bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New System for Comparative Functional Genomics of Saccharomyces Yeasts
Authors: Caudy Amy A , Guan Yuanfang , Jia Yue , Hansen Christina , DeSevo Chris , Hayes Alicia P , Agee Joy , Alvarez-Dominguez Juan R , Arellano Hugo , Barrett Daniel , Bauerle Cynthia , Bisaria Namita , Bradley Patrick H , Breunig J Scott , Bush Erin , Cappel David , Capra Emily , Chen Walter , Clore John , Combs Peter A , Doucette Christopher , Demuren Olukunle , Fellowes Peter , Freeman Sam , Frenkel Evgeni , Gadala-Maria Daniel , Gawande Richa , Glass David , Grossberg Samuel , Gupta Anita , Hammonds-Odie Latanya , Hoisos Aaron , Hsi Jenny , Hsu Yu-Han Huang , Inukai Sachi , Karczewski Konrad J , Ke Xiaobo , Kojima Mina , Leachman Samuel , Lieber Danny , Liebowitz Anna , Liu Julia , Liu Yufei , Martin Trevor , Mena Jose , Mendoza Rosa , Myhrvold Cameron , Millian Christian , Pfau Sarah , Raj Sandeep , Rich Matt , Rokicki Joe , Rounds William , Salazar Michael , Salesi Matthew , Sharma Rajani , Silverman Sanford , Singer Cara , Sinha Sandhya , Staller Max , Stern Philip , Tang Hanlin , Weeks Sharon , Weidmann Maxwell , Wolf Ashley , Young Carmen , Yuan Jie , Crutchfield Christopher , McClean Megan , Murphy Coleen T , Llinás Manuel , Botstein David , Troyanskaya Olga G , Dunham Maitreya J 
Published: July 2013

Abstract
Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.
Viability, Longevity, and Egg Production of Drosophila melanogaster Are Regulated by the miR-282 microRNA
Authors: Vilmos Péter , Bujna Ágnes , Szuperák Milán , Havelda Zoltán , Várallyay Éva , Szabad János , Kucerova Lucie , Somogyi Kálmán , Kristó Ildikó , Lukácsovich Tamás , Jankovics Ferenc , Henn László , Erdélyi Miklós 
Published: July 2013

Abstract
The first microRNAs were discovered some 20 years ago, but only a small fraction of the microRNA-encoding genes have been described in detail yet. Here we report the molecular analysis of a computationally predicted Drosophila melanogaster microRNA gene, mir-282. We show that the mir-282 gene is the source of a 4.9-kb-long primary transcript with a 5′ cap and a 3′-poly(A) sequence and a mature microRNA of ∼25 bp. Our data strongly suggest the existence of an independent mir-282 gene conserved in holometabolic insects. We give evidence that the mir-282 locus encodes a functional transcript that influences viability, longevity, and egg production in Drosophila. We identify the nervous system-specific adenylate cyclase (rutabaga) as a target of miR-282 and assume that one of the main functions of mir-282 is the regulation of adenylate cyclase activity in the nervous system during metamorphosis.
Association of Maternal mRNA and Phosphorylated EIF4EBP1 Variants With the Spindle in Mouse Oocytes: Localized Translational Control Supporting Female Meiosis in Mammals
Authors: Romasko Edward J , Amarnath Dasari , Midic Uros , Latham Keith E 
Published: July 2013

AbstractIn contrast to other species, localized maternal mRNAs are not believed to be prominent features of mammalian oocytes. We find by cDNA microarray analysis enrichment for maternal mRNAs encoding spindle and other proteins on the mouse oocyte metaphase II (MII) spindle. We also find that the key translational regulator, EIF4EBP1, undergoes a dynamic and complex spatially regulated pattern of phosphorylation at sites that regulate its association with EIF4E and its ability to repress translation. These phosphorylation variants appear at different positions along the spindle at different stages of meiosis. These results indicate that dynamic spatially restricted patterns of EIF4EBP1 phosphorylation may promote localized mRNA translation to support spindle formation, maintenance, function, and other nearby processes. Regulated EIF4EBP1 phosphorylation at the spindle may help coordinate spindle formation with progression through the cell cycle. The discovery that EIF4EBP1 may be part of an overall mechanism that integrates and couples cell cycle progression to mRNA translation and subsequent spindle formation and function may be relevant to understanding mechanisms leading to diminished oocyte quality, and potential means of avoiding such defects. The localization of maternal mRNAs at the spindle is evolutionarily conserved between mammals and other vertebrates and is also seen in mitotic cells, indicating that EIF4EBP1 control of localized mRNA translation is likely key to correct segregation of genetic material across cell types.
First Example of Alkyl–Aryl Negishi Cross-Coupling in Flow: Mild, Efficient and Clean Introduction of Functionalized Alkyl Groups
Authors: Egle Brecht , de Muñoz Juan M. , Alonso Nerea , De Borggraeve Wim M. , de la Hoz Antonio , Díaz-Ortiz Angel , Alcázar Jesús 
Published: July 2013

