dataesr/scientific-paragraphs-categorization huggingface dataset:
The grouping of insulins into categories which implies that both human and anologue insulins may be included in the original article DIABETES, OBESITY AND METABOLISM same category enables adequate numbers of subject in each insulin per group, and was also required by regulatory bodies. However this approach may obfuscate benefits of a specific regimen as part of an 'average' effect with a less successful insulin. While the propensity analysis is a powerful tool for pair matching groups to remove possible hidden confounders in the data, by its very nature it is not possible to validate fully the success of this analysis. Furthermore it is clear from the smaller ill-matched groups that such confounders do exist in the original dataset, confirming our caution in not comparing insulins without propensity pair-matching, and providing support for the approach we have taken over others that involve attempting statistical adjustment for difference in patient characteristics (which would have compared patients who did not share characteristics in our excluded analyses).
Background: Assessing the accuracy of influenza epidemic periods determined by statistical models is important to improve the performance of algorithms used in real-time syndromic surveillance systems. This is a difficult problem to address in the absence of a reliable gold standard. The objective of this study is to establish an expert-based determination of the start and the end of influenza epidemics in France. Methods: A three-round international web-based Delphi survey was proposed to 288 eligible influenza experts. Fifty-seven (20%) experts completed the three-rounds of the study. The experts were invited to indicate the starting and the ending week of influenza epidemics, on 32 time-series graphs of influenza seasons drawn using data from the French Sentinelles Network (Influenza-like illness incidence rates) and virological data from the WHO-FluNet.
Background The primary objective of sentinel surveillance is to provide sensitive, specific, and timely alerts at the beginning of increased disease activity. Timely detection of the start and the end of influenza outbreaks is crucial for a number of reasons such as improving communication towards persons eligible for vaccination, better planning of the organization of the health care system and estimating the vaccine effectiveness  [1, 2]. The French Sentinelles Network (http://www. sentiweb. fr/? page=database)  [3, 4] , like other surveillance systems  [5] [6] [7] , uses an approach based on a seasonal regression model proposed by Serfling for influenza outbreak monitoring  [8]. Under this model, influenza-like illness (ILI) incidence rates from non-epidemic weeks in the previous years are used to compute a time-varying threshold.
Questionnaire The first round questionnaire included 34 questions (Figure  2 ) of which 32 were time-series graphs. On each of the 32 graphs, experts were invited to indicate the starting and the ending week of the influenza epidemic period by using a slider (Figure  1 ). Each graph included data from the French Sentinelles Network (www. sentiweb. fr) [3, 4]  and from WHO-FluNet  [17]  (Figure  3 ): weekly national ILI incidence rates, weekly national proportions of confirmed influenza positive samples (virological data, available since 1997-1998), numbers of virological samples analyzed per week. Data were shown from the beginning of July (week 27) of the year to the end of June (week 26) of the following year, called seasons thereafter. Weeks were not numbered on the graphs and no indication to the year was given to the experts.
Determination of the start and end of each outbreak and level of consensus The detailed results are available in Table  2  and in Additional file 2, and the complete database of the study is available upon request. Overall, a high level of consensus was achieved for 20 beginning bounds (77%) of the 26 initial graphs, and for 15 ending bounds (58%). The mean IQR of the answers was 1. 8 weeks (1. 5 weeks for beginning bounds, 2. 0 weeks for ending bounds). We obtained consensual results for 88% (23/26) of epidemic periods. A high level of consensus was obtained for the beginning and the end of 12 epidemic periods in 26 (46%). For 10 epidemic periods (38%), a high level of consensus was obtained for one bound, and a medium level of consensus for the other bound. For one epidemic period (4%) the consensus was medium for the two bounds, and for three epidemic periods (12%) there was a low level of consensus for one of the bounds or for the two bounds.
Acknowledgements The authors would like to thank all the experts who participated in the study, and  Marie-Lise Grisoni  who took part in initial discussions about this study. DelFluWeb Study Group members: Akwar H ( Public Health Agency of Canada, Canada), Alexandrescu V (National Influenza Center, Cantacuzino Institute, Romania ),  Baumbach J (New Mexico Department of Health, USA), Blozik E (Swiss Center for Telemedicine Medgate, Switzerland), Bonovas S (Hellenic Centre for Disease Control and Prevention, Greece) ,  Born R  ( Swiss Federal Office of Public Health, Switzerland), Carnahan A (Swedish Institute for Communicable Disease Control, Sweden ),  Cojocaru R (National Center of Public Health ,.
