dataesr/scientific-paragraphs-categorization huggingface dataset:
A case was considered positive when the scored nuclei displayed a break-apart signal in at least 20% of the counted nuclei. Gain of 1q was also assessed, using the ZytoLight® SPEC 1p36/1p25 Dual Color Probe kit (ZytoVision, Bremerhaven, Germany) according to the manufacturers' instructions. Assays were considered non-informative if the FISH signals were either lacking or too weak to be interpreted. Results were recorded using a DM6000 imaging fluorescence microscope (Leica Biosystems, Nanterre, France) fitted with appropriate filters, a CCD camera and digital imaging software (CytoVision, v7. 4).
RNA sequencing RNA sequencing was performed on three primary tumor samples. Total RNA was extracted from frozen specimen using Allprep® DNA/RNA Extraction kit from Qiagen (Hilden, Germany). Libraries were prepared from 1 µg of total RNA using the TruSeq Stranded mRNA Sample preparation kit (Illumina, San Diego, CA, USA) following the supplier recommendations. Paired-end sequencing was carried out by Integragen on Illumina NextSeq500 to generate a mean of 150 million reads of 75 base-pairs per sample. Trimmed reads were then mapped using TopHat2 2. 1. 0 to the reference genome, and TopHat-Fusion algorithm was then used to detect RNA fusions. In-house scripts were used to annotate and translate these gene-fusions, which were finally validated by blast.
RELA-fused or YAP-fused ependymomas Finally, 22 cases were classified as RELA-fused ependymoma (WHO grade III) (Table  2  and supplementary Table  1 ). In two other cases, occurring in infants (one WHO grade II, case 27 and one WHO grade III, case 26), a YAP1 rearrangement was detected by PCR and  FISH (data not shown). IHC positivity for YAP1 protein was observed in YAP-fused ependymomas as well as in RELA-fused ependymomas and did not allow to distinguish these two subgroups (data not shown). In RELAfused ependymoma, the DNA methylation-based classification failed to diagnose with certainty two tumors (#21 and #22) (Table  1 ). FISH analysis of tumor from patient #21 showed a rearrangement both for RELA and C11orf95 genes in concordance with nuclear p65-RelA expression. The analysis of the copy number profile of this case revealed chromothripsis of chromosome 11.
Imaging data may add another layer of information in the differential diagnosis of RELA ependymomas Imaging may also be helpful in the differential diagnosis of supratentorial brain tumors, especially if a corticalbased, predominantly cystic lesion is observed, favoring RELA-fused ependymomas  (5, 13). For multinodular tumors, particularly in young children, a YAP-fused ependymoma should be ruled out. Subependymal histopathological features should be systematically searched for. Although imaging findings for RELA-fused ependymomas have been reported  (5, 13) , the specificity and sensitivity of the individual radiological features for the diagnosis of this entity and its differential diagnosis remains to be determined. Mixed ependymomas/subependymomas should be diagnostically separated from ependymomas with RELA fusions Subependymomas are rare WHO grade I tumors, often intraventricular, which occur exceptionally in children  (9, 14).
Research methodology The literature for English-language articles published from January 1990 up to June 2017 was reviewed by searching the following three databases: ISI Web of Knowledge/Web of Science (Thomson Reuters, UK), PubMed (US National Library of Medicine National Institutes of Health) and Google Scholar (Google, UK). Search terms included 'dairy', 'milk', 'cheese', 'yoghurt', 'calcium', 'obesity', 'adiposity', 'overweight', 'body fatness', 'body weight', 'children', 'adolescent', 'girls', 'boys' and combinations of these. In addition, reference lists of identified published articles as well as of previous narrative, systematic reviews and meta-analyses were searched for citations of relevant publications. A total of 981 hits were retrieved. All observational and intervention studies conducted in adults, in nonhealthy children and those which assessed body weight in infants (<1 year) were not included in this review.
Fig. 1  summarises the literature search strategy. Using the same three databases and predefined publication dates, the search terms 'dairy', 'milk', 'calcium', 'mechanisms', appetite', 'fat oxidation', 'fat metabolism', 'gut microbiota', 'energy intake', 'satiety', 'children', 'adolescent', 'girls', 'boys' and combinations of these were used for the studies mentioned in the mechanistic section of the present review. Mechanistic studies in cells or animals were limited to searches of the reference lists of identified published studies and relevant reviews for citation of relevant publications. We have summarised the evidence base, which we identified by study design; cross-sectional studies, longitudinal studies, and intervention studies and provided a narrative summary for the studies we identified by study design.
