bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grouped False-Discovery Rate for Removing the Gene-set-Level Bias of RNA-seq
Authors: Yang Tae Young , Jeong Seongmun 
Published: November 2013

In recent years, RNA-seq has become a very competitive alternative to microarrays. In RNA-seq experiments, the expected read count for a gene is proportional to its expression level multiplied by its transcript length. Even when two genes are expressed at the same level, differences in length will yield differing numbers of total reads. The characteristics of these RNA-seq experiments create a gene-level bias such that the proportion of significantly differentially expressed genes increases with the transcript length, whereas such bias is not present in microarray data. Gene-set analysis seeks to identify the gene sets that are enriched in the list of the identified significant genes. In the gene-set analysis of RNA-seq, the gene-level bias subsequently yields the gene-set-level bias that a gene set with genes of long length will be more likely to show up as enriched than will a gene set with genes of shorter length. Because gene expression is not related to its transcript length, any gene set containing long genes is not of biologically greater interest than gene sets with shorter genes. Accordingly the gene-set-level bias should be removed to accurately calculate the statistical significance of each gene-set enrichment in the RNA-seq. We present a new gene set analysis method of RNA-seq, called FDRseq, which can accurately calculate the statistical significance of a gene-set enrichment score by the grouped false-discovery rate. Numerical examples indicated that FDRseq is appropriate for controlling the transcript length bias in the gene-set analysis of RNA-seq data. To implement FDRseq, we developed the R program, which can be downloaded at no cost from http://home.mju.ac.kr/home/index.action?siteId=tyang .
RNA Expression Profiling from FACS‐Isolated Cells of the Drosophila Intestine
Authors: Dutta Devanjali , Xiang Jinyi , Edgar Bruce A. 
Published: November 2013

AbstractThis unit describes a protocol for the isolation of Drosophila intestinal cell populations for the purpose of cell type–specific transcriptome profiling. A method to select a cell type of interest labeled with green or yellow fluorescent protein (GFP, YFP) by making use of the GAL4‐UAS bipartite system and fluorescent‐activated cell sorting (FACS) is presented. Total RNA is isolated from the sorted cells and linear RNA amplification is used to obtain sufficient amounts of high‐quality RNA for analysis by microarray, RT‐PCR, or RNA sequencing. This method will be useful for quantitative transcriptome comparison across intestinal cell types under normal and various experimental conditions. Curr. Protoc. Stem Cell Biol. 27:2F.2.1‐2F.2.12. © 2013 by John Wiley & Sons, Inc.
Direct Organocatalytic Asymmetric Mannich Addition of 3‐Substituted‐2H‐1,4‐Benzoxazines: Access to Tetrasubstituted Carbon Stereocenters
Authors: Wang You‐Qing , Zhang Yongna , Pan Kun , You Junxiong , Zhao Jin 
Published: November 2013

Abstract3‐Substituted‐2H‐1,4‐benzoxazines undergo a highly enantioselective direct Mannich reaction with acetone in the presence of an L‐proline catalyst at room temperature. The corresponding N‐heterocycles with α‐tetrasubstituted carbon stereocenters were obtained in good yields (48–92%) and excellent enantioselectivity (up to >99% ee). Furthermore, a novel modification involving the diastereoselective reduction of the Mannich adduct was carried out leading to the formation of a 1,3‐amino alcohol with a chiral tetrasubstituted carbon stereocenter in high yield.magnified image
A Rhodium‐Catalyzed Tandem Alkyne Dimerization/ 1,4‐Addition Reaction
Authors: Lerum Ronald V. , Russo Christopher M. , Marquez Jocellie E. , Chisholm John D. 
Published: November 2013

AbstractA convenient three‐component coupling reaction for the construction of conjugated enynes using rhodium catalysis is reported. Dimerization of a monosubstituted alkyne followed by trapping of the vinyl metal intermediate with an electron‐deficient alkene, such as methyl vinyl ketone, provided moderate to good yields of these enynes. The use of the hindered electron‐rich tris(ortho‐tolyl)phosphine as a ligand for the rhodium catalyst provided the best conversions to these complex products.magnified image
Combined Catalytic System of Scandium Triflate and Boronic Ester for Amide Bond Cleavage
Authors: Kita Yusuke , Nishii Yuji , Onoue Akihiro , Mashima Kazushi 
Published: November 2013

