dataesr/scientific-paragraphs-categorization huggingface dataset:
Estimating effective population size Two methods were applied to estimate the effective population sizes of H. schachtii. We used the pseudolikelihood method of  Wang (2001)  implemented in the software MLNE 1. 0  (Wang and Whitlock 2003). This method has been demonstrated to be the most reliable among 14 estimation methods, including seven temporal methods  (Gilbert and Whitlock 2015). We also used the moment-based method developed by  Jorde and Ryman (2007)  and implemented in the software NeEstimator v2  (Do et al. 2014). Alleles with frequencies below 0. 05 were excluded to avoid any bias caused by rare alleles, as described in  Do et al. (2014). Both methods are complementary: the moment-based method yields unbiased but rather imprecise N e estimates, while the pseudo-likelihood method gives N e estimates that can be slightly upwardly biased, but that are more precise  (Jorde and Ryman 2007; Do et al.
To verify this hypothesis, we performed an exact test of homogeneity in allele frequencies between temporal samples to detect significant changes in allele frequencies using the software Genepop v4. 2  (Raymond and Rousset 1995). Populations with significant changes were then selected as candidates to test for the presence of nonrandom variation in allele frequencies (which would be caused by migration or selection) using the generalized test described in  Waples (1989). The generalized test was performed a posteriori because it requires an estimation of effective population size. To this end, we used the pseudo-likelihood estimation of N e , thought to be more accurate, assuming the median number of generations (see below) between the temporal samples to perform this test. Waples and Wilcoxon tests were computed with R (R Core Team 2014, version 2.
However, all infinite N e estimates remained infinite when we decreased the number of generations from ten to four. Overall, our findings suggest that infinite population sizes correspond to nematode populations lacking significant temporal variations in allele frequencies, probably because new nematode generations were not produced between the two sampling sessions. Temporal methods assume no significant influence of other micro-evolutionary forces, such as migration or selection. The relevance of this assumption in our dataset was tested by applying a generalized test developed by  Waples (1989) : only population two exhibited a significant impact of nonrandom forces. The effective population size estimated by the pseudo-likelihood method, used to compute this test, was much higher than that of the moment-based method, for which the Waples test was nonsignificant (data not shown).
Acknowledgement We are grateful to  Delphine Eoche-Bosy  and  Didier Fouville  ( UMR IGEPP ) for technical help. We thank  Eric Grenier ,  Josselin Montarry , and  Stephen Strelkov  ( UMR IGEPP ) for their useful comments on the manuscript, and  Stephen Strelkov  and  Carolyn Engel  for proofreading the language. This work was funded by the  French Ministry of Agriculture , the  French Ministry of Education and Research , the  Institut Technique de la Betterave sucri ere , and the  Union Franc ßaise des Semenciers.
(B) Cell spreading area of C2C12 cells cultured for 4 h on soft films with bBMP-2 in the presence of the same inhibitors as for A was quantified. For cell spreading analyses, 60 cells were analyzed per condition (n = 3). Data are mean ± SEM. The control condition (bBMP-2 on soft films) was normalized to 1 or 100% for luciferase signal and cell spreading, respectively. (C) Effect of inhibitors on Smad1,5,8 phosphorylation. Western blot of phospho-Smad1,5,8 (C, top) and corresponding quantitative analysis (bottom) after cell culture for 4 h on soft films with bBMP-2 in the presence of various inhibitors: dorsomorphin (BMPR), PP2 (Src), PF228 (FAK), Pyr1 (LIMK), Y27632 (ROCK), and Secramine (Cdc42). (D) Measurement of luciferase activity after 15 h of culture on soft film with matrix-bound BMP-2 upon siRNA treatment against Src, FAK, ILK, ROCK1&2, and Cdc42.
