dataesr/scientific-paragraphs-categorization huggingface dataset:
SCIAMACHY BESD algorithm The BESD retrieval algorithm has been developed at the University of Bremen to retrieve XCO 2 from SCIAMACHY nadir measurements. BESD aims to minimise scatteringrelated errors of the retrieved XCO 2. For this purpose, the algorithm explicitly accounts for scattering. The theoretical basis of BESD and a study of synthetic retrievals is presented in the publication of  Reuter et al. (2010)  and validation results are presented in  Reuter et al. (2011). The algorithm is a core algorithm within ESA's CCI  (Hollmann et al. , 2013; Buchwitz et al. , 2013b; Dils et al. , 2014)  aiming at delivering high-quality satellite retrievals. Here we use the most recent product version (02. 00. 08) of SCIA-MACHY BESD, which is part of the Climate Research Data Package (CRDP#2) of the CCI project.
Simultaneous fitting in both fit windows transfers information, e. g. in case of scattering parameters, mostly obtained from the O 2 -A band to the CO 2 band. The forward model is the radiative transfer model SCI-ATRAN  (Rozanov et al. , 2014). SCIATRAN calculates the needed radiance spectra and weighting functions, which are the derivatives of the measured radiation. The correlated-k approach of  Buchwitz et al. (2000)  is used to accelerate the radiative transfer calculations. Line parameters from NASA's absorption cross section database ABSCO v4. 0  (Thompson et al. , 2012)  is used for O 2. The HITRAN 2008 database  (Rothman et al. , 2009)  are used for the other gases. The calculated spectra are convolved with a Gaussian slit function. Although BESD has been designed to minimise scatteringrelated retrieval errors, clouds are still an important potential error source and strict cloud filtering is necessary.
Level 1C data generation GOSAT BESD uses GOSAT Level 1B data (L1B) version 161160. These data have been obtained from the GOSAT User Interface Gateway (http://data. gosat. nies. go. jp/GosatUserInterfaceGateway/guig/GuigPage/open. do) and from ESA's GOSAT Third Party Mission data archive. The (uncalibrated) L1B data have been converted into calibrated Level 1C (L1C) data, by using e. g. the radiance correction scheme described by  Yoshida et al. (2012). The L1C data consist of the fully calibrated total intensity, an estimation of the measurement error and a priori information. The total intensity is computed by using the polarisation synthesis method described by  Yoshida et al. (2011)  using the Mueller matrices described by  Kuze et al. (2009). The measurement noise (ε meas ) is estimated by the standard deviation of the first 500 and the last 500 off-band spectral points of GOSAT bands 1, 2 and 3.
The coefficients are listed in Table  1. The a priori information includes profiles of temperature, pressure and humidity obtained from ECMWF data and height information from a digital elevation model (DEM). The used DEM (obtained from http://www. viewfinderpanoramas. org) is mostly based on data collected in 2000 by the Shuttle Radar Topography Mission and has a spatial resolution of 15 arc s. A priori estimates for the zeroth-order polynomial coefficient of the albedo (P 0 ) are obtained by computing the 95 % percentile of the reflectance (sun-normalised GOSAT intensity divided by the cosine of the solar zenith angle).
GOSAT XCO 2 (Level 2) generation The GOSAT XCO 2 (Level 2) data have been generated by using a modified version of the SCIAMACHY BESD retrieval algorithm. The main modifications are the following: we have used three bands instead of two bands (as used for SCIAMACHY) for the retrieval of GOSAT XCO 2. Band 1 includes the O 2 -A band (12 920-13 195 cm -1 or 758-774 nm), band 2 contains a weak CO 2 absorption band (6170-6278 cm -1 or 1593-1621 nm) and band 3 includes a strong CO 2 absorption band (4804-4896 cm -1 or 2042-2082 nm). The state vector of GOSAT BESD consists of 38 elements instead of 26 for SCIAMACHY BESD. The state vector elements, their a priori values and uncertainties are listed in Table 2. A second-order albedo polynomial is additionally fitted in the third fit window. Besides a spectral shift of the nadir radiance, a shift of the solar spectrum is fitted.