Abstract
The first example of an alkyl-aryl Negishi coupling in a practical, sustainable, and high-yielding process using a silica-supported catalyst in flow is described. Excellent conversions and good functional group compatibility were obtained under very mild conditions. Functionalized alkyl groups were also introduced to provide access to synthetically useful molecules and to demonstrate the versatility of the method. The scalability was assessed, and a throughput of 7.5 mmol/h of processed substrate was achieved. All crude products were free from phosphine derivatives and ready for use in subsequent reaction steps.
Low Temperature Annealing of Inkjet-Printed Silicon Thin-Films for Photovoltaic and Thermoelectric Devices
Authors: Drahi Etienne , Gupta Anshul , Blayac Sylvain , Saunier Sébastien , Lombez Laurent , Jubault Marie , Renou Gilles , Benaben Patrick 
Published: July 2013

ABSTRACTSilicon nanoparticles-based inks were investigated in respect of their suitability for photovoltaic and thermoelectric applications. Nanoparticles with a diameter ranging between 20 to 150 nm were functionalized in order to avoid oxidation as well as having a good stability in suspension. After inkjet-printing and drying, they were annealed up to 1000 °C under nitrogen atmosphere by both rapid thermal and microwave annealing. The influence of the annealing treatment on the structural, electrical, optical and thermal properties was investigated by Raman, SEM, electrical and optical measurements. SEM and Raman demonstrate evolution of the microstructure at temperature as low as 600 °C. Optical, electrical and thermal properties depend strongly on the annealing temperature and tend to exhibit a modification of physical properties above 800 °C when the smallest nanoparticles begin to melt. The annealing method has been identified to be of primary importance on the layer microstructure and its thermal behavior.
Neoadjuvant Doxorubicin/Cyclophosphamide Followed by Ixabepilone or Paclitaxel in Early Stage Breast Cancer and Evaluation of βIII-Tubulin Expression as a Predictive Marker
Authors: Saura Cristina , Tseng Ling-Ming , Chan Stephen , Chacko Raju T. , Campone Mario , Manikhas Alexy , Nag Shona M. , Leichman Cynthia G. , Dasappa Lokanatha , Fasching Peter A. , Hurtado de Mendoza Fernando , Symmans W. Fraser , Liu David , Mukhopadhyay Pralay , Horak Christine , Xing Guan , Pusztai Lajos 
Published: July 2013

Abstract

Background.
This randomized phase II trial was designed to compare the rate of pathologic complete response (pCR) induced by neoadjuvant cyclophosphamide plus doxorubicin (AC) followed by ixabepilone or paclitaxel in women with early stage breast cancer (BC). Expression of βIII-tubulin as a predictive marker was also evaluated.

Patients and Methods.
Women with untreated, histologically confirmed primary invasive breast adenocarcinoma received four cycles of AC followed by 1:1 randomization to either ixabepilone 40 mg/m2 (3-hour infusion) every 3 weeks for four cycles (n = 148) or weekly paclitaxel 80 mg/m2 (1-hour infusion) for 12 weeks (n = 147). All patients underwent a core needle biopsy of the primary cancer for molecular marker analysis prior to chemotherapy. βIII-Tubulin expression was assessed using immunohistochemistry.

