dataesr/scientific-paragraphs-categorization huggingface dataset:
The participants sat in a double-walled sound attenuated booth. The sounds were presented using Matlab, through an ASUS Xonar Essence STX soundcard, a TDT PA4 attenuator, a TDT HB7 headphone buffer, and Sennheiser HD 650 headphones. Stimulus levels were checked using a KEMAR Type 45DA head assembly. Trials with each of the two frequency regions were mixed together in a single block. Participants performed the jitter detection task in a first 2-h session and came back a week later to do the rate discrimination task in a second session. The acoustic stimuli consisted of monophasic pulses. The stimuli were sampled at 44,100 Hz, 16 bits, and the pulses were one-sample wide. The interpulse intervals were rounded off to the nearest sample, and the resulting pulse train was then filtered in a specific frequency band.
Methods This multicenter retrospective observational study was conducted in 7French kidney transplant centers. We identified 16 patients (11 male) aged 46. 5 years (34-51. 8) from the ASTRE prospective database of the Spiesser Kidney Transplantation Group (Angers, Caen, Clermont-Ferrand, Reims, and Strasbourg University Hospitals) and the DIVAT prospective database (Necker and Toulouse University Hospitals). Patients aged at least 18 years who had undergone kidney transplantation and received anti-TNFa treatment were included in this study. The ethical committee of the institution approved the extraction of data from the patient charts. Patient medical charts and demographics were retrieved from the hospital registries, and the following data were recorded: age, gender, nephropathy, past history of infection or malignancy, date of transplantation, and postoperative immunosuppressive regimen.
Statistics All analyses were performed using Stata software (version 13, StataCorp, College Station, TX) and were performed for a 2-sided type I error of a5%. Baseline characteristics are presented as the mean ± standard deviation (SD) or the median (interquartile range) for continuous data (assumption of normality assessed via the Shapiro-Wilk test) and as numbers and percentages for categorical data. Quantitative variables were compared between independent groups (infection yes/no and death yes/no) by Student t test or the Mann-Whitney U test if the conditions of the t test were not met (normality and homoscedasticity were analyzed using the Fisher-Snedecor test). When appropriate, comparisons between independent groups were analyzed using a Chi-squared test or Fischer exact test for categorical variables.
Flow cytometry The proportion of T cells expressing activation (HLA-DR and CD38) and maturation (CD27 and CD45R0) markers was determined in fresh, anti-coagulated whole blood as previously described  [25]. Briefly, fresh blood samples were incubated for 30 min using the following fluorochrome-labelled monoclonal antibodies (mABs): CD3-Pacific Blue (BD), CD4 Per-CP Cy5. 5 (eBioscience), CD8 V500 or CD8 Amcyan, CD27 APC-H7, CD45RO APC, HLA-DR FITC and CD38 PE (all from BD). Acquisition was performed on a FACS CANTO II (BD). Compensation was conducted with antibody capture beads (BD) stained separately with the individual antibodies used in the test samples. Flow cytometry data was analysed using FlowJo (version 9. 5. 3; Tree Star Inc. ).
Statistical analysis Data analyses were performed using Prism version 5 (GraphPad Inc. ), Microsoft Excel (Microsoft) and Stata version 13 (StataCorp, TX). Groups were compared using the Mann-Whitney U-test, the Wilcoxon signed rank test or Fisher's exact test as appropriate. For association analyses, the Spearman rank correlation was determined. P-values ≤ 0. 05 were regarded as significant. Associations of different anti-Tat antibody isotypes with CD4 + T cell count and viral load were calculated using uni-and multi-variate Poisson regression with robust variance estimates. Figure and table legends describe which test was used in which case. Heatmaps were created and hierarchical clustering performed with Qlucore Omics Explorer 3. 2.