However, in order to accelerate the radiative transfer calculations for GOSAT BESD retrievals, tabulated cross sections (based on the absorption cross sections database ABSCO v4. 0 described by  Thompson et al. , 2012)  have been used and the linear-k scheme of  Hilker (2015)  has been implemented. A high spectral resolution solar irradiance spectrum based on the "OCO TOON spectrum"  (O'Dell et al. , 2012)  is used to calculate the total intensity instead of the sun-normalised intensity as used by SCIAMACHY BESD. The simulated intensity is convolved with the GOSAT ILS (Eq. 2). In Fig. 1  a typical example of observed and fitted GOSAT spectra in all three fitting windows is presented. The observed and fitted spectra show reasonable agreement. The reduced χ 2 (computed as described by  Yoshida et al.
Acknowledgements. We thank  JAXA ,  NIES  and  ESA  for providing us with the  GOSAT L1B  and  L2 IDS data. We are also grateful to  Jonathan de Ferranti  for the development of the digital elevation model, which we used for our evaluations. We thank  TCCON  for providing FTS XCO 2 data obtained from the  TCCON Data Archive , operated by the  California Institute of Technology , from the website at http://tccon. ipac. caltech. edu/. The CarbonTracker CT2013B results has been provided by  NOAA ESRL, Boulder, Colorado, USA , from the website at http://carbontracker. noaa. gov. We thank  NASA  for providing us with the ABSCOv4 tables and ECMWF for the meteorological data. This work has been funded by the  EU   FP7  ( MACC-II ),  EU Horizon 2020 (MACC-III) ,  ESA  ( GHG-CCI  project and  Living Planet Fellowship  project  CARBOFIRES ) and the state and the  University of Bremen.
We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computergenerated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft.
RiboSoft usage Before the design algorithm can run, valid input from the user must be entered. The required input takes the form of (i) a target nucleotide sequence, which may be provided by: direct entry into a text box, uploading a pure text (. txt) or FASTA format file, or typing in a GenBank sequence number (Figure  2 ); and (ii) a set of design parameter values (Figure  3 ). The design parameters are: (i) the target environment: whether it is in vitro or in vivo, and if it is in vivo, then the name or code of the intended organism; (ii) environment properties: temperature as well as oligomer, sodium and magnesium ion concentrations; (iii) potential cut-sites (e. g. GUC); (iv) ribozyme structure: minimal or extended (i. e. involving loop-loop interaction, designated as wishboneshaped) (5); (v) advanced options: the minimum and maximum lengths of helices I and III (the targeting arms of the ribozyme), the presence or absence of a T7 promoter (usually used for in vitro experiments) and whether specificity should take into consideration off-target sites that allow annealing only or annealing and cleavage by the designed ribozyme.
Ribozyme structure Every hhRz candidate surviving the annealing temperature phase is evaluated for its structure. This is a measure of how open (single-stranded) the arms are, which makes it easier for a ribozyme to find and anneal to its intended target sequence and hence, perform its trans-cleavage function. The Sfold program (  25 ) is used on the server side to fold all the candidates; it uses a statistical Boltzmann ensemble model to generate possible secondary structures for the candidate RNAs. Sfold reports 10 secondary structures, each with its own probability. This probability is used as a weight when considering the structure of a ribozyme. RiboSoft gets the quality of one or many secondary structures for one hhRz with an algorithm that uses the sum of the melting temperatures of all continuous stretches of double-stranded RNA as an (inverse) measure of the openness of the two arms of the ribozyme.
The result of this calculation is the raw cut-site accessibility value (both cut-site inaccessibility and disruption energy are succinctly described in pseudocode, supplementary information). The calculation of disruption energy is done per cut-site. The reason for this is the significant computational cost associated with the computation of the secondary structure for a long RNA strand; typical gene transcripts are one to several thousand bases long. We use 23 bases for both arms' binding sites and hence compute G disruption. This allows the evaluation of the structures likely to compete most strongly with hhRz binding. Since Sfold returns 10 possible secondary structures for the target transcript, we will also have 10 G disruption values. These values are used to calcu-late a weighted linear sum in a fashion identical to what was done for cut-site accessibility.
Specificity assessment For in vivo applications it is important that a given ribozyme affects the targeted transcript and no other. Typically, a hhRz would affect a transcript by cleaving it. It is possible, however, for a hhRz to anneal to a transcript and hence, lead to the transcript's destruction or to a reduction in its translational efficiency, without cleaving it. This is part of what is known as off-target effects. Hence, the 'advanced options' section of RiboSoft's input pages allow the user to check for either off-target hits that would potentially result in cleavage or all off-target hits, including those that do not lead to cleavage. The NCBI BLAST web-service is queried with a high threshold (sensitivity) using the region around the targeted cut-site corresponding to the maximal possible lengths of hhRz arms.
