dataesr/scientific-paragraphs-categorization huggingface dataset:
edu/CaMgATPEGTA-TS. htm programme  [40]. For each enzymatic reaction, 150 L of reaction buffer were incubated at 37 °C and the reaction was triggered by adding 5-10 µg purified protein. The reaction was quenched with EGTA or thapsigargin (TG). The data were analysed using SigmaPlot Systat software. The slope obtained after quenching was subtracted from the slope obtained after addition of the protein to eliminate any contaminant activity. Specific activity was determined over time intervals where the change in absorbance was linear minus any background activity observed after calcium removal or TG inhibition.
An example of The yields were estimated from SDS-Page gels and Western Blots, using ImageJ software  [36, 70]. The cultures were grown in rich media unless specified otherwise. Data was estimated for each construct on at least two batches of protein sample, using rabbit SERCA1a and free GFP as control standards; n/d-not determined. assessment of hSERCA2a-GFP-His 8 expression levels in different clones using in-gel fluorescence and Western blotting techniques is shown in Figure  1. To ensure the highest possible expression levels of functional hSERCA2a-GFP-His 8 , we used rich medium and lowered the temperature to 18 °C, before two steps of galactose induction of protein expression  [16]. In addition, the use of baffled flasks for cell growth significantly improves media aeration and allows routine yields of 50-60 g of yeast per litre culture to be obtained.
Purified hSERCA2a (from hSERCA2a-GFP-His 8 construct) showed calcium-dependent and thapsigargin-sensitive activity. The calcium K 0. 5 for hSERCA2a of 0. 6 μM found herein is within previously reported values  [57]. A significant difference observed in the turn-over rate between previously purified samples of SERCA2a may be explained by the different lipid 100% specific ATPase activity corresponds to 3 µmol hydrolysed ATP/min/mg of hSERCA2a. The results are the means of seven measurements, using protein obtained from three independent membrane preparations; error bars represent ±S. D. doi: 10. 1371/journal. pone. 0071842. g006 content, since previous data were measured on vesicular microsomes which contain some natural lipids associated with SERCA2, whereas SERCA2a purified from S. cerevisiae was not reconstituted into liposomes and was analysed in the presence of detergent.
Amplification and sequencing of TS genes Two upstream and two downstream primers to the region containing the T/C transition of TS-encoding genes were designed (59 primers: TS-51, 59-GGAGGCTGTCGG-CACGCTCTC-39 and TS-5, 59-GCTTCACTGCCGTGAC-CATCG-39; 39 primers: TS-31, 59-TCACGCAGCGGTACG-CATCCT-39 and TS-3, 59-CAGCGGGACCACAACCACGCT-39), so that all the TS sequences annotated in the GenBank were targeted in at least one of the four PCR reactions to be performed. Amplification was carried out with 0. 4 mM of each primer, 5 U of Pfu polymerase enzyme (Promega), 2. 5 mM of dNTPs, and 100 ng of genomic T. cruzi DNA as template in 50 ml final reaction volume. The PCR cycle consisted of 30 rounds of 94uC for 45 s, 63uC for 45 s, and 72uC for 45 s, with a first step of 2 min at 94uC and one last step of 5 min at 72uC.
PCR products were analyzed by electrophoresis in 2% agarose gel. Amplicons were purified and both strands sequenced with the primers used for amplification. Chromatograms were visually examined to determine the presence of C and/or T in the first position of the codon 342. Firstly TS-51/TS-31 primer set was used and those genomes rendering only the Tyr 342 codon were then subjected to the other three PCR reactions. The IUPAC nomenclature for the genetic code was used to define single nucleotide polymorphism (SNP) positions with mixed base identification set to 15% of the highest peak. Sequences were deposited in the GenBank with the accession numbers KC286514, KC286515, KC286516, KC286517, KC286518, KC286519, KC286520, KC286521, KC286522, KC286523, KC286524, KC286525, KC286526, KC286527, KC286528, KC286529, KC286530, KC286531, KC286532, KC286533, KC286534, KC286535, KC286536, KC286537, KC286538, KC286539, KC286540, KC286541, KC286542, KC286543, KC286544, KC286545, KC286546, KC286547, KC286548, KC286549, KC294586 and KC294587.