(A, bottom) Quantification of GSK3β phosphorylation in the different conditions. Data are mean ± SEM (n = 3). (B) Measurement of luciferase activity at 15 h upon siRNA treatment against β3 integrin, ILK, Src, and FAK with or without GSK3 inhibitor on soft film with bBMP-2. Data are mean ± SEM (n = 3). (C) Monitoring of the life time of Smad1 and phospho-Smad1,5,8 in C2C12 cells spread on TCPS with sBMP-2. C2C12 cells depleted or not with β3 integrin were incubated with 100 µg/ml cycloheximide. Cycloheximide and sBMP-2 were added at t = 0. Phospho-Smad1,5,8 and Smad1 protein contents in total lysates were visualized as a function of time from 1 to 18 h by Western blotting. The results are representative of three independent experiments. *, P ≤ 0. 05 compared with siRNA control. shown that GSK3 phosphorylation regulates the duration of Smad signaling  (Fuentealba et al.
In brief, cells were rinsed in PBS and incubated in ice-cold DTS SP (in 1 mM final concentration in PBS) for 30 min. Unreacted cross-linker was quenched with 50 mM Tris in PBS for 15 min and bulk cellular components were extracted in 0. 1% SDS in PBS. The slides were then blocked in 0. 1% BSA in TBS. After this, bound integrins were immunostained with antibodies against α or β chains and Alexa Fluor 488-conjugated secondary antibody. All the slides were mounted onto coverslips with antifade reagent (Prolong; Invitrogen) and viewed under fluorescence microscopy (LSM 710, Axiovert 200M; ZEI SS) using a 10×/0. 25 NA, 20×/0. 8 NA, or 63×/1. 4 NA objectives. Images were acquired with Metaview software using a CoolSNAP EZ CCD camera (Roper Technologies). To quantify cell spreading, fluorescence images were analyzed with the ImageJ software to determine mean cell area.
Immunoblotting Cells were lysed in Laemmli buffer. Detection of proteins by Western blotting was done according to standard protocols. After electrotransfer and blocking (10 mM Tris, pH 7. 9, 150 mM NaCl, 0. 5% Tween 20, and 3% dry milk at RT for 1 h), the PVDF membrane was incubated with antibodies overnight at 4°C. Immunological detection was achieved with HRP-conjugated secondary antibody. Peroxidase activity was visualized by ECL (West pico signal; Thermo Fisher Scientific) using a ChemiDoc MP imaging system (Bio-Rad Laboratories). Densitometric quantification of the bands was performed using the Image Lab program (Bio-Rad Laboratories). As control, detection of actin was also performed.
Time-lapse image acquisition Cells were plated on either low-or high-CL films without BMP-2 or with sBMP-2 or bBMP-2 in standard GM at 37°C in 5% CO 2. Timelapse images were acquired every 15 min over a 16-h period (after the initial 4-h adhesion period) using a 10×/0. 3 NA objective in phase-contrast microscopy (Axiovert 200M; ZEI SS). Images were acquired with Metaview software using a CoolSNAP HQ2 CCD camera (Roper Scientific). Migration velocities were measured using "Manual Tracking" and "Chemotaxis and Migration Tool" plugins from ImageJ. For both analyses, at least 60 cells were analyzed for each time point.
FRAP experiment C2C12 cells transfected with EGFP-paxillin were cultured on stiff film with sBMP-2 or bBMP-2 12 h before the experiment. FRAP experiments were performed in standard GM at 37°C in 5% CO 2. with a confocal microscope (LSM710; ZEI SS) using a 63× objective (Plan-Apochromat 63×/1. 4 oil DIC III, WD 190) equipped with onstage incubator. One 0. 03-µm 2 area located in the center of one focal adhesion was processed by FRAP. EGFP fluorescence in this adhesion area was eliminated by 10 bleach cycles at 100% intensity of the 488nm argon laser. The fluorescence recovery was then sampled with low laser power (3%) each 5 s for 3 min. The recovery curves were obtained using Zen software. The corrected curve was adjusted with origin software using monoexponential fit. The characteristic recovery time (τ) of EGFP-paxillin deduced from the fit of the experimental data was the mean of at least 20 individual focal adhesions.