The results are weighted based on the number of matched pairs, thus a perfect match yields a weight of one (the targeted transcript). It should be noted that RNAs with accession numbers starting with XM or XR (RNA predicted sequences) are ignored in the count, but are still reported in the results' page. The program will only return 0 if the RNA sequence does not exist, since there is not necessarily a priori knowledge of the transcript being targeted (users can enter arbitrary sequences directly). Optimally, the value of specificity is 1, entailing a perfect match to only one cut-site on the targeted transcript. Higher specificity values are detrimental to the quality of the hhRz candidate, and as such this measure of quality should be minimized (pseudo-code in supplementary information briefly describes this).
Western blotting Total proteins were extracted in SUB buffer at different time points (containing 8M urea, 2% mercaptoethanol and 0. 5% SDS), and electrophoresed in 12% SDS-PAGE gels. Proteins were blotted into nitrocellulose membrane and probed with specific antibodies against PABPN1 (1:2000) (Abcam, USA). Parallel samples were probed using monoclonal actin antibody (Chemicon International, USA) to confirm the equal loading of lysates between lanes. After incubation with specific secondary HRP-conjugated antibodies, the membranes were revealed using the western blot chemiluminescence reagent plus kit (NEN Life Sciences Products, Boston, MA, USA). Quantification of the band intensity was performed using the ImageJ software. Values were normalized by ␤-actin. Quantification of PABPN1 protein level was determined by western blot using the ImageJ software, normalized to actin and presented as fold change relative to the level of PABPN1 in untransfected HEK293T cells.
Single ribozyme cleavage and additive effect of combinations In addition to specifying and devising a comprehensive hhRz design algorithm, then implementing it as web service, we have also used the service for a particular gene silencing application. This involved the PABPN1 gene, whose mutation results in a muscular dystrophy disease known as OPMD. Before proceeding to in vivo trials in various model organisms, which is a costly affair, we proceeded to test the validity of ribozymes generated by RiboSoft, in vitro, for their efficiency in cleaving the transcript (mRNA) of the PABPN1 gene. The following two sections describe in detail the wet lab experimental methods followed to test the ribozymes and the results of these tests. The results were positive and provide preliminary evidence of the value of the new web service.
This result confirms that the design of the ribozymes, amongst many generated by RiboSoft, were correct, in that they led to functional ribozymes. To ensure the universal applicability of RiboSoft, we assayed 15 additional hhRz designed by our software against two very different targets, a RFP mRNA and a portion of a 16S ribosomal RNA, the latter is notably structured and likely much less accessible than the average mRNA. All the ribozymes that were ranked 1 against these targets could cleave similarly to the results obtained for PABPN1-hhRzs, except for one inactive ribozyme, as well as most ribozymes with ranks as low as 7 (Supplementary Figures  S1, S2 , Table  S1  and data not shown). However, for two ribozymes that had poor rankings, and interestingly had an accessibility 2 measure of zero, no significant cleavage was observed (Supplementary Table  S1 ).
DISCUSSION This paper presents two main contributions to the world of ribozyme design and ribozyme application. The first part of the paper describes the algorithm and implementation of RiboSoft, a completely automated program (offered as a web service) for hhRz design. It can be used to design hhRz to target any RNA sequence, including the transcript of any gene. The program has clear and valuable advantages over existing hammerhead design services, related to usability, ribozyme quality assessment and multi-objective optimization. It unifies in a single tool the functionalities of targeting ribozyme design software that have been done in the last decade: it finds target sites, computes target accessibility, ribozyme structure validity and potential off-target effects. More importantly for the future community of users, it provides a user friendly interface with the flexibility required for any application: from in vitro assays, to gene targeting in Escherichia coli, in humans or in any desired species and computes all the complexity of the analysis to simply pro-vide ribozymes that will likely be active over 90% of the time as demonstrated by our in vitro assays.