Sequence comparison of the region around the codon 342 A 455-bp consensus sequence of each T. cruzi stock was obtained by comparison of forward and reverse sequences of the TS-51/TS-31 PCR reactions. Sequences from the different stocks were aligned and compared by using ClustalW2 program  [42]. A clustering tree was built by using SplitsTree4  [43]  with the following options: i) the ''UncorrectedP'' method which computes the proportion of positions at which two sequences differ was used; ii) the ambiguous state codes (such as W, M, V …) were handled with the option 'Average' meaning that the contribution at a site is averaged over all possible resolutions of the ambiguous codes, with the exception that sites having the same ambiguous code contribute zero; iii) the distance-based method used was UPGMA because we considered that evolution rate must be the same upon all branches; the bootstrap was conducted with 1,000 iterations.
Presence of the T/C SNP in codon 342 of TS genes The findings presented above strongly suggest the intriguing absence of iTS genes in TcI parasite genome. To further test the differential distribution of aTS and iTS among T. cruzi stocks belonging to different DTUs, the T/C SNP was directly searched by sequencing PCR-amplified gene fragments comprising the surrounding region. To assess the representation of the Tyr 342 His mutation among these different parasite stocks, two primers were designed upstream and two other downstream the target codon. All TS genes deposited at GenBank were covered given that all these known sequences were targeted at least once in the PCR strategy designed. Table  2  summarizes the biological sources and geographical origins of the parasite isolates tested and the findings observed.
In addition, increased circulating TS activity correlates with several abnormalities observed early during the infection  [26, 28]. The involvement of shed aTS in the alterations of the histoarchitecture of the spleen, thymus and ganglia, as well as in the induction of thrombocytopenia has been evaluated by both the administration of recombinant aTS to naive mice and the neutralization of the enzymatic activity during the acute infection  [26, 28, 48]. Here the fine quantitative SNP mapping allowed us to identify aTS/iTS differences that remain hidden in genomic analyses  [49]  because iTS genes are not included in databases taken as reference. The present quantification of TS genes in parasite stocks exposed the absence of iTS genes together with the presence of similar copy number of aTS in all TcI parasite stocks tested (28 to 32 copies/ haploid genome).
Ethical approval and study design This randomised, double-blind, parallel, controlled study was approved by the Institutional Review Board of Tours, France (Région Centre, Ouest-1) (Trial registration: EudraCT 2008-004153-15 and NCT00847977). Patients were enrolled after their next-of-kin provided written informed consent. Retrospective consent, when available, was obtained from patients. Patients were enrolled from October 2008 to October 2010, when recruitment was completed in three ICUs of the Nantes University Hospital.
Data handling The following data were recorded: general characteristics, including demography, initial GCS score, WFNS grade, time from tracheal intubation to study inclusion, vasopressor therapy, fluid challenges and surgical procedures prior to inclusion. Natraemia, chloraemia, kalaemia, magnesemia, phosphatemia, ionized calcaemia, azotaemia, albuminaemia, osmolarity, lactataemia, arterial gases and haematocrit were measured immediately before and at 6, 12, 24, 36 and 48 hours after starting the treatment. The total volume of fluid administered and the evolution of ICP were recorded during the study period (48 hours). Episodes of ICH, modifications on the control CT (bleeding, herniation or brain swelling), osmotherapy and/or barbiturate use, transfusion, vasopressor use, time to achieve more than 50% of goal calories of enteral nutrition, duration of mechanical ventilation, length of ICU stay and mortality rate were also recorded in the ICU.
Acknowledgements We gratefully acknowledge  Delphine Flattres  for her critical help with the study and the nurses and medical team of the  Surgical Intensive Care Units of Nantes University Hospital  for technical assistance. This work was supported by  B-BRAUN MEDICAL. B-BRAUN MEDICAL  provided the solutions but was not involved in the study design, patient recruitment, data collection and analysis, report writing and publication. The  University Hospital of Nantes (UHN)  sponsored the study. UHN stored the data, ensured the monitoring of the study. The biostatistics unit (Christelle.
Study population The CML patients included in this analysis were in CP, resistant to TKI according to the IRIS study definitions 2 or ELN recommendations  16, 17  and harbored a T315I BCR-ABL mutation detected prospectively or retrospectively on frozen samples, by any validated means, between 1999 and 2010. CP CML patients with a T315I mutation were extracted from a previously described updated international database containing information from 222 T315I + CML patients (all phases and those with Philadelphia chromosome-positive acute lymphoblastic leukemia). 14 In that study,  14  the survival of T315I + patients did not differ between countries (unpublished data). In this study, the comparison group was CML patients in CP at diagnosis and at IM-resistance, previously screened at IM-resistance for BCR-ABL mutations and found to be T315I negative (they could harbor other mutations).