Acknowledgments We thank  D. Logeart-Avramoglou  for providing the C2C12-A5-transfected cells;  P. Knaus ,  S. Bailly , and  F. Bruckert  for fruitful discussions; and  M. Billaud ,  J. Almodovar ,  T. Boudou , and  E. Van Obberghen-Schilling  for comments on the manuscript. We thank  C. Oddou ,  A. -S. Riba ,  M. Regent ,  M. Mignot ,  F. Gilde , and  C. Fournier  for their technical help. This work was supported by the  European Commission ,  FP7 , via a  European Research Council   starting grant  to  C. Picart  ( BIO MIM, GA 239370 ), by the  Institut Universitaire de France  (C. Picart), by the  Fondation pour la Recherche Médical (C. Albiges-Rizo) , and by the  Ligue Contre le Cancer for Equipe labelisée Ligue 2014  ( C. Albiges-Rizo ). The groups of  C. Picart  and  C. Albiges-Rizo  belong to the  Centre National de la Recherche Scientifique consortium CellTiss.
BMMCs were stimulated with 20 ng/ml DNP-HSA for 10 min and then lysed. Cell lysates were immunoprecipitated (IP) with a polyclonal anti-Rab27 antibody or with isotype control antibody. The immunoblots were analyzed using anti-Kif5b, anti-Slp3, and anti-Rab27 antibodies. Data are representative of three independent experiments. (C, left) IgE-sensitized BMMCs were preincubated in medium containing DMSO, 100 µM LY-294002, or 20 mM BAP TA. BMMCs were stimulated with 20 ng/ml DNP-HSA for 10 min. Cells were fixed, permeabilized, and stained with anti-STX3 and antitubulin antibodies. (Right) More than 100 cells PI3K regulate kinesin-1's accessibility to cargo receptors like Slp3. This may require investigation of kinesin-1's phosphorylation status under unstimulated and stimulated conditions to establish whether this posttranslational modification modulates kinesin-1's access to its cargo receptor (as has been shown for kinesin-5 and -7 families;  Cahu et al.
Each sample was amplified in triplicate on a real-time PCR cycler (ABI 7900) and analyzed with Sequence Detection Systems software (version 2. 2. 2; Applied Biosystems). The relative mRNA levels were quantified using the comparative Cτ method and normalized against the mean values of ACTB as an endogenous control. Levels of KIF5A, KIF5B, and KIF5C transcripts were then expressed as a proportion of the mean value for KIF5B. Levels of RAB27A, RAB27B, SYTL1, SYTL2, SYTL3, SYTL4, and SYTL5 transcripts were expressed as a proportion of the mean value of the gene showing the highest level of expression (arbitrarily set to 1 U).
BMMCs were stimulated with 20 ng/ml DNP-HSA for 10 min. Cells were fixed, permeabilized, and stained with anti-STX3 and antitubulin antibodies (left). Bars, 2 µm. (Right) More than 100 cells were counted per setting. Statistical analyses were performed using unpaired t tests. ***, P < 0. 0001. (F) IgE-sensitized BMMCs were preincubated in normal medium containing DMSO or 20 µM nocodazole. BMMCs were stimulated with 20 ng/ml DNP-HSA for 10 min before lysis. Cell lysates were immunoprecipitated with a polyclonal anti-Rab27 antibody or with isotype control antibody. The immunoblots were analyzed using anti-Kif5b, anti-Slp3, and anti-Rab27 antibodies. Data are representative of three independent experiments. Error bars represent mean ± SD. MFI, mean fluorescence intensity.