008). Anti-Tat antibody-negative subjects were more likely to have low CD4 + T cell counts, although this difference was not significant (p-value = 0. 27). Since these data suggest that anti-Tat IgM responses are associated with a better disease prognosis, and usually IgM responses tend to disappear over time  [37] [38] [39] , we sought to investigate whether the presence of this isotype and its  Frequency of the different anti-Tat antibody isotypes was calculated in every stratum and compared using Freeman-Halton extension of the Fisher's exact probability test for a two-rows by three-columns contingency table association with high CD4 + T cell counts was dependent on the duration of HIV infection. Thus, subjects were stratified according to the duration of infection: less (n = 20) or more (n = 69) than 3 years.
Concurrence of anti-Tat IgG and IgM protects from disease progression To determine whether the presence of anti-Tat antibodies could protect against AIDS progression, CD4 + T Frequency of the different anti-Tat antibody isotype was calculated in every stratum and compared using Fisher's exact probability test cell counts were measured 1 year after the baseline anti Tat measurements. These data were available for 65 of the 96 subjects (67. 7 %). For these individuals we calculated the difference in CD4 + T cell counts measured at baseline and after 1 year follow up, expressed as a percentage decrease (or increase) and grouped the subjects into tertiles based on this measure  [40, 41]. Subjects with the lowest CD4 T cell counts (third tertile) experienced the fastest CD4 + T cell decline (median change: -25.
Acknowledgments We would like to thank the study volunteers as well as the WHIS field and laboratory teams for their support throughout the study. We also thank  Onesmo Mgaya ,  Dr. Lilli Podola ,  Dr. Stefano Buttò ,  Dr. Alessandra Cenci  and  Dr. Maria Josefina Ruiz Alvarez  for technical assistance and helpful data discussion, and  Dr. Eleonora Gallerani  and  Associate Professor Anthony Jaworowski  for their editorial assistance.
Funding This work was conducted under the umbrella of the EMINI study which was funded by the  European Commission  [ SANTE/2004/078-545  and  SANTE/2006/ 129-931 ] and the WHIS study, funded by the  German Research Foundation [DFG , grant  SA 1878/1-1 ] with additional support by the  European Community 's  Seventh Framework Programme  [FP7/2007-2013 and FP7/ 2007-2011 under EC-GA nu 241642]. FN was partially supported by the  Italian Center of Biotechnology (CIB)  and from  Consorzio Spinner  ( Regione Emilia Romagna and European Commission ). MC was partially supported by the  University of Ferrara  [iCOP Project]. The funding organizations did not play a role in the design of the study and collection, analysis, and interpretation of data and did not contribute to the writing the manuscript.
Materials and Methods Fungal strains and preparation of the bio-inocula. The strain of B. brongniartii was isolated on a selective medium  32  from the soil of a potato field highly infested by M. melolontha. The soil samples were collected in May 2012 in Romanów locality (Lublin voivodship, Eastern Poland). The strain was deposited in the Fungal Collection of the Department of Plant Protection and Breeding, Siedlce University of Natural Sciences and Humanities. The sequence has been deposited in the GenBank database and can be accessed to ID KT932309. The strain of B. bassiana was selected from rhizospheric soil of an apple orchard located in Valle d' Aosta by the company CCS Aosta, (Aosta, Italy) and named BB59. The sequence has been deposited in the GenBank database and can be accessed to ID KT932307.
The quality of amplification products was checked by 1. 5% agarose gels and ethidium bromide staining. PCR products resulting from three replicate reactions were pooled and purified with a Qiaquick PCR purification kit (Qiagen Inc. Chatsworth, CA, USA). Purified products were quantified by Qubit ® 2. 0 Fluorometer following manufacturer's instructions kit. Specificity was tested by PCR following the instructions reported above in the section 2. 5. SSR marker detection for the locus Bb4H9 was performed according to the method of Enkerli et al. 22  and was applied to all selected species (Table  1 ). SSR marker detection for the locus Ba01 was performed according Rehner S. A. , and Buckley E. P. 30. Statistical analyses. Data of qPCR quantification of DNA were obtained from soil samples where B.
Acknowledgements This work was supported by the  Polish Ministry of Agriculture and Rural Development ,  Sadownictwo metodami ekologicznymi -Określenie dobrych praktyk ochrony przed szkodnikami i chorobami w uprawach sadowniczych " (Grant nr. HORre-029-31-29/14(103 )) through funding of equipment and other expenses. We thank  Dr. Anna Benedetti  for sharing laboratory facilities.
