna , Szymański Jędrzej , Malinska Dominika , Patalas-Krawczyk Paulina , Michalska Bernadeta , Duszyński Jerzy , Giorgi Carlotta , Bonora Massimo , Dobrzyn Agnieszka , Wieckowski Mariusz R. 
Published: February 2018

Abstract
Sites of close contact between mitochondria and the endoplasmic reticulum (ER) are known as mitochondria-associated membranes (MAM) or mitochondria-ER contacts (MERCs), and play an important role in both cell physiology and pathology. A growing body of evidence indicates that changes observed in the molecular composition of MAM and in the number of MERCs predisposes MAM to be considered a dynamic structure. Its involvement in processes such as lipid biosynthesis and trafficking, calcium homeostasis, reactive oxygen species production, and autophagy has been experimentally confirmed. Recently, MAM have also been studied in the context of different pathologies, including Alzheimer's disease, Parkinson’s disease, amyotrophic lateral sclerosis, type 2 diabetes mellitus and GM1-gangliosidosis. An underappreciated amount of data links MAM with aging or senescence processes. In the present review, we summarize the current knowledge of basic MAM biology, composition and action, and discuss the potential connections supporting the idea that MAM are significant players in longevity.
Emerging molecular mechanisms in chemotherapy: Ca2+ signaling at the mitochondria-associated endoplasmic reticulum membranes
Authors: Kerkhofs Martijn , Bittremieux Mart , Morciano Giampaolo , Giorgi Carlotta , Pinton Paolo , Parys Jan B. , Bultynck Geert 
Published: February 2018

AbstractInter-organellar communication often takes the form of Ca2+ signals. These Ca2+ signals originate from the endoplasmic reticulum (ER) and regulate different cellular processes like metabolism, fertilization, migration, and cell fate. A prime target for Ca2+ signals are the mitochondria. ER–mitochondrial Ca2+ transfer is possible through the existence of mitochondria-associated ER membranes (MAMs), ER structures that are in the proximity of the mitochondria. This creates a micro-domain in which the Ca2+ concentrations are manifold higher than in the cytosol, allowing for rapid mitochondrial Ca2+ uptake. In the mitochondria, the Ca2+ signal is decoded differentially depending on its spatiotemporal characteristics. While Ca2+ oscillations stimulate metabolism and constitute pro-survival signaling, mitochondrial Ca2+ overload results in apoptosis. Many chemotherapeutics depend on efficient ER–mitochondrial Ca2+ signaling to exert their function. However, several oncogenes and tumor suppressors present in the MAMs can alter Ca2+ signaling in cancer cells, rendering chemotherapeutics ineffective. In this review, we will discuss recent studies that connect ER–mitochondrial Ca2+ transfer, tumor suppressors and oncogenes at the MAMs, and chemotherapy.
A key role for MAM in mediating mitochondrial dysfunction in Alzheimer disease
Authors: Area-Gomez Estela , de Groof Ad , Bonilla Eduardo , Montesinos Jorge , Tanji Kurenai , Boldogh Istvan , Pon Liza , Schon Eric A. 
Published: February 2018

AbstractIn the last few years, increased emphasis has been devoted to understanding the contribution of mitochondria-associated endoplasmic reticulum (ER) membranes (MAM) to human pathology in general, and neurodegenerative diseases in particular. A major reason for this is the central role that this subdomain of the ER plays in metabolic regulation and in mitochondrial biology. As such, aberrant MAM function may help explain the seemingly unrelated metabolic abnormalities often seen in neurodegeneration. In the specific case of Alzheimer disease (AD), besides perturbations in calcium and lipid homeostasis, there are numerous documented alterations in mitochondrial behavior and function, including reduced respiratory chain activity and oxidative phosphorylation, increased free radical production, and altered organellar morphology, dynamics, and positioning (especially perinuclear mitochondria). However, whether these alterations are primary events causative of the disease, or are secondary downstream events that are the result of some other, more fundamental problem, is still unclear. In support of the former possibility, we recently reported that C99, the C-terminal processing product of the amyloid precursor protein (APP) derived from its cleavage by β-secretase, is present in MAM, that its level is increased in AD, and that this increase reduces mitochondrial respiration, likely via a C99-induced alteration in cellular sphingolipid homeostasis. Thus, the metabolic disturbances seen in AD likely arise from increased ER-mitochondrial communication that is driven by an increase in the levels of C99 at the MAM.
The role of the mitochondria and the endoplasmic reticulum contact sites in the development of the immune responses
Authors: Martinvalet Denis 
Published: February 2018