TIRF The TIRF assay was performed using WGA-488-loaded BMMCs sensitized with DNP-specific IgE overnight. Cells were allowed to attach to fibronectin-coated glass coverslips (10 µg/ml; Sigma-Aldrich) before stimulation with 20 ng/ml DNP-HSA. TIRF images were then acquired for 15 min (exposure time of 200 ms). During the observation, the cells were cultured at 37°C in a 5% CO 2 atmosphere. Fluorescence data were acquired with a TIRF imaging system (Eclipse Ti-E; Nikon). Images were acquired with a QuantEM 512 SC camera (Roper Technologies) and NIS-Elements AR software (version 3. 1; Nikon). Image sets were processed with ImageJ software. A WGA-containing granule was defined by a minimum of a square of 3 × 3 pixels (1 pixel = 0. 16 µm) of strong intensity signal, orange to white intensity from the pseudocolor scale.
Calcium flux 5 × 10 6 IgE-sensitized BMMCs were loaded with 5 µg indo-1 (Thermo Fisher Scientific) in RPMI medium supplemented with 10 mM Hepes, pH 7. 0, for 30 min at 37°C. RPMI medium supplemented with 10 mM Hepes, pH 7. 0, and 5% FCS was then added for 30 min at 37°C. Cells were washed and resuspended in RPMI medium supplemented with 5% FCS before the addition of 20 ng/ml DNP-HSA (to induce calcium flux). Calcium flux was measured by using a FAC SAria flow cytometer (BD) to monitor the fluorescent emission ratio (405 nm/475 nm). Time course analyses were performed using the FlowJo software package (Tree Star).
Passive systemic anaphylaxis A temperature probe (Bio Medic Data Systems) was implanted into the subcutaneous tissue on the back of 8-wk-old WT and cKO mice. On the next day, mice were passively sensitized i. v. using 1 µg/g anti-DNP mouse IgE antibody (H1-ε-26). 24 h later, mice were challenged by the i. v. administration of 500 µg DNP-HSA (Sigma-Aldrich). The body temperature was recorded every 5 min for 60 min using a wireless reader (DAS-7007S; Bio Medic Data Systems). At the end of the recording, blood samples were collected and the serum concentration of MCPT-1 was measured with an ELI SA kit (eBioscience).
Acoustophoretic resolution of food particles from intrinsic natural microflora Fig. 7  shows the effect of acoustophoresis on the levels of TVC in the food streams emerging from the chip outlets (1* and 3*), with/without application of the acoustic radiation. No significant loss of viable microorganisms was observed, although there was a significant reduction in the optical density in the streams emerging from the outlets (1* and 3*) on application of acoustophoresis (Fig. 4  and 6 ). In the absence of acoustic radiation, TVC (range 10 6 -10 8 CFU g -1 ) was enumerated in the outlets (1* and 3*) as expected, but not in the buffer stream emerging from the central outlet (data not shown), confirming establishment of a laminar flow. In the 'ON' position, an equivalent level of TVC was measured in all the outlet channels, indicating that organisms may be associated with the particles and/or microbial aggregation may lead to larger particle sizes that partition in the central channel.
Acknowledgements BN and NP would like to thank  C. Murphy  for her kind support on biological sample preparation and analyses. Microfluidic chip fabrication by  S. Clark  is also gratefully acknowledged. Our sincere gratitude is expressed to  Dr M. D. Tarn  for all helpful input to the manuscript. The work was financially supported by bioMérieux s. a. ,  Chemin de I'Orme ,  Marcy I'Etoile ,  69280 , France.