Acknowledgments: We are grateful to  Andrew Cuthbertson  and  Eric Riddick  for inviting us to write this review. We thank the three anonymous reviewers for their insightful comments on previous versions of the manuscript. This review was inspired by several root defense-related research projects that are funded by the  Swiss National Science Foundation  ( PBNE33-114692 ,  PA0033_121483 , and  31003A_159869  to  Sergio Rasmann ).
Despite several tools developed to predict the secondary structures of pre-mRNA (ViennaRNA Package a ; RNAfold b ; mfold c …), it remains quite difficult to estimate the final shape of RNA and thus to design binding sequences based on this information. Interestingly, a recent report suggests that it is also important to consider the sequence of the target intron, and particularly the homology of the splice sites to the consensus sequences. 38 Based on this characteristic, the authors showed that it is possible to rank the different introns of a target pre-mRNA to determine which are the most likely to lead to an efficient trans-splicing reaction. To progress on this purpose, we can count on progress of bioinformatic tools in terms of 3D structure prediction, and, as discussed above, PTM screening using randomlygenerated libraries.
DNA sequencing and SNP polymorphisms detection After purification using the Wizard SV Gel and PCR Clean-Up System (Promega), the amplified fragments were sequenced using Big Dye ® Terminator Cycle Sequencing Ready Reaction version 3. 1 (Applied Biosystems) and ABI PRISM DNA Analyzer 3730 (Applied Biosystems)  [30]  at the Genomic Platform/PDTIS/Fiocruz. The direct DNA sequencing from PCR products was compared with the reference wild type Sal I GenBank accession nº AY571984  [24, 25]. Forward and reverse sequences were analysed using the free software Bioedit Sequence Alignment Editor version 7. 2. 5. Statistical significance of differences of pvmdr1 genotypes frequencies among Brazilian localities was assessed using Fisher's tests.
Acknowledgements CTDR and MFFC are recipients of a  Research Productivity Fellowship  from the  National Brazilian Council for Scientific and Technological Development (CNPq)  and from the  Foundation for Research Support in the State of Rio de Janeiro (Faperj) as Cientistas do Nosso Estado. LRG receives a doctoral fellowship from  CAPES ,  Brazilian Ministry of Education. The work was supported by the  POM (Fiocruz) , the  PNCM, Secretary for Health Surveillance, Brazilian Ministry of Health  and  Fiocruz-Pasteur network. Sponsors had no role in the collection, analysis and interpretation of data, in the writing of the manuscript and in the decision to submit the manuscript for publication.
Agradecimientos El Dr. Jordi Bover pertenece a la Red Nacional RedinRen (RD06/0016/0001 y RD12/0021/0033), a la Red de Biobancos Nacional Espa ñola (RD09/0076/00064) y al Grupo Catalán de Investigación AGAUR (2009 SGR-1116). Además, colabora con la Fundación Í ñigo Álvarez de Toledo (FRIAT). Queremos agradecer también al Sr. Ricardo Pellejero por su importante labor de asistencia bibliográfica. b i b l i o g r a f í a.
5 l de producto de PCR. La reacción de secuenciación se realizó con Big Dye Terminator 3. 1 (Applied Biosystems) según las instrucciones del fabricante. Se obtuvieron las secuencias de ambas direcciones en un secuenciador ABI 3100 (Applied Biosystems) en el Laboratorio de Secuenciación Genómica de la Biodiversidad y la Salud del Instituto de Biología, UNAM. Las secuencias se editaron y ensamblaron en Geneious Pro R7 (Biomatters). Se construyó una matriz de secuencias con especies de Agaricus sección Bivelares utilizadas en estudios filogenéticos previos  (Challen, Kerrigan y Callac, 2003; Geml, Geiser y Royse, 2004)  y también se incluyeron aquellas secuencias de GenBank que resultaron similares a la secuencia de la región ITS de la cepa IE 623 mediante una búsqueda en Blast. Las secuencias fueron alineadas en Muscle  (Edgar, 2004 ) y la matriz de datos se analizó mediante los métodos Neighbor-Joining, máxima verosimilitud e inferencia bayesiana en Geneious Pro R7 (Biomatters).