AbstractWe have found that the combination of scandium with boronic ester enables the cleavage of amide bonds. Primary amides were converted to the corresponding esters in the presence of catalytic amounts of scandium triflate and boronic ester under mild and neutral conditions. This unique catalytic system can be applied to the deprotection of acetylaniline derivatives. In addition, control NMR experiments were carried out to examine the effect of the boronic esters.magnified image
Synthesis and Characterization of Lithium Bis(fluoromalonato)borate for Lithium‐Ion Battery Applications
Authors: Liao Chen , Han Kee Sung , Baggetto Loïc , Hillesheim Daniel A. , Custelcean Radu , Lee Eun‐Sung , Guo Bingkun , Bi Zhonghe , Jiang De‐en , Veith Gabriel M. , Hagaman Edward W. , Brown Gilbert M. , Bridges Craig , Paranthaman M. Parans , Manthiram Arumugam , Dai Sheng , Sun Xiao‐Guang 
Published: November 2013

A new orthochelated salt, lithium bis(monofluoromalonato)borate (LiBFMB), is synthesized and purified for application in lithium‐ion batteries. The presence of fluorine in the borate anion of LiBFMB increases its oxidation potential and also facilitates ion dissociation, as reflected by the ratio of ionic conductivity (σexp) and ion diffusivity coefficients (σNMR). Half‐cell tests using 5.0 V lithium nickel manganese oxide (LiNi0.5Mn1.5O4) as a cathode and ethylene carbonate (EC)/dimethyl carbonate (DMC)/diethyl carbonate (DEC) as a solvent reveals that the impedance of the LiBFMB cell is much larger than those of LiPF6‐ and lithium bis(oxalato)borate (LiBOB)‐based cells, which results in lower capacity and poor cycling performance of the former. X‐ray photoelectron spectroscopy (XPS) results for the cycled cathode electrode suggest that because of the stability of the LiBFMB salt, the solid electrolyte interphase (SEI) formed on the cathode surface is significantly different from those of LiPF6 and LiBOB based electrolytes, resulting in more solvent decomposition and a thicker SEI layer. Initial results also indicate that using a high dielectric constant solvent, propylene carbonate, alters the surface chemistry, reduces the interfacial impedance, and enhances the performance of LiBFMB‐based 5.0 V cell.
Design, Synthesis, and X‐Ray Crystal Structure of a Fullerene‐Linked Metal–Organic Framework
Authors: Peng Ping , Li Fang‐Fang , Neti Venkata S. Pavan K. , Metta‐Magana Alejandro J. , Echegoyen Luis 
Published: November 2013

AbstractGiven the unique structural and electronic properties of C60, metal–organic frameworks (MOFs) containing C60 linkers are expected to exhibit interesting characteristics. A new hexakisfullerene derivative possessing two pairs of phenyl pyridine groups attached to two methano‐carbon atoms located at the trans‐1 positions was designed and synthesized. The four pyridyl nitrogen atoms define a perfectly planar rectangle. This new C60 derivative was used to assemble the first fullerene‐linked two‐dimensional MOF by coordination with Cd2+.
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution
Authors: Schönknecht Gerald , Weber Andreas P. M. , Lercher Martin J. 
Published: November 2013

In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red algaGaldieria sulphurariato its hot, acid, toxic‐metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice‐binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism.Editor's suggested further reading in BioEssaysJumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract
Microfluidic perfusion culture of human induced pluripotent stem cells under fully defined culture conditions
Authors: Yoshimitsu Ryosuke , Hattori Koji , Sugiura Shinji , Kondo Yuki , Yamada Rotaro , Tachikawa Saoko , Satoh Taku , Kurisaki Akira , Ohnuma Kiyoshi , Asashima Makoto , Kanamori Toshiyuki 
Published: November 2013