The authors adjusted their analysis for age, sex, ethnicity, education of mother, and energy intake, soda intake, physical activity, and milk substitutes intake. Wiley  (30)  analysed National Health and Nutrition Examination Survey data from 1999 to 2004 and suggested that a dietary pattern characterised by greater milk consumption was associated with increased BMI among children aged 2-10 years, and dairy product intake among 2-to 4-year-old children. The sample included 1493 participants, of which 68 % were Caucasian, 15 % Hispanic and 15 % African/African American. The authors adjusted their analysis for age, birth weight and ethnicity. We understand that the associations between the exposure (milk and other dairy product consumption) and outcome (body weight/composition) may reflect reverse causality, which means that the presence of adiposity in children may affect their dairy product consumption habits.
For instance, twenty-six of the thirty-one studies reviewed included data on both boys and girls, and only sixteen adjusted for sex. Similarly, five  (35, 38, 41, 42, 48)  of the fifteen studies, which analysed data in school-age children and adolescents, adjusted for pubertal growth development. This is important given that children and adolescents' body size and composition are influenced by the sex and pubertal growth rate, for example, change in height  (65)  , with notable differences in growth rate in the period from early childhood to adolescence. Thus, assumptions that the body composition measures would be independent of pubertal growth stage are invalid and both observational and controlled randomised trials need to consider the influence of pubertal development on the effect of milk and other dairy product consumption on indicators of adiposity.
Consistent with this result, IPs from the control serum were not recognized by mAb2C2 or mAb1D9 (Figure  3B ). The 93 kDa bands were subjected to mass spectrometric analysis followed by a database search using the T. cruzi CL Brener (hybrid clone) genome database (Supplementary Table  S1 ). The mAb2C2 immunoprecipitates from the CL strain showed high identity with sequences from two CL Brener haplotypes, namely, TcCLB. 507089. 170 (Esmeraldolike haplotype) and TcCLB. 506725. 20 (non-Esmeraldo-like haplotype), with 16% coverage. Both sequences code for the same 67 kDa hypothetical protein. Interestingly, mass spectrometric analysis of the 93 kDa band from the immunoprecipitation of the G strain with mAb2C2 and mAb1D9 also identified the same protein (TcCLB. 506725. 20) with 19. 6 and 17. 2% coverage, respectively (Supplementary Table  S1 ).
Only MAP2 was selected for polyclonal antibody production in mice. The polyclonal antibody against the MAP2 peptide reacted with a band of 93 kDa from EA lysates immunoprecipitated with mAb2C2 (Figure  3E ), confirming that the MAP2 peptide is part of the protein core of Ssp-4. These data confirm that the hypothetical protein identified by mass spectrometry is Ssp-4, as previously identified by mAb2C2  (Andrews et al. , 1988). We sequenced nucleotides from the T. cruzi CL Brener, G and CL strains, and the protein alignment revealed that the Ssp-4 sequence is well conserved across all strains and among CL Brener haplotypes, clone Dm28c, and the Sylvio strain from the genome database (Supplementary Figure  S2A ). Protein identity between all strains was analyzed and was found to be at least 95.
These challenges led us to identify Ssp-4 using approaches other than immunostaining, such as mass spectrometry (MS) of mAb2C2and mAb1D9-immunoprecipitated proteins, protein sequencing with bioinformatic analysis and quantitative PCR. Based on the CL Brener hybrid clone genomic database, haplotype sequences encode a hypothetical protein that is highly expressed (mRNA and protein) in amastigote forms  (Atwood et al. , 2005; Minning et al. , 2009). Additionally, Ssp-4 sequences exhibit homology with a hypothetical protein from Trypanosoma rangeli and Leishmania ssp. , but not Trypanosoma brucei, which indicates that these proteins could be associated with the presence of an intracellular cycle defined by the amastigote form. In silico analysis of the amino acid sequences identified by MS led to the identification of Ssp-4 domains previously described by  Andrews et al.