Análisis molecular Se obtuvieron 4 secuencias de ADN en ambos sentidos de la cepa IE 623 de diferentes resiembras y medios de cultivo con entre 620 y 710 pares de bases. Entre ellas existió una similitud nucleotídica de 99. 99% y su secuencia consenso de 712 pares de bases quedó registrada en GenBank bajo el número de acceso KM677957. Todos los análisis dieron resultados similares y se recuperó para Agaricus sección Bivelares, una estructura similar a la registrada por  Challen et al. (2003). En todos los casos, el clado de A. bisporus tuvo un soporte alto -bootstrap de Neighbor Joining 99. 4%, bootstrap de máxima verosimilitud 94. 6%, probabilidades posteriores bayesianas 1-. En los 3 análisis la cepa IE 623 se ubicó dentro del clado de A. bisporus. La figura 3 muestra los resultados del análisis de máxima verosimilitud.
Si bien dentro de A. bisporus hay poca estructura y los clados que se forman tienen poco soporte, la secuencia de la cepa IE 623 tiene una similitud genética mayor a cepas silvestres que a variedades cultivadas. Se encontraron 4 posiciones -39, 510, 516, 552-, en las que se presentaron heteroalelismos en A. bisporus var. bisporus. La cepa IE 623 mostró C, Y, C y C en estas posiciones, respectivamente, y solo una de las secuencias de GenBank (JF223230) tiene la misma secuencia, pero esta última difiere, además, por una A en la posición 522. La cepa IE 623 tiene, por lo tanto, una secuencia única. En las 4 posiciones de importancia heteroalélica el genotipo «CYCC» de A. bisporus var. bisporus indica que uno de sus núcleos tiene un genotipo «CCCC» que aparece con mayor frecuencia (8/58; 13% de las secuencias), mientras que el otro núcleo que es «CTCC» es menos frecuente (2/58; 3%) (tabla 2).
En la posición heteroalélica 510 de la región ITS las 63 secuencias de GenBank son C (18), T (41), o C/T = Y (4) (tabla 3). Sin embargo, estas 4 últimas secuencias difieren en otras posiciones de la cepa IE 623, lo que corrobora que no existe ninguna secuencia idéntica a la secuencia de dicha cepa. Id: identidad con el tipo de núcleo; N. o GB: número de acceso de GenBank. Por lo tanto, entre los 2 núcleos de la cepa heterocariótica IE 623 un núcleo que se podría denominar A contiene el nucleótido C, mientras que el otro núcleo llamado B contiene el nucleótido T. Se compararon las secuencias de estos 2 núcleos, A y B, con las 18 y 41 secuencias de GenBank, respectivamente conteniendo C o T en la posición 510. Entre ellas se encontró que 2 secuencias eran idénticas al núcleo A y 5 al núcleo B (tabla 4).
Entre las 2 secuencias de tipo A se observó que una corresponde a una cepa silvestre proveniente de Alaska (EF460354; Geml, Laursen y Taylor, 2008); mientras que entre las 5 de tipo B, una es un homocarión aislado por el método de protoplastos a partir de una cepa silvestre procedente de Francia (AF465403;  Callac et al. , 2003)  y otra es una cepa silvestre de Dinamarca (AF432886;  Challen et al. , 2003) ; de las 4 secuencias restantes de GenBank no existe información en la base o publicada sobre su procedencia.
Agradecimientos Este trabajo fue financiado en el marco de la cooperación bilateral México-Francia, a través del proyecto Agasub 115790 Conacyt-ANR. La secuenciación de ADN fue financiada por la red MEXBOL a través del proyecto Conacyt 1251085. Se agradece al técnico Ranulfo Castillo-del Moral, del INIFOR-UV, su asistencia en el trabajo de gabinete y elaboración de figuras. Al Dr. Gastón Guzmán y al técnico Juan Lara-Carmona, de la colección de hongos del Herbario XAL del INECOL, por su ayuda en la consulta y búsqueda de materiales. Al ingeniero Juan Carlos Sucarrats, de la empresa Riojal, la donación de compost para el cultivo de las cepas aisladas. Se agradece al M. en C. Rodolfo Ángeles-Argaiz, del Instituto de Biología de la UNAM, su apoyo en la obtención de las secuencias de ADN.