ABSTRACTHuman induced pluripotent stem cells (hiPSCs) are a promising cell source for drug screening. For this application, self‐renewal or differentiation of the cells is required, and undefined factors in the culture conditions are not desirable. Microfluidic perfusion culture allows the production of small volume cultures with precisely controlled microenvironments, and is applicable to high‐throughput cellular environment screening. Here, we developed a microfluidic perfusion culture system for hiPSCs that uses a microchamber array chip under defined extracellular matrix (ECM) and culture medium conditions. By screening various ECMs we determined that fibronectin and laminin are appropriate for microfluidic devices made out of the most popular material, polydimethylsiloxane (PDMS). We found that the growth rate of hiPSCs under pressure‐driven perfusion culture conditions was higher than under static culture conditions in the microchamber array. We applied our new system to self‐renewal and differentiation cultures of hiPSCs, and immunocytochemical analysis showed that the state of the hiPSCs was successfully controlled. The effects of three antitumor drugs on hiPSCs were comparable between microchamber array and 96‐well plates. We believe that our system will be a platform technology for future large‐scale screening of fully defined conditions for differentiation cultures on integrated microfluidic devices. Biotechnol. Biotechnol. Bioeng. 2014;111: 937–947. © 2013 Wiley Periodicals, Inc.
Co‐regulation of primary mouse hepatocyte viability and function by oxygen and matrix
Authors: Buck Lorenna D. , Inman S. Walker , Rusyn Ivan , Griffith Linda G. 
Published: November 2013

ABSTRACTAlthough oxygen and extracellular matrix cues both influence differentiation state and metabolic function of primary rat and human hepatocytes, relatively little is known about how these factors together regulate behaviors of primary mouse hepatocytes in culture. To determine the effects of pericellular oxygen tension on hepatocellular function, we employed two methods of altering oxygen concentration in the local cellular microenvironment of cells cultured in the presence or absence of an extracellular matrix (Matrigel) supplement. By systematically altering medium depth and gas phase oxygen tension, we created multiple oxygen regimes (hypoxic, normoxic, and hyperoxic) and measured the local oxygen concentrations in the pericellular environment using custom‐designed oxygen microprobes. From these measurements of oxygen concentrations, we derived values of oxygen consumption rates under a spectrum of environmental contexts, thus providing the first reported estimates of these values for primary mouse hepatocytes. Oxygen tension and matrix microenvironment were found to synergistically regulate hepatocellular survival and function as assessed using quantitative image analysis for cells stained with vital dyes, and assessment of secretion of albumin. Hepatocellular viability was affected only at strongly hypoxic conditions. Surprisingly, albumin secretion rates were greatest at a moderately supra‐physiological oxygen concentration, and this effect was mitigated at still greater supra‐physiological concentrations. Matrigel enhanced the effects of oxygen on retention of function. This study underscores the importance of carefully controlling cell density, medium depth, and gas phase oxygen, as the effects of these parameters on local pericellular oxygen tension and subsequent hepatocellular function are profound. Biotechnol. Biotechnol. Bioeng. 2014;111: 1018–1027. © 2014 Wiley Periodicals, Inc.
Simultaneous analysis of polygala acid, senegenin and 3,6′‐disinapoylsucrose in rat plasma by liquid chromatography–tandem mass spectrometry: application to a pharmacokinetic study after oral administration
Authors: Lin Longfei , Yan Lei , Zhang Hui , Li Xuechun , Zhang Jin , Dou Haoran , Shen Mingrui , Yin Xingbin , Qu Changhai , Ni Jian 
Published: November 2013

ABSTRACTA rapid and specific LC‐MS/MS method has been developed for the simultaneous analysis of polygala acid, senegenin and 3,6′‐disinapoylsucrose (DSS) in rat plasma. The method was applied to the pharmacokinetics studies of polygala acid, senegenin and DSS. The analysis was carried out on an Agilent Eclipse plus C18 reversed‐phase column (100 × 4.6 mm, 3.5 µm) by gradient elution with methanol and ammonia (0.01%, v/v). The flow rate was 0.4 mL/min. All analytes including internal standard (IS) were monitored by selected reaction monitoring with an electrospray ionization source. Linear responses were obtained for polygala acid and DSS ranging from 2.5 to 2000 ng/mL, and senegenin ranging from 5 to 2000 ng/mL. The intra‐ and inter‐day precisions (relative standard deviation) were <11.34 and 8.99%. The extraction recovery ranged from 70.89 ± 4.60 to 88.49 ± 3.26%, and that for the IS was 77.23 ± 3.68%. Stability studies showed that polygala acid, senegenin and DSS are stable during the preparation and analytical process. The validated method was successfully used to determine the concentration–time profiles of polygala acid, senegenin and DSS. Copyright © 2013 John Wiley & Sons, Ltd.
α‐Crystallin Modulates its Chaperone Activity by Varying the Exposed Surface
Authors: Palmieri Valentina , Maulucci Giuseppe , Maiorana Alessando , Papi Massimiliano , De Spirito Marco 
Published: November 2013