Results.
There was no significant difference in the rate of pCR in the ixabepilone treatment arm (24.3%; 90% confidence interval [CI], 18.6–30.8) and the paclitaxel treatment arm (25.2%; 90% CI, 19.4–31.7). βIII-Tubulin-positive patients obtained higher pCR rates compared with βIII-tubulin-negative patients in both treatment arms; however, βIII-tubulin expression was not significantly associated with a differential response to ixabepilone or paclitaxel. The safety profiles of both regimens were generally similar, although neutropenia occurred more frequently in the ixabepilone arm (grade 3/4: 41.3% vs. 8.4%). The most common nonhematologic toxicity was peripheral neuropathy.

Conclusions.
Neoadjuvant treatment of early stage BC with AC followed by ixabepilone every 3 weeks or weekly paclitaxel was well tolerated with no significant difference in efficacy. Higher response rates were observed among βIII-tubulin-positive patients.
Aminoguanidine Inhibits the AGE–RAGE Axis to Modulate the Induction of Periodontitis but Has Limited Effects on the Progression and Recovery of Experimental Periodontitis: A Preliminary Study
Authors: Chang Po‐Chun , Chong Li Yen , Tsai Sheng‐Chueh , Lim Lum Peng 
Published: July 2013

Background: Advanced glycation end products (AGE) have been found in inflamed gingival tissue and have been shown to interfere with the integrity of extracellular matrix and cell–matrix interactions. This study aims to investigate the modulatory effect of aminoguanidine (AG), an AGE inhibitor, in various stages of experimental periodontitis.Methods: Thirty‐six Sprague‐Dawley rats were used. AG or normal saline (NS) was systemically administered in the induction, progression, and recovery phases of ligature‐induced periodontitis. Dynamic changes of the periodontium were evaluated by microcomputed tomography, histology, and immunohistochemistry of the receptor for AGE (RAGE). Molecular mechanisms were evaluated by myeloperoxidase activity, gene expression of RAGE, and markers associated with tissue repair and homeostasis, including vascular endothelial growth factor (VEGF), type I collagen, fibronectin, and periostin.Results: AG appeared to inhibit the degradation of the collagen matrix in the induction phase but promoted collagen reorganization in the progression and recovery phases of experimental periodontitis. In the induction sites, periodontal bone loss was significantly reduced (P <0.05), with significantly reduced RAGE (P <0.05) and significantly elevated fibronectin and periostin levels (P <0.01). No significant alterations in the levels of myeloperoxidase, VEGF, and collagen were noted. In the progression and recovery sites, similar trends were observed, with insignificant differences relative to NS‐treated animals.Conclusions: AG reduced periodontal bone loss during the induction of experimental periodontitis, and the effects appeared to be insignificant in the progression and recovery phases. This modulation was related to the inhibition of the AGE–RAGE axis to resume cell–matrix interactions and maintain tissue integrity.
Trimerization of aldehydes with one α-hydrogen catalyzed by sodium hydroxide
Authors: Li Yu-Gang , Luo Chen-Xi , Qian Chao , Chen Xin-Zhi 
Published: July 2013

AbstractTrimerization of 2-methylpropanal (isobutyraldehyde) is a simple and effective method to synthesize 2,2,4-trimethyl-1,3-pentanediol monoisobutyrate and 2,2,4-trimethyl-1,3-pentanediol-3-monoisobutyrate which are often used as film forming auxiliaries in paints. The use of solid sodium hydroxide as a catalyst provides an excellent yield of above 85 % after the optimization of the reaction time and the catalyst dosage. Furthermore, trimerization of four other aldehydes with one α-hydrogen catalyzed by solid sodium hydroxide can also take place and the yield of 1,3-diol monoesters reaches 50–70 %. Trimerization of aldehydes with one α-hydrogen can be explained by a three-step reaction mechanism: (i) aldol condensation of aldehyde; (ii) crossed Cannizzaro reaction; and (iii) esterification of carboxylic acid and alcohol.
A retrospective review of cytogenetic studies on methyl isocyanate with special reference to the Bhopal gas tragedy: Is the next generation also at risk?
Authors: Samarth Ravindra , Gandhi Puneet , Maudar Kewal 
Published: July 2013