2 kV and 100 V, respectively. All analyses were performed in positive ion mode. The spectra were acquired from 50 to 2000 m/z. Peptides from the IPs of the G strain were injected onto an LTQ-Orbitrap Velos (Thermo). Masses from the raw Q-TOF files were corrected using a lock mass of m/z 784. 823, and the raw data were converted to the. pkl format using the ProteinLynx Global Server (Waters). Orbitrap raw files were converted into. mgf files using MSConverter. Searches were performed in MASCOT (2. 4. 1 version) against a Trypanosoma cruzi CL Brener database (downloaded in 2017/05, 21,169 sequences) by considering a peptide and fragment mass tolerance of 0. 5 Da (for Q-TOF files) and peptide and fragment mass tolerance of 10 ppm and 0. 6 Da, respectively. Carbamidomethylation of cysteine and oxidation of methionine residues were specified as fixed and variable modifications, respectively.
In Silico Analysis Bioinformatics was performed using the ExPASy 1 platform. The signal peptide was predicted by SignalP v. 4. 1. The TargetP v. 1. 1 platform was used to predict subcellular location. Hydrophobic domains were predicted by the TMHMM 2. 0 server. Potential sites of N-and O-glycosylation were identified by NetNGlyc 1. 0 and NetOGlyc 4. 0, respectively. Interproscan v. 4. 8 software was used to identify different protein domains. Prediction of GPI-anchoring sites was performed with the PredGPI 2 program.
Sequences were aligned by BioEdit v. 7. 2. 5 using the ClustalW algorithm. The assembled nucleotide sequences encoding the putative Ssp-4 protein from the G and CL strains were deposited in GenBank under accession numbers KX581696 and KX581697, respectively. Relative Quantification of mRNA by Real-Time PCR (qPCR) For real-time quantitative PCR (qPCR), we synthesized the following primers: GAPDH Forward (5 -agcgcgcgtctaagacttaca-3 ) and Reverse (5 -tggagctgcggttgtcatt-3)  (Cordero et al. , 2008)  1 www. expasy. org 2 http://gpcr. biocomp. unibo. it/predgpi/pred. htm and Ssp-4 Forward (5 -cctctgacattgacccgttatt-3 ) and Reverse (5gtaagttggattggtgtggta-3 ). RNA extraction from the EAs of the G and CL strains was performed with the RNeasy Protect Mini Kit (Qiagen). Next, cDNA was generated using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
1 M Tris (pH 8. 6) and 0. 1% p-phenylenediamine. Samples were examined by a Leica TCS SP5 confocal system (Leica Microsystems, Wetzlar, Germany) using a 100 × NA 1:44 oil immersion objective. Images were processed by Imaris software (Bitplane AG, Andor Technology, Belfast, United Kingdom).
Funding was provided by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) through grants and fellowships number (2011/51475-3 and 2012/23150-5), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) fellowship number 302068/2016-3 to RM, and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
FUNDING Funding was provided by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) through grants and fellowships number (2011/51475-3 and 2012/23150-5), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) fellowship number 302068/2016-3 to RM, and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
The topic guide included questions to elicit participants' perceptions and experiences of implementing and delivery of treatments within the Pain Platform and how it compared to pre-existing process of care delivery. The opportunity was also offered to participants to make any additional comments about issues relating to implementation of the Platform. One member of the research team, not directly involved with any of the referral or delivery services, conducted all interviews face-to-face or by telephone, dependent on participant preference. All participants provided written consent which included consent to audio record the interview. Interviews lasted from 24 to 71 min and were transcribed verbatim. Data was managed using NVivo software  [28]  and independently analysed by the researcher who conducted the interviews with the assistance from a Psychological Wellbeing Practitioner (PWP) who had supported patients accessing T-CBT using thematic analysis  [29]  informed by NPT.
Limitations and strengths The study time restrictions meant interviews were conducted relatively soon after implementation had occurred and on one occasion only. Therefore the data captured may reflect only initial experiences of the Pain Platform. Future work exploring the experiences and views of implementation could include studies of a longitudinal design to better capture if perceptions altered over time. Although professional stakeholders varied in terms of their role within the Pain Platform it is acknowledged that the sample is restricted to one locality and is relatively small which could limit generalisability to other pain management settings. Participants provided representation for the key routes through the Pathway, however, as the Pathway was early in conception/implementation, routes were developing and to some extent limited.