Variación en el número de esporas por basidio (%) y en el número promedio de esporas en diferentes cepas mexicanas silvestres de Agaricus bisporus. Número de casos que comparten el orden en las 4 posiciones heteroalélicas (39, 510, 516, 552) de los genotipos encontrados en las 63 secuencias de Agaricus bisporus de las variedades bisporus, burnettii y eurotetrasporus, obtenidas de GenBank. Frecuencia heteroalélica en las 4 posiciones relevantes de los genotipos encontrados en las 63 secuencias de Agaricus bisporus obtenidas de GenBank.
Variación en el número de esporas por basidio (%) y en el número promedio de esporas en diferentes cepas mexicanas silvestres de Agaricus bisporus. Número de casos que comparten el orden en las 4 posiciones heteroalélicas (39, 510, 516, 552) de los genotipos encontrados en las 63 secuencias de Agaricus bisporus de las variedades bisporus, burnettii y eurotetrasporus, obtenidas de GenBank. Frecuencia heteroalélica en las 4 posiciones relevantes de los genotipos encontrados en las 63 secuencias de Agaricus bisporus obtenidas de GenBank. Tabla 1 Tabla 2 Ejemplar del que se obtuvo la cepa Colector Cepa Esporas por basidio ASN Posición heteroalélica 1 2 Agaricus bisporus 3 4 Mata 641 39, 510, 516, 552 PC-GM IE 623 var. bisporus 0 47. 5 var. burnettii 50. 0 2. 5 2. 53 var. eurotetrasporus Ramírez Guillén 174 CTCT GM 35 IE 673 0 44.
AF465400, Agaricus bisporus var. eurotetrasporus DQ404388, Agaricus bisporus AF432886, Agaricus bisporus Tabla 4 FJ223227, Agaricus bisporus AF465399, Agaricus bisporus var. eurotetrasporus Secuencias idénticas a los 2 tipos de núcleo de la cepa heterocariótica IE 623, encontrados en 63 secuencias depositadas en GenBank. AF465404, Agaricus bisporus N. o GB Id Ref Material EF460355, Agaricus bisporus FJ755218, Agaricus bisporus Región Tipo EF460354 JN807464 A A Geml et al. , 2008 Cepa GAL18055 Cepa Tarimg01 FJ869182, Agaricus bisporus Alaska, EE. UU. HM561976, Agaricus bisporus JN234843, Agaricus bisporus (¿China?) Silvestre AF432886 B Challen et al. , 2003 Cepa RWK1885 JN234841, Agaricus bisporus Copenhague, Dinamarca Silvestre FJ755218 AF465403 FJ223225 B B B Callac et al. , 2003 Cepa CZ450-1 Cepa Bs 261-150 Cepa AGRHS202 HM561978, Agaricus bisporus (¿China?) AF187270, Agaricus bisporus Francia (protoplasto de Bs261) FJ223224, Agaricus bisporus FJ223229, Agaricus bisporus (¿China?) Silvestre FJ223228 B Cepa AS2796 FJ223230, Agaricus bisporus (¿China?) C623, Agaricus bisporus JN807464, Agaricus bisporus GU327643, Agaricus bisporus var.
Material y métodos Los datos proceden de la base de datos utilizada para la evaluación genética de la población Rasa Aragonesa de UPRA-Grupo Pastores  (Jurado, 2014)  e incluyen: 1) los partos procedentes de monta natural de 269. 503 ovejas, que se componen de 918. 956 registros effect of the genotype on the variability of prolificacy. All the models were run using the ASReml software. The effect of the presence of the ROA ® allele of the BMP15 gene on the mean prolificacy was 0. 32 extra lambs per lambing. Due to the selection on prolificacy performed during many years in this population ignoring the presence of this major gene, animals carrying the mutation were found to have lower remaining polygenic estimated breeding values than non-carrier animals, and there was no interaction between the BMP15 genotype and the polygenic background.