AbstractThe world’s worst industrial disaster, at Union Carbide, Bhopal, India, took place on 2–3 December 1984, leading to the leakage of poisonous methyl-isocyanate into the environment, causing thousands of deaths, pregnancy loss and for some, incapacitation for life. More than a quarter of a century later, the Indian Council of Medical Research undertook to redefine the abysmal consequences of the toxic gas exposure on the exposed population. This invigorated the interest of scientific community in the evaluation of the long-term effects, with reference to cytogenetic parameters. The thrust area was identified in terms of genetic disorders, low birth weight, developmental/growth disorders and congenital malformations. Also the impact on epigenetic factors, which may have contributed to variations in the functional expression of genes, was not negated, stimulating intense scientific research on in utero exposure and the progeny of the exposed population. To accomplish this mammoth task, molecular cytogenetic investigations must be undertaken in conjunction with conventional cytogenetics, using techniques such as FISH, Immuno-FISH, SKY and SNP analysis, to build up a cytogenetic database of the surviving population.
Impairment‐driven cancer rehabilitation: An essential component of quality care and survivorship
Authors: Silver Julie K. , Baima Jennifer , Mayer R. Samuel 
Published: July 2013

Answer questions and earn CME/CNEAdult cancer survivors suffer an extremely diverse and complex set of impairments, affecting virtually every organ system. Both physical and psychological impairments may contribute to a decreased health‐related quality of life and should be identified throughout the care continuum. Recent evidence suggests that more cancer survivors have a reduced health‐related quality of life as a result of physical impairments than due to psychological ones. Research has also demonstrated that the majority of cancer survivors will have significant impairments and that these often go undetected and/or untreated, and consequently may result in disability. Furthermore, physical disability is a leading cause of distress in this population. The scientific literature has shown that rehabilitation improves pain, function, and quality of life in cancer survivors. In fact, rehabilitation efforts can ameliorate physical (including cognitive) impairments at every stage along the course of treatment. This includes prehabilitation before cancer treatment commences and multimodal interdisciplinary rehabilitation during and after acute cancer treatment. Rehabilitation appears to be cost‐effective and may reduce both direct and indirect health care costs, thereby reducing the enormous financial burden of cancer. Therefore, it is critical that survivors are screened for both psychological and physical impairments and then referred appropriately to trained rehabilitation health care professionals. This review suggests an impairment‐driven cancer rehabilitation model that includes screening and treating impairments all along the care continuum in order to minimize disability and maximize quality of life. CA Cancer J Clin 2013;63:295‐317. ©2013 American Cancer Society.
Autochtones et récit policier en Amérique hispanique
Authors: Ponce Néstor 
Published: July 2013

Cet article a comme objectif l’analyse d’un sujet peu abordé dans les études consacrées à la littérature policière en Amérique hispanique : la présence des indigènes dans ces récits. Pour cela, l’auteur étudie l’œuvre de Leonardo Castellani, Luis Sepúlveda y Marisol Ceh Loo, qui a écrit le roman bilingue maya/espagnol X-Teya, u puksi’ik’al koolel, Teya, un corazón de mujer (2009), de Marisol Ceh Moo.
El delincuente en la literatura testimonial venezolana
Authors: Hernández Argenis Monroy 
Published: July 2013

En este artículo se analiza cómo la literatura testimonial venezolana de los años 70 escrita por delincuentes, construye modelos alternativos de ciudadanías que, epistémicamente, rompen con los patrones éticos, antropológicos, pedagógicos y sociológicos heredados de la modernidad. El análisis está centrado en las novelas-testimonios Retén de Catia (1972) de Juan Sebastián Aldana, Soy un delincuente (1974) de Ramón Antonio Brizuela y Cárcel Modelo Máxima Seguridad (1976) de Yon Calletano Franco. Las tres obras se inscriben en el género testimonial que comienza a manifestarse a finales de los años 60 en Latinoamérica y que, según algunos teóricos como Beverley (1987), surge de una experiencia vivencial de represión, pobreza, explotación, marginalización, etc. La investigación muestra a través de las teorías expuestas por Michel Foucault (1993), que a partir del acto denunciatorio, estos testimonios se enmascaran en un discurso « fuera de la ley » para imaginar un proyecto alternativo de nación a través de la lectura y la escritura.
El Cadillac en la configuración del protagonista
Authors: Vera Elvia Estefanía López 
Published: July 2013