These tensors were rotated to test changes in stress orientation, but only number 48 presented noticeable changes and reasonable field arguments showing its tilting (Figs. 5b, c ; see discussion below). Accordingly, only tensor 48 was kept rotated in the final database. The overall stress map (Fig. 7 ) includes comparable strain axes; shortening and stretching directions published by  Diraison et al. (2000)  and  Lagabrielle et al. (2004). The obtained stress field is quite complex, and presents the three main deformational modes  (extension, compression, strike-slip). Looking at the strike-slip tensors (about 55% of the total) two major directions arise from our database (Fig. 7 ), with subhorizontal σ 1 at az. ~30º and ~110º, associated to subhorizontal σ 3 axis at az. ~120º and ~20º, respectively.
Acknowledgements This work was carried out thanks to the financial support of grants projects Agencia PICT-2013PICT- -1291;; CONICET PIP 2014-2016 GI directed by M. G. ,  Argentinian-French ECOS-SUD  project  A15U02  (CS, and MG), and thanks to the  French projects Franco-Suisse (Franche-Comté region) , and  SYSTER (INSU CNRS ) directed by C. S. The authors are grateful to  Parques Nacionales of Argentina  for permitting access to  Perito Moreno  and  Patagonia National Parks. Special thanks to the park rangers at  Lago Belgrano ,  Comisión de Fomento de Hipólito Yrigoyen , and the people of Lago Posadas, especially to Luciana and Gendarmería for allowing access to outcrops, kind logistical support and assistance. This is contribution R-223 of the  Instituto de Estudios Andinos IDEAN Don Pablo Groeber (UBA-CONICET ).
Methods Patients were identified from the hospital patient database of the Orthopedic Department in the Specialist Hospital in Rudna Mała, Poland. Patients who had undergone arthroscopic reconstruction of the rotator cuff from 2015 to 2016 by one orthopedic surgeon (supraspinatous, infraspinatous or subscapularis, and additionally after the damage to the tendon of the long head of the biceps brachi), were eligible for the study. Patients who were ≥ 18 years of age, were native Polish speakers and signed an informed consent participated in the study. Exclusion criteria was: previous surgeries within the shoulder complex and the upper limb, dislocations of the shoulder complex, fractures of the shoulder blade, clavicle or upper limb, and who had co-existing rheumatological or neurological conditions.
Participant characteristics After screening of the database of Specialist Hospital in Rudna Mała we identified 140 patients who were operated on for rotator cuff disorders in 2015-2016 (72 people in 2015 and 68 people in 2016) of which 111 met the inclusion criteria. These patients were contacted by phone, the study explained to them and were asked for their willingness to complete questionnaires. Those that agreed signed an informed consent form and the outcome tools were sent by post according to the measurement protocol. Sixty-nine subjects (62. 2%) returned the completed questionnaires. Patient gender, age, operated limb, hand dominance, time from surgery and diagnosis were recorded (Table  1 ). In order to assess test-retest reliability and agreement of the scale, the respondents filled in the WORC questionnaire a second time.
The median time between administrations was 13 days (range 10-14 days). In the test-retest analyzes, data from 57 people were used; 4 subjects who participated in the first test were excluded due to reporting changes in the functioning of the operated shoulder joint during the assessed period in GRS scale, and 8 people did not return the completed questionnaire for the second time. The absolute values of all scores are given in Table  2.
Primers and probe designs The N gene sequences for ten RABV-TWFB strains, according to the whole-genome sequences first reported in 2013  [1] , were used to design gene-specific primers and the probe. The N gene sequences of the ten strains, with accession numbers KF501180, KP881353, KF501181, KP881355, KF501182, KF501183, KP881354, KP881356, KF501184 and KF501185, were extracted from GenBank. Of these sequences, KF501180 and KP881353 belonged to the TW-II group isolated from Eastern Taiwan, whereas the remaining eight were from the TW-I group isolated from Western Taiwan  [18]. Three identical stretches of nucleotide sequence were identified among the N gene sequences of the ten virus strains. These sequences were used for the primer set and the probe used to generate and screen for the amplicon of 201 nucleotides, using the TaqMan real-time RT-PCR assay.
The two strains of viruses used for animal inoculations were demonstrated to have the same nucleotide sequences as the primers and probe. The probe was labeled with fluorescent reporter dye 6-carboxy-fluorescein (FAM) at the 5′-end, and 6-carboxytetramethylrhodamin at the 3′-end (Biosearch, Novato, CA, U. S. A. ). Table  1  shows the detailed sequence information for the primers and probe used. The identities of the N gene sequences derived from 63 RABV-TWFB strains published by Chiou et al. [4]  and Tsai et al. [18]  were compared in the regions of our primers and the probe by using the multiple-alignment functions of DNASTAR ® software (DNASTAR, Madison, WI, U. S. A. ).