The annealed DNA was ligated with linearized pSilencer 2. 0-U6 (Ambion) at BamHI and HindIII sites. The sequence of resulting plasmids: pSilencer-STAT3. 1_hs and STAT3. 2_hs was further verified by direct sequencing. The plasmid DNA was isolated with Qiagen Plasmid Maxi Kit. STAT3 siRNA which is a pool of three target-specific 20-25 nt siRNA designed to knock down gene expression was obtained from Santa Cruz Biotechnology (sc-29493). Control siRNA-A was obtained from Santa Cruz Biotechnology (sc-37007), is a non-targeting 20-25 nt siRNA designed as a negative control. sc-29493: Stat3 siRNA (h) is a pool of 3 different siR-NA duplexes: sc-29493A: • Sense: GAGACAUGCAAGAUCUGAATT • Antisense: UUCAGAUCUUGCAUGUCUCTT sc-29493B: • Sense: GGAUCCCGGAAAUUUAACATT  PT3027-5, GenBank Accession #U55762 Catalog #6085-1) coding for green fluorescence protein and analyzed after 48 h with fluorescent microscopy to determine efficacy of transfection.
siRNA transfection efficiency was assessed by co-transfecting the cells with siGlo Red siRNA (557-570 nm) from Thermo Scientific Dharmacon and control and STAT siRNA and analysed after 48 h using flow cytometry analysis (FACSCalibur using CellQuest software). After transfection cells were plated into 24-wells plate at a density of 2 9 10 5 /well and incubated for 48 h. To study NFjB activation, the cells were cotransfected with 2. 5 lg of the reporter plasmid carrying a firefly luciferase gene under promoter consisting multiple of binding sites for NFjB (NF-jB p65 cis-Reporting System, Stratagene-Agilent Technologies Company, CA, USA) and p-Super vector (VEC-PBS-0002 OligoEgine) and PCMV6-XL5(Origene) using Lipofectamine TM 2000 Reagent (Invitrogen, Carlsbad, CA). Twenty four hours after transfection the cells were lysed in a passive lysis buffer and luciferase activity was measured using a Promega luciferase kit.
Cell nuclei extracts were collected 48 h after transfection and 2 lg of nuclear extract was subjected to an NFjB DNA binding assay (Active Motif-TransAM Ò NFjB Family Kit, Carlsbad, USA). The NFjB -ELISA assay results demonstrated an increase in the NFjB binding to DNA after silencing the expression of STAT3. Data are presented as mean ± S. D. from three experiments. g-h. STAT3 knockdown with siRNA induces specifically NFjB-Luciferase activity in WM209 and T1 melanoma cell lines. The NFjB-Luciferase activity measured in WM209 and T1 cells untreated (mock), treated with electroporation only or in cells transfected with two empty plasmids such as p-Super and PCMV6-XL5, or plasmids coding for shRNAs or siRNAs. An increase of the NFjB transcriptional activity was observed in melanoma cells transfected with plasmids encoding shRNA against STAT3 and control shRNAs and siRNA against STAT3 and control.
Electroporation itself or transfection with empty plasmids do not induce NFjB activation. Data are presented as mean ± S. D. from three experiments Quantitative evaluation of gene expression RNA was extracted using the RNeasy Mini Kit from Qiagen. The quality and concentration of RNA was checked using Nanodrop 2000 spectrophotometer from Thermo Scientific. Total RNA from each sample was converted into cDNA using the SuperScript First-Strand Synthesis System (Invitrogen) for PCR according to manufacturer's instructions. TaqMan/Syber green real time quantitative reverse transcription-PCR (qRT-PCR) was used to measure the mRNA expression levels for STAT3 and IRF7. The primers sequences were: IRF7: GCGGTGCAAGAGCCCAGCCC -CGTGCAGCTCGGGTGTCCCA; STAT3: ATTGCCCGG ATTGTGGCCCG -CTCCGTCACCACGGCTGCTG; and 18S AACGAACGAGACTCTGGCATG -CGGACATCT AAGGGCATCACA; The amount of target mRNA was normalized to the expression level of the 18S rRNA amplified from the same sample.