AbstractThe α‐crystallin family of small heat shock proteins possesses chaperone activity in response to stress and is involved in several neurological, muscular, and ophthalmic pathologies. This family includes the vertebrate lens protein α‐crystallin, associated with cataract disease. In this study, by combining small‐angle X‐ray and light scattering techniques, the structure and shape of α‐crystallin was revealed in its native state and after a transition caused by heat stress. Below critical temperature (Tc), α‐crystallin appears as an ellipsoid with a central cavity; whereas at high temperatures the cavity almost disappears, and the protein rearranges its structure, increasing the solvent‐exposed surface while retaining the ellipsoidal symmetry. Contextually, at Tc, α‐crystallin chaperone binding shows an abrupt increase. By modelling the chaperone activity as the formation of a complex composed of α‐crystallin and an aggregating substrate, it was demonstrated that the increase of α‐crystallin‐exposed surface is directly responsible for its gain in chaperone functionality.
Mechanistic Insights from Substrate Preference in Unsaturated Glucuronyl Hydrolase
Authors: Jongkees Seino A. K. , Yoo Hayoung , Withers Stephen G. 
Published: November 2013

AbstractNatural and synthetic unsaturated glucuronides were tested as substrates for Clostridium perfringens unsaturated glucuronyl hydrolase to probe its mechanism and to guide inhibitor design. Of the natural substrates, a chondroitin disaccharide substrate with sulfation of the primary alcohol on carbon 6 of its N‐acetylgalactosamine moiety was found to have the highest turnover number of any substrate reported for an unsaturated glucuronyl hydrolase, with kcat=112 s−1. Synthetic aryl glycoside substrates with electron‐withdrawing aglycone substituents were cleaved more slowly than those with electron‐donating substituents. Similarly, an unsaturated glucuronyl fluoride was found to be a particularly poor substrate, with kcat/Km=44 nM−1 s−1—a very unusual result for a glycoside‐cleaving enzyme. These results are consistent with a transition state with positive charge at carbon 5 and the endocyclic oxygen, as anticipated in the hydration mechanism proposed. However, several analogues designed to take advantage of strong enzyme binding to such a transition state showed little to no inhibition. This result suggests that further work is required to understand the true nature of the transition state stabilised by this enzyme.
Cyclopalladation and Reactivity of Amino Esters through CH Bond Activation: Experimental, Kinetic, and Density Functional Theory Mechanistic Studies
Authors: Laga Eduardo , García‐Montero Angel , Sayago Francisco J. , Soler Tatiana , Moncho Salvador , Cativiela Carlos , Martínez Manuel , Urriolabeitia Esteban P. 
Published: November 2013

AbstractThe orthopalladation, through CH bond activation, of a large number of amino esters and amino phosphonates derived from phenylglycine, and having different substituents at the aryl ring and the C‐α atom, as well as on the N‐amine atom, has been studied. The experimental observations indicated an improvement in the yields of the orthopalladated compounds when the N‐amine and/or the C‐α atom are substituted, when compared with the unsubstituted methyl phenylglycinate derivatives. In contrast, substitutions at the aryl ring do not promote significant changes in the orthometalation results. Furthermore, the use of hydrochloride salts of the amino esters has also been shown to have a remarkably favorable effect on the process. All these observations have been fully quantified at different temperatures and pressures by a detailed kinetic study in solution in different solvents and in the presence and absence of added Brønsted acids and chloride anions. The data collected indicate relevant changes in the process depending on these conditions, as expected from the general background known for cyclopalladation reactions. An electronic mechanism of the orthopalladation has been proposed based on DFT calculations at the B3LYP level, and a very good agreement between the trends kinetically measured and the theoretically calculated activation barriers has been obtained. The reactivity of the new orthopalladated amino phosphonate derivatives has been tested and it was found that their halogenation, alkoxylation and carbonylation resulted in formation of the corresponding functionalized ortho‐haloaminophosphonates, ortho‐alkoxyaminophosphonates and oxoisoindolinylphosphonates.
Patterns of care of radiation therapy in patients with stage IV rectal cancer: A Surveillance, Epidemiology, and End Results analysis of patients from 2004 to 2009
Authors: Logan Jennifer K. , Huber Kathryn E. , DiPetrillo Thomas A. , Wazer David E. , Leonard Kara L. 
Published: November 2013