These T315 - patients were identified in the individual databases from three representative European centers (Lyon and Bordeaux in France and London, UK). All patients who had received an allogeneic transplant were eliminated from this study. Patients with the T315I mutation were pair-matched to T315I -IM-resistant patients according to three different variables: age at CP CML diagnosis (± 5 years), time elapsed between CP CML diagnosis and initiation of IM (± 5 years), and the duration of IM treatment (± 31 months). All patients were in CP at diagnosis and at IM-resistance and none had received ponatinib. These CML patients provided written consent whenever possible. This retrospective analysis was approved by the institutional review board/ethical review committee in each participating site/country whenever necessary.
Data collection Demographic, clinical, treatment, mutation, and survival data were collected from each of the three European centers for the control group or extracted -and updated whenever possiblefrom the epidemiological study database previously described. 14 tation screening was performed using different techniques (predominantly direct sequencing, but also polymerase chain reaction-restriction fragment length polymorphisms and denaturing high performance liquid chromatography in combination with sequencing) and, for some patients, included assaying frozen material. Patients with any T315I clone levels were included. A mutated clone was considered the major clone if it accounted for the highest percentage of cells among all detected clones, when this information was available.
Demographic information Sixty-four patients with CP CML at diagnosis and at IMresistance were identified in the initial international T315I + database and matched with 53 T315I negative counterparts (Table  1 ). Importantly, among the T315I + patients, the T315I clone was predominant in 42 patients (78%) out of 53 cases evaluable for quantification, being predominant over wild-type transcripts in 31 patients or other mutated transcripts in 11 patients (21%). In 10 patients (19%) the wild-type clone or another mutated clone was predominant. Significantly more patients had received interferon-α prior to IM in the T315I + group (64% versus 37. 7%; P=0. 008), but the duration of interferon-α treatment did not differ between the two groups (10 versus 12 months, P=0. 98). The initiation of IM occurred at a median of 33 months after diagnosis in the T315I -group versus 63.
Acknowledgments F-EN thanks  Mrs M. Etienne ,  CRA, Pierre-Bénite, France , for help with the data collection;  Mr Mohamad Sobh, PharmD ,  CRA ,  Pierre Bénite , France for editorial assistance, the association " Regarde un jour le monde " for its constant support, and  Mrs Barbara White , for her critical proof-reading of this manuscript. We also thank the hematolog tumor bank of the  CHU of Bordeaux, France.
These include the study of Feltens et al. [33]  in Drosophila melanogaster, by far the most in depth exploration of the method, Kaufmann et al. [34, 35]  in biting midges and Karger et al. [36]  in ticks. The prospect of MALDI-TOF MS to discriminate arthropod species motivated us to set out and further explore this techniquetogether with a computational approach developed for ''omics'' data -for its use in malaria vector biology. Here, we measured MALDI-TOF MS spectra from 32 Anopheles laboratory colonies and 2 field populations representing 12 Anopheles species. The Anopheles colonies included key members of the A. gambiae species complex (i. e. A. gambiae s. s. of the M and S molecular form, A. arabiensis, the zoophagic A. quadriannulatus and one saltwater (red) colonies. The spectra were taken from crude suspensions of heads and thoraces in SA solution.
The spectra obtained by the spectrometer were then loaded into Launchpad TM 2. 8 software (Shimadzu-Biotech Corp. , Kyoto, Japan) to create a peak list for each sample spotted on the plate (i. e. four lists for each mosquito specimen). The peak lists with size (m/z value) and intensity values (arbitrary units) were then saved as ASCII text files for further data analysis. The peak lists and additional information are provided in Dataset S1 and Table  S1. The software parameters were set to the following values: parent peak cleanup = ''advanced scenario''; peak width = ''80 chans''; smoothing filter width = ''50 chans''; baseline filter width = ''500 chans''; peak detection method = ''threshold apex''. For the ''threshold apex'' peak detection, the threshold type was set as dynamic and the threshold offset to 0.