Este artículo estudia la poética del espacio del escritor mexicano Martín Luis Guzmán (1887-1976), que a través del Cadillac configura al protagonista en La sombra del Caudillo. La obra de Guzmán se ubica dentro del subgénero conocido como narrativa de la Revolución Mexicana. La propuesta de análisis del artículo está centrada en la presencia de un espacio simbólico en el que Ignacio Aguirre se desenvuelve a través de un proceso de ascenso que culmina con su sacrificio. Analizo las diversas funciones del automóvil en la novela : la caracterización del personaje a través de un estatus económico debido a la sustitución habitual del caballo por el Cadillac dentro de la clase política mexicana ; así como la atmósfera de intimidad ; la manifestación metonímica de los sentimientos del protagonista y el espacio dinámico que acompaña al personaje hacia su destino fatal, es decir, el tránsito que va desde su cenit político hasta su muerte. Los diversos planos de significación le dan al Cadillac una dimensión simbólica que es necesario advertir para complementar la comprensión de la propuesta estética de la obra de Guzmán.
Violence homicide, drogues et déstructuration sociale
Authors: González Olga L. 
Published: July 2013

On parle souvent de la « colombianisation du Mexique » pour décrire le phénomène de la violence au Mexique. La connaissance de processus sociaux de ces deux pays, ainsi que l’examen des données et l’étude des rapports spécialisés sur la violence homicide dans ces deux pays nous permettent de nous pencher sur les différences, les similarités de cette violence, et aussi sur les réponses de la société.Dans un premier temps, nous étudions les niveaux de la violence homicide au Mexique et en Colombie et nous rappelons que ceux-ci sont trois fois plus élevés dans ce dernier pays. Aussi, le parallélisme entre les deux pays se trouve ailleurs, dans les caractéristiques communes à la montée de cette violence. En effet, l’arrivée des mafias, mais surtout la concurrence avec d’autres acteurs armés (l’armée légale ou d’autres groupes) entraîne une hausse brutale de la violence homicide. Par la suite, nous montrons comment les mafias provoquent la hausse des violences homicides dans des régions, vastes en Colombie, localisées au Mexique, où le tissu social est déjà affaibli. Les contextes de déstructuration sociale sont favorables à la pénétration de ces acteurs au sein de la société, qu’ils fragilisent davantage.La dernière partie de cet article explore les différentes réponses (mobilisations sociales) face à ce problème. C’est ici où le contraste entre les deux pays est le plus remarquable. Nous concluons avec quelques questions sur les capacités d’action devant le grave problème de la violence homicide en Amérique latine.
L’évangélisation des Indiens d’Amérique
Authors: Benoit Jean-Louis 
Published: July 2013

La légende noire consiste en une lecture très négative de l’histoire de l’Espagne et plus particulièrement de la conquête de l’Amérique. L’Espagne aurait évangélisé par la violence les Indiens au prix d’une extermination massive et d’expropriations. Bartolomé de las Casas, vibrant défenseur des Indiens a dressé un tableau très sombre de la Conquista. Certains de ses jugements doivent être nuancés. La « Controverse de Valladolid » n’a pas eu pour but de savoir si les Indiens avaient une âme, mais de faire le point sur la colonisation et l’évangélisation. La Couronne espagnole a voulu par le système de l’encomienda et de nombreuses lois éviter les abus des colons et protéger les Indiens. L’évangélisation n’a pas pu se faire sans la colonisation. Elle a été marquée par un souci d’acculturation et de métissage. Son succès a été réel. La conquête de l’Amérique du Nord par les Anglais a été plus brutale. La colonisation y a entraîné une exclusion voire une extermination des Indiens. C’est pourtant les Américains du Nord qui ont le plus contribué à la diffusion de cette légende noire antiespagnole.
Carlos Pellicer y Germán Pardo García
Authors: Gutiérrez León Guillermo 
Published: July 2013

The purpose of this essay is letting the readers to know about the love story between two of the most relevant latinamerican poets (Carlos Pellicer and German Pardo Garcia) and the very first gay poem in mexican poetry during the 20th century. The large poem « Recinto » (Enclosure), written by Carlos Pellicer in 1931 (and published 10 years later), has two major values, being the first homoerotic poem in mexican poetry, and expressing in verses the love story between Carlos Pellicer and German Pardo Garcia.