2e, f ) only after STAT3 was knocked down. The results showed that the control siRNA did not significantly increase the NFjB-luciferase activity. The results were corroborated by a NFjB DNA binding ELISA assay that measures how activated NFjB in the cell extract binds to the consensus-binding site. The NFjB DNA binding ELISA results indicated that after silencing the expression of STAT3, there was an increase in the NFjB binding to DNA (Fig. 2f ). These results confirmed our data collected using NFjB-luciferase activity and the pIjBa Western blotting. Fig. 3  STAT3 knockdown with specific shRNA, but not siRNA, reduces cell survival and induces DNA fragmentation in melanoma cells. a-b Cells (1 9 10 7 cells/per group) were mock transfected or were transfected with a control or STAT3 siRNA or plasmids coding for control or STAT3 specific shRNAs.
Cell viability was determined using the MTT metabolism assay 48 h after the transfection of the indicated shRNA or siRNA. Measurements were related to respective controls (cells transfected with ctr siRNA or shRNA were taken as 100 %) and data represent mean ± S. D. from three experiments, each in triplicate. c STAT3 knockdown with two specific shRNAs results in induction of apoptotic cell death. The levels of phosphorylated and total STAT3 and cleaved PARP proteins in cells transfected with plasmids coding for control or STAT3 specific shRNA were examined by Western blotting. Immunoblots were re-probed with an antibody recognizing b-actin to ensure equal loading. Similar results were obtained in three independent experiments. d Quantification of the Western blots by using b-actin as the loading control using Image J.
Main study The main study, conducted from April 2009 to February 2011, included patients receiving CRS plus HIPEC for PC (group 1), patients with colorectal cancer or a history of cancer undergoing abdominal surgery (group 2), and patients without cancer undergoing abdominal surgery (group 3). A standard data form was created to collect information on the origin of PC and the status of the patient before undergoing the combined procedure, including age, sex, extent of the PC, and any previous treatment with systemic chemotherapy regimens. The Sugarbaker Peritoneal Cancer Index (PCI) was used to assess the extent of PC (1, 2). Information recorded about the combined procedure included the date; a score for the extent of cytoreduction (CC-0, no disease left; CC-1, nodule(s) size <2. 5 mm; CC-2, nodule size 2.
Statistical analysis All values are expressed as the mean±SD. The Mann-Whitney nonparametric U test was performed to compare independent data, and the Wilcoxon signed-rank test was applied to paired data. Spearman's rank correlation (ρ) was used to assess the correlation among Hsp27 protein expression levels, the CRP values, and the duration of surgery. A two-tailed p<0. 05 was considered statistically significant. Statistical analyses were performed using the SAS software package (version 9. 2, SAS Institute, Cary, NC).
Introduction Leksell GammaPlan (LGP; ELEKTA Instruments AB, Stockholm, Sweden) is dedicated computer-aided software that disorders. The current versions of these systems provide extensive options for highly accurate and precise coregistration and fusion of various images (computed tomography [CT], magnetic resonance imaging [MRI], digital subtraction angiography, positron emission tomography, magnetoencephalogram, etc. ) within the same workspace, their magnification and reconstruction in axial, coronal, and sagittal planes. Moreover, various anatomical structures delineated on the different images may be combined on the composite view and evaluated three-dimensionally from the different angles and directions. These capabilities can be used not only for radiosurgery or stereotactic interventions, but for planning of open neurosurgical procedures as well.
Methods and Materials LGP v. 8. 3 was used before the surgical resection of cerebral gliomas for (1) delineation of the subdural grid electrodes and detailed evaluation of their position relatively to cortical structures, and (2) fusion of the structural MRI and diffusion tensor imaging (DTI) for detailed visualization of the corticospinal tract (CST) and optic radiation. Several functions available within the software were used. Fusion of images obtained with various neuroimaging modalities and at different time was done with "Coregistration. " Besides the main automatic algorithm, it also provides a manual mode that may be useful if correction and/or modification of the fusion technique are required. Delineation of the various intracranial anatomical structures was performed with "Regions and Volumes.
Fusion of Structural Magnetic Resonance Imaging and Diffusion Tensor Imaging Simultaneous 3D visualization of the tumor, CST, and optic radiation with the use of LGP was applied for the planning of a parieto-occipital glioma resection (►Fig. 2) and the planning of a stereotactic biopsy for a bilateral thalamic glioma (►Fig. 3). Volumetric MRI, as well as high signal-to-noise ratio and low-distortion DTI with 6 and 32 directions of diffusion sensitizing gradient and nearly isotropic voxel size were acquired on at 3-T MR Philips ACHIEVA scanner. Raw data   of DTI were analyzed with the dedicated software (Stealth DTV, Medtronic Co. , USA). A fractional anisotropy (FA) map was created with tracking of the CST (region of interest [ROI]  in the lower brainstem) and optic radiation (ROI in the lateral geniculate nucleus).