Material and Methods Participants. Fourteen participants (6 female; mean age: 30. 2, SD: 7. 5 ) were recruited from our local subject database and participated in the experiment. All observers were naive to the purpose of the experiment and had normal or corrected-to-normal vision. They provided informed written consent before the experiment and filled out a post-questionnaire thereafter. The study was approved by the ethics review board of the Max Planck Society and conducted in accordance with relevant guidelines and regulations.
e. , purely emotional facial expressions), "emotional in social interaction" (i. e. , emotional and facial speech movements occurring in a social interaction) and "conversational" (i. e. , conversational and facial speech movements with little affective content occurring in a social interaction). Details of each facial movement and its corresponding exemplary scenario eliciting the movement are listed in Table  1. Second, we chose one female avatar head in Poser 8 (SmithMicro, Inc. , Watsonville, CA, USA) and modified it, to give it an average appearance (e. g. , the lips were made thinner). The resulting head was animated by each of the motion-recorded facial movements. To this end, we used a system that decomposes the recorded motion data into time-courses of meaningful facial action activation (e.
g. , eyebrow raising)  24, 36. The activat on for each of the 30 facial actions  8, 24, 36  during a recorded facial expression can range from 0 (no activation) to 1 (maximum intensity), thus representing the amplitude of this facial action at a given time point (see middle column of Fig. 3 ). Those time-courses of facial action activation were used to animate the same avatar head and hence ensured that animations were independent of an actor's individual facial form. Finally, the 48 animations were rendered as Quicktime movies of 3. 5 s duration (300 × 400 pixels, Codec H. 264, 60 Hz) in 3ds Max 2012 (Autodesk, Inc. , San Rafael, CA, USA). Stimuli were presented and responses recorded using PsychToolbox 3 for Matlab (http://www. psychtoolbox. org)  9, 10, 37. Observers were seated approximately 60 cm from a Dell 2407WFP monitor (24 inch screen diagonal size, 1920 × 1200 pixel resolution; 60 Hz refresh rate).
Animation stimuli were scaled to a size of 9° × 12°. In the first step (motion capture, left), facial expressions are recorded from different actors using a marker-based motion capture system (41 markers shown as white dots). In the second step (facial action time courses, middle), the facial animation system decomposes the motion capture data of each facial expression into 30 time courses of facial action activation (e. g. , eyebrow raising). Here a subset of 13 facial actions is depicted for demonstrative purposes. In the last step (facial animation, right), the time courses of facial action activation are used to animate a single 3D face model designed in Poser 8 (SmithMicro, http://poser. smithmicro. com/poser. html).
Data Analysis. Human and model observer data analysis. We assessed human sensitivity to identity information by calculating the d' value for the three types of facial movement. We used the differencing rule for match-to-sample tasks to calculate d'; this assumes that observers compare each of the test stimuli a and b with the sample x and base their decision on these two comparisons  [12] [13] [14] 40. We  pplied the same formula to the model observer data. T-tests were used to assess whether sensitivity was significantly different from chance and to reveal differences in sensitivity between types of facial movement. A two-way mixed measures ANOVA with facial movement type as within factor and observer type as between subjects factor assessed behavioral effects of facial movement type and differences between human and model observers.
Determinants of treatment failure were explored by univariate log-rank test and unadjusted Cox analysis. Statistical analysis used SPSS 17. 0 software (SPSS Inc, Chicago, IL, USA). The research was conducted in accordance with the Declaration of Helsinki and national and institutional standards. The study received the approval of the French South-East II and III ethics committee with the reference number CAL2011-021 and n°QH 20/2014. In accordance with French legislation, written informed consent was not required for any part of the study, as (i) daptomycin was used as salvage therapy in the usual care of patients addressed to our regional reference center for complex BJI; (ii) patients were informed orally and by letter that data were being collected using a national database established by the DGOS (in line with ruling n°2012-220 of the French national data protection commission: Commission Nationale de l'Informatique et des Liberté).
Discussion Despite its non-comparative, non-randomized, singlecenter design, this cohort study provides important data concerning off-label use of prolonged high-dose daptomycin therapy in complex BJI, reflecting the real-life use of daptomycin in a BJI referral center. Daptomycin therapy in patients with complex BJI shows a high rate of treatment success (77 %), despite the patient population being at high risk of relapse. Age, non-optimal surgery and daptomycin discontinuation for serious adverse events were the three determinants of treatment failure. Daptomycin was safe, but a higher incidence of  eosinophilic pneumonia than expected was recorded, in contexts of daptomycin C min > 24 mg/L. Daptomycin does not have approval for the treatment of BJI by the US and European authorities. However, based on retrospective data and one randomized controlled trial, it was proposed as an alternative option in patients with staphylococcus or enterococcus prosthetic joint infection in the recent IDSA guidelines, at the standard dose of 6 mg/kg/d  [4, 5, 7].