023; heterocigota  [R+] , n = 10. 013; o desconocida [desc. ] n = 258. 467), el efecto permanente ligado a cada oveja productiva (Perm: 269. 503 niveles), y finalmente, el efecto genético aditivo que corresponde al número de animales en el pedigrí (u: 305. 703 niveles). En este estudio, los partos de más de 3 corderos fueron agrupados en la categoría "4+". La distribución por genotipos en función del tipo de parto observado en esta muestra global aparece en la Tabla 1. El tipo de parto (TP) es una variable discreta que se analizó mediante el software ASReml  (Gilmour et al. , 2009) , utilizando varios modelos umbral  (Gianola, 1982). La parametrización utilizada para todos los modelos supone que la variable subyacente sigue una distribución normal estandarizada l ~ N (0, 1) y que el vector de umbrales t = (τ 1 , τ 2 , τ 3 ), que determina las cuatro categorías de parto, está afectado por efectos ambientales y genéticos.
Distribución de Weibull Los datos del módulo de elasticidad y dureza, hallados por las dos técnicas de indentación, fueron analizados mediante la distribución estadística de Weibull. Esta distribución es un indicador de la variabilidad de la resistencia de los materiales, debido a una distribución de tamaños de las imperfecciones  [22]  y cuanto mayor es su valor, menor es la variabilidad de la propiedad medida. Las curvas se construyeron en el software Ori-ginPro 8. 5 y a partir de éste se obtuvo el módulo de Weibull, que representa el grado de variabilidad de cada una de las propiedades halladas. Además el valor de la dureza y del módulo de elasticidad fue hallado gráfi-camente como el percentil 50.
Análisis estructural del recubrimiento La sección transversal del recubrimiento 8YSZ elaborado por SPS se muestra en la Figura 2. Se observa que el recubrimiento presenta una estructura homogénea en general (Figura 2a), con presencia de poros y una baja densidad de grietas. Además el recubrimiento presenta un espesor de 83 2 µm promedio de 5 medidas a 10 imágenes analizadas mediante el software ImageJ, según la norma ASTM B487-07  [23]. En la Figura 2b se muestra una ampliación del recubrimiento, el cual presenta una estructura compuesta por dos zonas: (i) una zona densa con partículas nanométricas semifundidas (ZS) y (ii) lamelas con mayor grado de fusión (ZF) que cubren la anterior zona. Figura 2: Sección transversal del recubrimiento 8YSZ (a) Vista de la interface recubrimiento -acero (b) Ampliación de la capa cerámica elaborada por SPS El resultado del análisis químico mediante FRX realizado al recubrimiento de 8YSZ mostró los siguientes compuestos (% en peso): ZrO2 con un 84.
AGRADECIMIENTOS Los autores agradecen a la Universidad de Antioquia (Colombia) por su financiación mediante los proyectos CODI MDC10-01-04, PR14-2-05 y al programa "Estrategia de Sostenibilidad 2014-2015 de la Universidad de Antioquia". El autor Andrés González agradece a Colciencias y Colfuturo por el apoyo financiero en sus estudios de doctorado realizados en la Universidad de Antioquia y en la Universidad de Limoges (Francia).
Mars Express dataset Since the Sun is the main source of ionization in the Martian upper atmosphere, the ionospheric behaviour as a function of solar cycle is directly dependent on its radiation behaviour with time. Only now, thanks to the more than 10 years of data from Mars Express  (Chicarro et al. , 2004) , is it possible to analyse the ionospheric response to changes in the solar activity during a full solar cycle with the same dataset and with an almost complete planetary coverage. The main dataset used in this study is the Mars Advanced Radar for Subsurface and Ionospheric Sounding (MARSIS)  (Picardi et al. , 2004)  on board the Mars Express (MEX) spacecraft  (Chicarro et al. , 2004). This instrument has been probing the ionosphere and subsurface of Mars since mid-June 2005  (Orosei et al.