AbstractMitochondria and endoplasmic reticulum (ER) contact sites (MERCs) are dynamic modules enriched in subset of lipids and specialized proteins that determine their structure and functions. The MERCs regulate lipid transfer, autophagosome formation, mitochondrial fission, Ca2+homeostasis and apoptosis. Since these functions are essential for cell biology, it is therefore not surprising that MERCs also play a critical role in organ physiology among which the immune system stands by its critical host defense function. This defense system must discriminate and tolerate host cells and beneficial commensal microorganisms while eliminating pathogenic ones in order to preserve normal homeostasis. To meet this goal, the immune system has two lines of defense. First, the fast acting but unspecific innate immune system relies on anatomical physical barriers and subsets of hematopoietically derived cells expressing germline-encoded receptors called pattern recognition receptors (PRR) recognizing conserved motifs on the pathogens. Second, the slower but very specific adaptive immune response is added to complement innate immunity. Adaptive immunity relies on another set of specialized cells, the lymphocytes, harboring receptors requiring somatic recombination to be expressed. Both innate and adaptive immune cells must be activated to phagocytose and process pathogens, migrate, proliferate, release soluble factors and destroy infected cells. Some of these functions are strongly dependent on lipid transfer, autophagosome formation, mitochondrial fission, and Ca2+flux; this indicates that MERCs could regulate immunity.
Anisotropic photoemission time delays close to a Fano resonance
Authors: Cirelli Claudio , Marante Carlos , Heuser Sebastian , Petersson C. L. M. , Galán Álvaro Jiménez , Argenti Luca , Zhong Shiyang , Busto David , Isinger Marcus , Nandi Saikat , Maclot Sylvain , Rading Linnea , Johnsson Per , Gisselbrecht Mathieu , Lucchini Matteo , Gallmann Lukas , Dahlström J. Marcus , Lindroth Eva , L’Huillier Anne , Martín Fernando , Keller Ursula 
Published: February 2018

AbstractElectron correlation and multielectron effects are fundamental interactions that govern many physical and chemical processes in atomic, molecular and solid state systems. The process of autoionization, induced by resonant excitation of electrons into discrete states present in the spectral continuum of atomic and molecular targets, is mediated by electron correlation. Here we investigate the attosecond photoemission dynamics in argon in the 20–40 eV spectral range, in the vicinity of the 3s−1np autoionizing resonances. We present measurements of the differential photoionization cross section and extract energy and angle-dependent atomic time delays with an attosecond interferometric method. With the support of a theoretical model, we are able to attribute a large part of the measured time delay anisotropy to the presence of autoionizing resonances, which not only distort the phase of the emitted photoelectron wave packet but also introduce an angular dependence.
Author Correction: Well-being, problematic alcohol consumption and acute subjective drug effects in past-year ayahuasca users: a large, international, self-selecting online survey
Authors: Lawn Will , Hallak Jaime E. , Crippa Jose A. , Dos Santos Rafael , Porffy Lilla , Barratt Monica J. , Ferris Jason A. , Winstock Adam R. , Morgan Celia J. A. 
Published: February 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: Divergent effects of Wnt/β-catenin signaling modifiers on the preservation of human limbal epithelial progenitors according to culture condition
Authors: Lee Hyun Jung , Wolosin J. Mario , Chung So-Hyang 
Published: February 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Interaction between alcohol consumption and methylenetetrahydrofolate reductase polymorphisms in thyroid cancer risk: National Cancer Center cohort in Korea
Authors: Yang Sarah , Lee Jeonghee , Park Yoon , Lee Eun Kyung , Hwangbo Yul , Ryu Junsun , Sung Joohon , Kim Jeongseon 
Published: February 2018

AbstractThe effect of alcohol intake on thyroid cancer is unestablished, and its interaction effects with genetic susceptibility are unclear. In this case-control study, the relationship among alcohol intake, the methylenetetrahydrofolate reductase (MTHFR) gene, and thyroid cancer risk has been evaluated. In total, 642 cases and 642 controls of Korean origin were included, and the genetic variants C677T and A1298C of the MTHFR gene were analysed. The interactions between alcohol-consumption behaviour and genetic variants were analysed with a likelihood ratio test, wherein a multiplicative interaction term was added to a logistic regression model. There was an independent association between the C677T polymorphism and thyroid cancer risk but not for drinking history. For C677T C/C homozygotes, individuals with a history of alcohol consumption showed a protective OR (95% CI) of 0.42 (0.15–1.13) when never drinkers were used as the reference. However, this protective association was not observed among individuals with a T+ allele with an OR (95% CI) of 1.27 (0.89–1.82), showing different directions for the association between genotypes with a significant interaction (Pinteraction = 0.009). Based on the genetic characteristics of individuals included, an interaction between alcohol intake and MTHFR C677T may modify the risk of thyroid cancer.
Tunable critical temperature for superconductivity in FeSe thin films by pulsed laser deposition
Authors: Feng Zhongpei , Yuan Jie , He Ge , Hu Wei , Lin Zefeng , Li Dong , Jiang Xingyu , Huang Yulong , Ni Shunli , Li Jun , Zhu Beiyi , Dong Xiaoli , Zhou Fang , Wang Huabing , Zhao Zhongxian , Jin Kui 
Published: February 2018