Acknowledgments This study was supported by  Grant-in-Aid for Scientific Research  (B) 22300093 and was done under the auspices of the  Global COE Program , namely the  Multidisciplinary Education and Research Centre for the Establishment of Regenerative Medicine (MERCREM). Additional support was obtained from  JST  and  CREST. The authors do not have any personal or institutional financial interests in drugs, materials, or devices described in this article. We thank  Drs. Gautam A. Deshpande  and  Mikhail Chernov  for their help with the preparation of the manuscript.
Entomological Data Mosquito sampling was performed in different locations of Nice conurbation, using ovitraps' networks placed mostly in sites shaded by vegetation. The surveillance of eggs was chosen for detecting invasive mosquito species such as Ae. albopictus in South-eastern France. It allows targeted and rapid sampling efforts and an optimal cost-benefit ratio  [5, 18]. Ovitraps are artificial egg-laying containers made up with 3 L black plastic buckets (Dillewijn Zwapak © , Aalsmeer, The Netherlands) filled with 2 L of tap water and the biolarvicide Bacillus thuringiensis israelensis (Bti) to prevent the production of mosquitoes in the trap  [19] , in which a floating polystyrene square (5  5 cm) was added to provide a support for oviposition. The sampling was conducted in six different locations of Nice conurbation, mainly in discontinuous urban fabric including individual houses with gardens: Nice (1: Nice downtown, 2: residential area on the outskirts of Nice), Cagnes-sur-Mer, La Gaude, Biot, and Villeneuve-Loubet.
Acknowledgments This study was conducted within the framework of the  European Life+ project ("Integrated Mosquito Control Management ",  LIFE08/ENV/F/000488 ). The authors thank  Didier Fontenille  ( Institut de Recherche pour le Dé veloppement-IRD), Benjamin Roche (IRD) ,  Lucas Lé  ger (IRD),  Yvon Perrin  ( Centre national d'Expertise sur les Vecteurs-CNEV ), and  Jean-Michel Roques  (AMENYS), for fruitful discussions on the modelling of Ae. albopictus populations, and  Nathalie Barras  ( EID ) for manuscript revision. Thanks are due to the four anonymous reviewers for valuable comments and advices for improving the text.
Characterising soft biological tissues outside the linear viscoelastic regime is challenging due to their complex behaviour. In addition, the viscoelastic properties of tissues have been shown to be sensitive to sample preparation and loading regime resulting in inconsistent data varying by orders magnitude in the literature. This paper presents a novel technique to characterise the non-linear behaviour of tissues which uses Fourier Transformation to decompose the stress output waveform under large amplitude oscillatory shear (LAOS) into harmonic contributions. The effect of varying preload, the compressive strain exerted on a liver tissue specimen prior to shear testing to minimise slip, was also investigated. Results showed that in the linear regime, preload affects the viscoelastic response of liver.
Measuring accurate data at LAOS is potentially a useful technique for measuring high strain rate large deformation tissue properties which are applicable to a wide range of practical situations, including tissue injury. The LVL of soft biological tissues such as the brain and liver is considered to be in the range of 0. 1-1%  (Bilston et al. , 1997; Brands et al. , 2000; Hrapko et al. , 2006; Cheng et al. , 2008). Fourier Transformation rheology (FT-rheology) is a relatively new method of analysing LAOS data by decomposing the stress output waveform into harmonic components using Fourier analysis  (Wilhelm et al. , 1998). When a material is loaded past its LVL, the non-sinusoidal stress output wave can be decomposed into a Fourier series. This decomposition can then be used to estimate harmonic components.
Samples with dimensions of 20 mm diameter and 3 mm thickness were harvested using a cylindrical corer. Samples were inspected and samples containing visceral peritoneum (double-layered membrane covering the liver) and large blood vessels were excluded  (Nicolle et al. , 2010; Gao et al. , 2010). To establish a uniform initial tissue state and to eliminate any residual surface strains  (Cheng et al. , 2009) , eight pre-conditioning cycles were applied to the specimen prior to testing. Strain sweep tests were conducted at frequencies of 1 Hz under three different preloads (1%, 10% and 20%) applied in the axial direction (i. e. normal to the direction of shear). Data were acquired at a log mode and for the LVL analysis, 20 data points per decade were collected between 0. 005% and 2% shear strain and for the LAOS analysis, 10 data points per decade were collected between 0.