BACKGROUNDAccording to the 2013 National Comprehensive Cancer Network guidelines, pelvic radiation therapy (RT) is one of the preferred regimens for patients with metastatic rectal cancer (mRC). The objective of this study was to analyze patterns of care and outcomes data for the receipt of RT among patients with mRC using the Surveillance, Epidemiology, and End Results (SEER) database.METHODSPatients with stage IV rectal or rectosigmoid cancer were identified in the SEER database (2004‐2009). Patients were stratified according to their primary disease site (rectum vs rectosigmoid), tumor (T) classification, and lymph node (N) classification. Treatment regimens (with or without surgical resection, with or without RT) were recorded. The Fisher exact test was used to compare RT rates based on stratified factors. Two and five‐year survival rates were compared among treatment groups.RESULTSIn total, 6873 patients with stage IV rectal cancer and 3417 patients with rectosigmoid cancer were identified. Overall, 20.5% of patients with rectal cancer underwent surgery alone, whereas 38.7% received RT with or without surgery. Within the rectosigmoid group, 51.4% of patients underwent surgery alone, and 15.1% received RT with or without surgery. The use of RT differed significantly between patients with in situ (Tis) through T2 tumors versus T3/T4 tumors (P < .001) and between those with N0 disease versus N1/N2 disease (P < .001). The 2‐year and 5‐year survival rates differed between treatment groups, with the highest survival rates observed among those who received combined surgery and RT.CONCLUSIONSThe primary treatments for patients with mRC include RT with or without surgery. RT is used more commonly in patients with primary rectal (vs rectosigmoid) tumors, N0 disease, or Tis‐T2 tumors. Treatment with combination surgery and RT is associated with prolonged survival. Cancer 2014;120:731–737. © 2013 American Cancer Society.
Efferent and afferent connections of the olfactory bulb and prepiriform cortex in the pigeon (Columba livia)
Authors: Atoji Yasuro , Wild J. Martin 
Published: November 2013

ABSTRACTAlthough olfaction in birds is known to be involved in a variety of behaviors, there is comparatively little detailed information on the olfactory brain. In the pigeon brain, the olfactory bulb (OB) is known to project to the prepiriform cortex (CPP), piriform cortex (CPi), and dorsolateral corticoid area (CDL), which together are called the olfactory pallium, but centrifugal pathways to the OB have not been fully explored. Fiber connections of CPi and CDL have been reported, but those of other olfactory pallial nuclei remain unknown. The present study examines the fiber connections of OB and CPP in pigeons to provide a more detailed picture of their connections using tract‐tracing methods. When anterograde and retrograde tracers were injected in OB, projections to a more extensive olfactory pallium were revealed, including the anterior olfactory nucleus, CPP, densocellular part of the hyperpallium, tenia tecta, hippocampal continuation, CPi, and CDL. OB projected commissural fibers to the contralateral OB but did not receive afferents from the contralateral olfactory pallium. When tracers were injected in CPP, reciprocal ipsilateral connections with OB and nuclei of the olfactory pallium were observed, and CPP projected to the caudolateral nidopallium and the limbic system, including the hippocampal formation, septum, lateral hypothalamic nucleus, and lateral mammillary nucleus. These results show that the connections of OB have a wider distribution throughout the olfactory pallium than previously thought and that CPP provides a centrifugal projection to the OB and acts as a relay station to the limbic system. J. Comp. Neurol. 522:1728–1752, 2014. © 2013 Wiley Periodicals, Inc.