Unsupervised Cluster Analysis For the unsupervised cluster analysis, the peak lists, previously saved as ASCII text files, were loaded into SARAMIS TM 3. 4. 1. 11 (AnagnosTec, Germany) to create a binary presence/absence table for each peak in the whole data set with columns for peaks and rows for spectra. Peaks were binned within 6800 ppm. A custom-written macro in Excel 2002 (Microsoft) then merged the peak lists into a single ''average'' peak list for each mosquito specimen. Here, a peak was deemed present if it was detected in at least three out of four lists. The consolidated table was then loaded into the freely available PAST 2. 14 software and a dendrogram generated using the ''Dice'' multivariate clustering algorithm for paired groups  [40]. The computed output was exported in nexus file format and displayed with the freely available FigTree 1.
Here, training of the classifier is based on James-Stein shrinkage estimates of correlations and variances, where regularisation parameters are chosen analytically without re-sampling and therefore computationally non-intensive. The approach applies a pooled centroids formulation of the multiclass LDA predictor function, in which the relative weights of Mahalanobis-transformed predictors are given by correlation-adjusted t-scores (CAT scores). The CAT scores allow for simple ranking and selection of peaks. For the supervised LDA, ASCII files containing the peak list for each measurement (i. e. four files per specimen) were imported into the open source statistical software package R version 2. 14. 1  [43]. The peaks from the original peak lists were dynamically binned with the R package ''caMaClass''  [44] , with a variable bin size between 800-1600 ppm.
For example, separating A. arabiensis from A. gambiae s. s. the same data could be used to first separate between the species and then to further classify A. gambiae s. s. into M and S molecular forms. Similarly this would allow for re-running the analysis should taxonomy change in one or the other way. Another approach that has been proposed to discriminate between A. gambiae s. s. and A. arabiensis specimens is NIRS, near infrared spectroscopy  [25]. Similar to our approach spectra are recorded and explored for discriminant patterns. The spectra themselves are, however, less conducive in drawing conclusion as to what causes them and what makes the differences between classes due to the complex nature of the spectra. An association between observed patterns and specific chemical components is extremely difficult if not impossible.
Acknowledgments We would like to express a special thanks to  Marcel Tanner  ( Swiss TPH ) for supporting this study and  Guido Vogel  ( Mabritec SA ) for useful discussions and scientific advice. We are grateful to  Danica Janc  ˇariovaand  Mohamad Abdul Rustom Sater  for mosquito rearing at Swiss TPH. We particularly thank  Paul Howell  from  MR4  for many of the mosquito specimens and all the donors of mosquito stocks:  Badria El Sayed  (DONGOLA),  Carles Aranda (EBRO) ,  Francis Atieli  ( ASEMBO1 ),  Greg Lanzaro  (MOPTI),  Hillary Ranson  ( RSP-ST  and  ZAN/U) ,  Jack Seawright  (ORLANDO and STECLA),  John Vulule  (RSP),  Mark Benedikt  ( IN22C+ ),  Maureen Coetzee  (KGB and SKUQUA),  Mustafa Dakeen  (SENN),  Nora Besansky (MALI-NIH  and PIMPERENA),  Rajendra Maharaj  (OPHANSI),  Vincent Corbel  ( KISUMU1 ) and  William Collins  ( F1 ,  G3 ,  MINIMUS1 ,  STE2  and  WRAIR2 ).
Justification and main hypothesis The notion of mental or intrapsychic conflict has been discussed for over a century by multiple theoretical approaches, but it has not been defined in measurable operational terms. The importance of said conflicts with regard to depression has not been described either. Based on PCT, we have developed a procedure to identify IDs, a type of cognitive conflict, using RECORD 5. 0 (  [44] ; the English version GRIDCOR 4. 0 is also available  [27] ), an application software for the analysis of RGT data. Preliminary results  [39]  indicate that about 90% of these patients have at least one of the cognitive conflicts (dilemmas) as formulated by our team based on their repertory grids. These results justify the development of a manualized intervention, DFT, to resolve these conflicts  [41] [42] [43].
Procedure This study was approved by the Committee for Ethics in Research of the University of Barcelona under the number (IRB00003099) and also by the ethical committees of the other centers involved in the study. It is registered at ClinicalTrials. gov under number NCT01542957 and also at Current Controlled Trials (ISRCTN92443999). Professionals of collaborating centers will be asked to inform their patients with major depression or dysthymia of the existence of this psychological treatment study and enable us to contact those who accept the opportunity to participate. For each center, an information sheet for potential participant patients and another for professionals with information on how to refer patients for the study were created. Finally, to reach a wider population range, a web page (www.