Discussion In this study, we demonstrated how normal preload affects the viscoelastic response of liver in dynamic oscillatory shear tests. The LVL decreases with preload and this shows that it is important to note the magnitude of preload when publishing data to allow meaningful comparison of data across research groups. It is possible that the LVL of liver decreased with preload due to the additional compressive strain exerted on the sample thus requiring less shear strain to reach the LVL. The samples were analysed at a microscopic level using histology. It was found that increasing preload resulted in redistribution of the blood in the tissue as shown by an accumulation of blood within the central veins and this may contribute to differences in the rheological properties if excessive preload is exerted on a sample during testing.
, 2006; Klatt et al. , 2010). Second, to minimise the effects of inertia, relatively low frequencies were used in this study. For the LAOS experiments at frequencies higher than 2 Hz, instrumental inertial effects began to dominate the torque response and data were considered unreliable. Based on a series of shear strain sweep experiments with varying preloads, this study showed that the magnitude of preload used will alter the storage modulus and LVL of bovine liver. It is recommended that a normal preload of no more than 10% be applied when using a parallel plate rheometer configuration to maximise grip while minimising slip. Histological analysis showed that structural changes under these conditions were minimal. This study introduces a method of meaningfully characterising soft tissues in the non-linear regime using FT-rheology.
Acknowledgements This research is supported by a  Discovery Grant  from the  Australian Research Council  ( DP0985147 ). L. E. Bilston  is supported by an  NHMRC  senior research fellowship. The authors thank  Heather McCann  and  Carla Scicluna  at the  Sydney Brain Bank  and  Dr. Elizabeth Clarke  and  Sue Smith  at the  Kolling Institute  for assistance with fixing and staining of the tissue. The authors would also thank  Dr. Randy Ewoldt  and his team for making the Matlab program, MITLaos, freely available.
Materials and methods Data from the medical files of the Department of Paediatric Neurosurgery of Ho ˇ p ital Necker Enfants Malades, Paris were assessed between 1 January 1993 and 31 December 2009 to provide results concerning epidemiological aspects, imaging features and clinical considerations. Charts and MRI studies of these patients were analysed retrospectively. Among 70 patients with clear radiological and/or pathological criteria of a cerebral cavernoma, 18 patients (26%) had additional black spot lesions in the context of a cavernomatosis and were included in the study. Children with a history of radiotherapy were excluded from the study. Genetic analysis had been intended in all 18 patients. However, consent of the patients' parents could be obtained only in seven of the 18 cases.
1e4 Consequently, recruiting a considerable number of paediatric patients with black spot lesions in a single centre can be an onerous task. Nonetheless, there is a need for better understanding of black spot lesions, as, for instance, the diagnosis of such a lesion in the brainstem poses the question as to whether a patient might or might not be at risk of a haemorrhagic event in the future. Therefore, even retrospective data may be helpful in daily clinical practice until there are prospective data dealing with the natural history of black spot cavernomas. Despite all its limitations, this first analysis concerning the natural history of black spot cavernomas in children may lead to a better understanding of these lesions. One hundred and eighty-seven asymptomatic lesions were analysed. The dynamic nature of black spot cavernomas and the rather high mean annual bleeding rate of 0.
Production of the PfDiCre cassette PCR amplification was conducted using AccuPrime™ Pfx SuperMix (Invitrogen, UK) and when required PCR products were subcloned into the pScB subcloning vector (Aligent Technologies, UK). A 'mock' promoter region was amplified from E. coli genomic DNA using primers EWmock1 and EWmock2. The resulting amplicon (corresponding to ~930 bp of the E. coli pmba gene, GenBank/EMBL Accession No. X54152) was subcloned into pScB. Restriction digestion of the intermediate vector using PstI and HindIII released the mock promoter fragment which was subsequently cloned into the pBlueScript SK+ phagemid (GenBank/EMBL Accession No. X52328) pre-digested with PstI and HindIII, to form pmockINT. The FKBP-Cre59 gene was amplified using primers EWCRE59For and EWCRE59Rev from plasmid TUB8FKBP-Cre59-HX  (Andenmatten et al.