Recent reports of poor daptomycin bone penetration encourage the use of higher doses  [6]. In addition to these pharmacological studies, doses up to 8 mg/kg are supported by in vitro  [9, 10]  and in vivo studies  [11] [12] [13]  High doses have been described in retrospective studies  [14] [15] [16] , but prospective studies including patients receiving high doses of daptomycin are crucial to determine efficacy and safety in BJI. Concerning safety, patients with BJI are particularly exposed to serious adverse events, as most antimicrobials are used in combination, at high doses and for several weeks or months  [3]. In the present study, 40 % of patients experienced at least one AE during treatment, which is notably higher than in previous reports  [7]. This difference can probably be explained by longer treatment duration (81 days, versus 28 days in the EU-CORE SM database), as AEs occurred after a mean 56 days.
Acknowledgements This work was supported by the  Lyon hospitals board (Hospices Civils de Lyon). Lyon Bone and Joint Infection Study Group  (collaborators):  Physicians -Tristan Ferry ,  Thomas Perpoint ,  André Boibieux ,  François Biron ,  Florence Ader ,  Julien Saison ,  Florent Valour ,  Fatiha Daoud ,  Johanna Lippman ,  Evelyne Braun ,  Marie-Paule Vallat ,  Patrick Miailhes ,  Christian Chidiac ,  Dominique Peyramond ;  Surgeons -Sébastien Lustig ,  Philippe Neyret ,  Olivier Reynaud ,  Caroline Debette ,  Anthony Viste ,  Jean-Baptiste Bérard ,  Frédéric Dalat ,  Olivier Cantin ,  Romain Desmarchelier ,  Michel-Henry Fessy ,  Cédric Barrey ,  Francesco Signorelli ,  Emmanuel Jouanneau ,  Timothée Jacquesson ,  Pierre Breton ,  Ali Mojallal ,  Fabien Boucher ,  Hristo Shipkov ,  Joseph Chateau ;  Microbiologists -Frederic Laurent ,  François Vandenesch ,  Jean-Philippe Rasigade ,  Céline Dupieux , Sophie Trouillet-Assant;  Nuclear Medicine -Isabelle Morelec ,  Marc Janier ,  Francesco Giammarile ; PK/PD specialists -Michel Tod,  Marie-Claude Gagnieu ,  Sylvain Goutelle ;  Clinical Research Assistant -Eugénie Mabrut.
Finally, the BS transmits its data through the Internet for storage and processing on more powerful devices which may then be accessed by the hospital staff. secure system (see  Section 6). It also provides the ability to isolate the malicious node(s) and form a new path free of any malicious node. Moreover, the related works mentioned above prove their methods using simulations only. However, this work here provides both simulation results (Tmote Sky platform) and hardware test bed results using the OpenMote platform. This allows real-world test bed results to be obtained and verified in conjunction with simulation based measurements.
System Overview In the medical-based WSN system used in this work there are components, processes, protocols, and objective(s): 1. Components refer to sensors, nodes, access points, base station(s), databases, and servers. Out of these components some of the important ones that will be covered in this paper are nodes, access points, and base stations. 2. Processes are the steps taken to achieve a particular objective. These may be acquiring patient data, sending control signals, network maintenance, route setup, and so on. This work will focus on route setup with basic maintenance to facilitate a self-healing network. 3. Protocols are the set of rules followed by the network communications. This work focuses on the lower-layers of the Contiki operating system (OS), namely the radio duty cycling layer and the network layer.