Detection and quantification of RABV-TWFB RNA using a one-step real-time RT-PCR Nucleic acid was amplified using real-time RT-PCR on a Roche LightCycler ® 480 II (Roche, Basel, Switzerland) using a KAPA PROBE FAST Universal One-step qRT-PCR Kit (Kapa, Cape Town, South Africa). A 20 µl reaction mixture composed of 0. 4 µl of KAPA RT Mix (50 ×), 10 µl of KAPA Probe Fast qPCR Master Mix (2×), 3 µl of RNA sample, 400 nM final concentrations of each primer and 500 nM of probe. The thermal cycling profile was as follows: a single stage for reverse transcription at 42°C for 20 min and reverse transcriptase inactivation at 95°C for 5 min, followed by 50 sequential cycles of 95°C for 3 sec and 60°C for 35 sec. Fluorescent signals were detected at the end of the elongation phases. According to the automatic calculation by the LightCycler ® 480 software, based on the second derivative maximum method, the time when the fluorescence curve of sample RNA turned sharply upward was automatically recorded as the crossing point (Cp) for a specific RNA concentration.
Data analysis The standard curve was estimated according to the error value and efficiency (E), E=10 (-1/slope) , which was automatically calculated by the LightCycler ® 480 software. To determine the limit of detection (LOD), 10-fold RNA standards at 10-100 copies/ reaction were analyzed in at least 20 replicates to assess the positive detection rate for each concentration. An LOD was assigned as the concentration with a Cp at which ≤5% of the true-positive standard RNA was found to be negative. To compare the four regression lines (generated from the T7 RNA transcripts suspended and diluted in the background of extracted RNA derived from the brain or ear emulsions of the rabies-negative mice or ferret badgers) with the dedicated standard curve (T7 RNA transcripts suspended in RNase-free water), an analysis of covariance (ANCOVA) with a 95% confidence interval was conducted using SAS 9.
4 software (SAS, Cary, NC, U. S. A. ). An RNA sample was considered positive if fluorescent signals were detected in all three wells, and the average Cp of the triplicate values was less than the upper limit Cp of the LOD (average value added to 1. 96 × standard deviations). Sensitivity and specificity were compared with FAT results, which were set as the gold standard. Statistical comparisons of the RNA copy numbers extracted from ferret badgers receiving different virus dilutions were first analyzed using the Shapiro-Wilk test to confirm distribution normality, and then the mean or median RNA copy numbers detected were compared using one-way analysis of variance (ANOVA) or the Kruskal-Wallis test using the SAS 9. 4 software.
ACKNOWLEDGMENTS. This study was financially supported by the  Bureau of Animal and Plant Health Inspection and Quarantine, Council of Agriculture, Executive Yuan, Taiwan (R. O. C. )  (grant nos. MOST 103-3114-Y-518-001 ,  MOST 104-3114-Y518-002 , and  1052101011001-101005B2 ). The authors would like to thank  Dr. Jyh-Mirn Lai  from  National Chia yi University  and  Dr. Ya-Jane Lee  from  National Taiwan University  for their guidance on the statistical analysis.
Monoclonal antibody 5-6 (Developmental Studies Hybridoma Bank) directed against muscle myosin was used as primary antibody, anti-mouse Alexa 555 (Molecular Probes) was used as secondary antibody, worms were mounted on Fluoroshield (Sigma). Images were acquired with a Leica DM6000 TCS SP5 confocal microscope using LAS AF (Leica) software. -Metabolic profiling by HPLC For an extraction, ~7500 young adult worms, 72 h after synchronization, were collected with ice cold water, onto 15 ml conical tubes, and centrifuged at 1000 rpm, 1 min and 4°C, supernatant was discarded eliminating most bacteria. The nematode pellet was washed with 10 ml of cold Hepes 10 mM and centrifuged. The worm pellet was resuspended in Hepes 10 mM, 1 ml of worm suspension is transferred onto 4 ml of absolute ethanol at 80°C, incubated for 5 min and cooled on ice for 10 min.