AbstractStabilized FeSe thin films in ambient pressure with tunable superconducting critical temperature would be a promising candidate for superconducting electronic devices. By carefully controlling the depositions on twelve kinds of substrates using a pulsed laser deposition technique single crystalline FeSe thin films were fabricated. The high quality of the thin films was confirmed by X-ray diffraction with a full width at half maximum of 0.515° in the rocking curve and clear four-fold symmetry in φ-scan. The films have a maximum T
c
~ 15 K on the CaF2 substrate and were stable in ambient conditions air for more than half a year. Slightly tuning the stoichiometry of the FeSe targets, the superconducting critical temperature becomes adjustable below 15 K with quite narrow transition width less than 2 K. These FeSe thin films deposited on different substrates are optimized respectively. The Tc of these optimized films show a relation with the out-of-plane (c-axis) lattice parameter of the FeSe films.
A Triplet Parallelizing Spiral Microfluidic Chip for Continuous Separation of Tumor Cells
Authors: Chen Hongmei 
Published: February 2018

AbstractInertial and deformability- based particles separations gradually attract more significant attentions. In this work, we present a hybrid chip by combining the advantages of inertial and deformability –based principle. The chip is a triplet parallelizing spiral inertial microfluidic chip interconnected with numerable tilted slits (Spiral-Slits Chip) for continuous separation of circulating tumor cells. Utilizing the inertial lift and viscous drag forces, different sized particles achieve different equilibrium at distinct streamlines of the spiral microchannel. Numerable tilted slits are organized along the flow direction. They frequently transport segregated streamline particles into a paralleled smaller microchannel. These frequent dragging results in the amount of certain sized particles in the original microchannel gradually and dramatically reduced. Inertial separation of distinct sized particles could be achievable. Two arrays of numerable tilted slits function as bridges. This Spiral-Slits Chip could substitute for Red Blood Cells Lysis (RBCL) and is most effective for ultra-high throughput. The overall arrangement of this triplet parallelizing spiral inertial microfluidic reflects stable streamlines distribution in the first main microchannel. Combining with Ellipse filters, robust and reproducible capture of CTCs could be achieved at high flow rates. Optical absorption detection has been tentatively tested, and this could simplify the process.
Cooperative catalysis of cellulose nanofiber and organocatalyst in direct aldol reactions
Authors: Kanomata Kyohei , Tatebayashi Naoko , Habaki Xin , Kitaoka Takuya 
Published: February 2018

AbstractCellulose nanofibers (CNFs) are finding a wide range of applications in the forthcoming sustainable society because of their carbon-neutral renewability and superior physicochemical properties. Here, we first show a cooperative organocatalysis by combining TEMPO-oxidized cellulose nanofiber (TOCN) and proline to enhance the catalytic efficiency in a direct aldol reaction. The yields of proline-catalyzed aldol products drastically increased in the presence of catalytically-inactive TOCN. This effect was also achieved by simply adding the TOCN to the reaction conditions where various proline analogues including structurally simple pyrrolidine and piperidine were used instead of proline. TOCN was superior to physically-pulverized CNF in the organocatalytic efficiency, and the nanofibrillation of cellulose microfibrils in reaction media was essential to induce the drastic enhancement in catalytic activity. The present finding will bring a new entry in the applications of CNFs, and open up a new phase in developing highly efficient molecular transformations in green chemical industries.
Zerumbone reduces proliferation of HCT116 colon cancer cells by inhibition of TNF-alpha
Authors: Singh Salam Pradeep , Nongalleima Khumukcham , Singh Ningthoujam Indrajit , Doley Pradip , Singh Chingakham Brajakisor , Singh Thiyam Ramsing , Sahoo Dinabandhu 
Published: February 2018

AbstractZerumbone is a known anti-cancer herbal compound. However, the actual protein target is not fully understood or known. This investigation focus on the association of zerumbone in HCT116 colon cancer cell proliferation and its link with TNF-alpha. The study shows that with the increasing concentration of zerumbone, there was a reduction of HCT116 cells proliferation based on the cell line study and hence higher TNF-alpha inhibition based on the TNF-alpha assay. The study also emphasizes on the computational aspect by investigating the molecular docking analysis of zerumbone against TNF-alpha. The docked complex was further validated using molecular dynamics simulation studies. The docking analysis observed that alpha-beta unsaturated carbonyl scaffold is an important moiety for the anti-cancer activity of zerumbone. Furthermore, the DFT analysis also confirms the reactivity nature of zerumbone based on the frontier molecular orbital analysis.