Initial assessment The initial assessment (T1) will be carried out in three phases. Firstly, the nature of the study is explained and, if the patient agrees to participate and signs the informed consent, the BDI-II is applied to verify the clinically significant presence of depressive symptoms (a score above  19). Secondly, patients meeting this criterion will be evaluated using the SCID-I interview to confirm the diagnosis of MDD or DD (if this is not the case, they will be excluded) and explore for other comorbid disorders. The section "Overview" included in this interview will also be used to collect socio-demographic data and information relative to previous treatments, to clarify that they are not receiving and will not receive any other concurrent psychological treatment, and to record psychotropic drug consumption.
A few other instruments will also be used in this and further assessment sessions as part of another study. With patients selected in this phase, a second assessment session will be scheduled in the following weeks. In this third phase, the CORE-OM and the RGT will be administered. The resulting data will be analyzed with the RECORD 5. 0 software  [27, 44]. On the following day, they will be contacted to confirm their inclusion in the study (if they have at least one cognitive conflict) or exclusion (in which case a way of providing the appropriate assistance to them will be sought together with the professionals from the center where they came from). The evaluators will be psychology graduate students (or advanced undergraduates) who will have been specially trained to perform the entire assessment process, as in particular the SCID-I and the RGT interviews require specific training, and they will be, at this point, blind in regard to the treatment modality which will be assigned to the patients.
Statistical analyses All data derived from the measurements and the clinical data (including use of psychotropic drugs) and sociodemographic information will be entered into Statistical Package for Social Sciences version 20. 0 or later (IBM Corporation, Armonk, New York, USA). The main statistical calculations will be performed on an intention-to-treat basis (patients will be analyzed as initially randomized). Categorical data will be summarized as frequencies and percentages. Means and standard deviations will be used for continuous data for which normality tests will also be performed. Analyses will include elementary head-to-head comparisons of the intervention groups as well as mixed models of repeated measures analysis of variance in which initial measures (baseline) of the dependent variables will be used as covariates.
Ninety-six well black bottom plates and their silicone lids were from Greiner Bio One (Fisher Scientific, Illkirch, France). The automated 96-well microtiter plate assay was conducted on a Freedom Evo® 100 liquid handling workstation (Tecan, Lyon, France). The liquid handling (LiHa) arm was equipped with four LiHA standard fixed washable tips (Teflon ® -coated stainless steel, resistant to DMSO, Tecan). Dispensing steps, i. e. , liquid class parameters, were optimized and programmed using Evoware software. AGE fluorescence was measured using a microplate spectrofluorometer infinite M200 (Tecan, Lyon, France) and Magellan software (Tecan).
5 M). A blank of control, i. e. , 100% inhibition of AGE formation, consisted of wells with only BSA. The final assay volume was 100 μL. Both vesperlysines-like (λ exc 370 nm; λ em 440 nm) and pentosidine-like (λ exc 335 nm; λ em 385 nm) AGE fluorescence were measured using a microplate spectrofluorometer. The percentage of AGE formation was calculated as follows for each compound/extract concentration: AGEs (%) = [fluorescence intensity (sample) -fluorescence intensity (blank of sample)]/[fluorescence intensity (control) -fluorescence intensity (blank of control)] × 100. Dose-effect curves were best fit with a sigmoidal dose-response equation using Sigma Plot 12. 0 software, which enabled calculation of the IC 50 values.
THREE DIMENSIONAL HYDRODYNAMICAL CONSTRAINTS ON MODE EIGENFUNCIONS In order to quantify the departure from adiabatic eigenfunction, we have derived at different layers the velocity profiles v 3D (r) of the dominant radial modes trapped in given 3D hydrodynamical models of the surface layer of stars. We consider two 3D hydrodynamical models. The first one is representative for a red giant star with log g = 2. 5 and T eff = 4964 ± 22 K (see details in  [29] ), and was computed with CO 5 BOLD code  [30]. The second one is representative for the Sun  [31]  and was computed with the STAGGER code  [32, 33]. Both 3D models have been run during a sufficient duration such as to resolve the dominant trapped radial modes. The procedure followed for the derivation of v 3D (r) will be detailed in a forthcoming paper.