A number of software exist to assist in ribozyme design. Up to now, the best tool in that regard was probably. Aladdin (SeArch computing tooL for hAmmerheaD ribozyme DesIgN) (http://aladdin. ifc. cnr. it/aladdin). This tool, which evolved from an earlier computational method  (29, 30) , is handy and scientifically sound. However, Ri-boSoft has several advantages: it uses the latest research on target-site accessibility; and it has off-target specificity analysis. Off-target accessibility could be evaluated with Ribo-Substrates  (31) , but the design of ribozymes would then require the use of two different tools, which makes automated design more complicated. RiboSoft also has the advantage of allowing specification of the nature of the environment, the type and size of the ribozyme and the nature of the application.
Similarly, the evaluation of possible hhRzs is easier with RiboSoft than Aladdin, because the former provides multi-objective ranking and allows sorting ribozymes according to each parameter, Our experience with these parameters seem to point toward a stronger impact of 'accessibility 2' on the ability of a chosen ribozyme to cleave its target. The other contribution is the design (by RiboSoft) of four hhRz targeting the transcript of the PABPN1 gene, and testing these ribozymes, in vitro and in vivo, for their cleavage efficiency. A mutated PABPN1 is the root cause of OPMD (oculopharyngeal muscular dystrophy) in humans, a late onset muscle disease associated with progressive ptosis of the eyelids, and dysphagia. The experiments validated the designs as they demonstrated cleavage by each of the four ribozymes.
It is worth noting that only a precisely delineated part of the ribozyme need to be altered to give the whole ribozyme this unique allosteric capability; the rest of the ribozyme stays fixed. Both of these allosteric ribozymes could be designed by a RiboSoft 2. 0. Another direction for development involves the modification of the design of the resulting hhRz to test their gene silencing functionality, as well as unwanted effects, in living organisms. Selected ribozymes against PABPN1 appear to cleave their target both in vitro and in vivo, which is promising for future work aiming to replace the mutant transcripts with healthy mRNAs in human cell, thus advancing toward a therapeutic approach to OPMD. Indeed, even when it is theoretically possible to target them, the exact regions harboring mutations are not necessarily ideal cleavage sites.
APPLICATIONS Code limitations While a range of reactive transport codes handle the Nernst-Planck equations for diffusive fl uxes in the bulk water, very few of them can handle transport processes in the diffuse layer  (Steefel et al. 2014 ). Available publications with reactive transport simulations considering diffusion in the diffuse layer are limited to PHREEQC and CrunchFlowMC application studies  (Appelo and Wersin 2007; Appelo et al. 2008 Appelo et al. , 2010;; Alt-Epping et al. 2014 ). To our knowledge, interlayer diffusion processes are handled by PHREEQC only, and the interlayer diffusion option has been applied in only two published studies  (Appelo et al. 2010; Glaus et al. 2013 ). In the following PHREEQC and CrunchFlowMC are used to illustrate the importance of considering coupled diffusion/surface reaction effects in order to understand and to predict migration processes and associated parameters in charged porous media, especially clays.
ACKNOWLEDGMENTS This work was supported by the Director,  Offi ce of Science, Offi ce of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division , of the  U. S. Department of Energy  under Contract No. DE-AC02-05CH11231 , and by the  European Atomic Energy Community Seventh Framework Programme  [ FP7 -Fission -2009]  under grant agreement n°624 249624 Collaborative Project Catclay. C. Tournassat acknowledges funding from  L'Institut Carnot BRGM  for his visit to the  Lawrence Berkeley National Laboratory.
Patient selection Tissue samples were collected from colonic biopsies of patients with CD. Thirty patients with CD treated at the Department of Gastroenterology (Nantes University Hospital, France) were included in this study. Colonic biopsies were obtained and stored in the bio-collection of the "Institut des Maladies de l' Appareil Digestif (IMAD)". The clinical and demographic data were collected and recorded in a computerized database securely coupled to the biological collection. This bio-collection was approved and registered by the French Ministry of Science and Research "DC-2008-402". CD was diagnosed on the basis of clinical and endoscopic criteria. Fifteen quiescent disease patients and fifteen active disease patients, with acute or chronic inflammation, were included in this study.
PCR amplifications were performed in duplicate using Light cycler 480 SYBR Green I master mix (Roche Diagnostics, Mannheim, Germany) according to the manufacturer's protocol. External standard curves were generated with serial 5-fold dilution of cDNA samples prepared with RNA extract from human mucosal biopsies. The relative amount of transcripts was calculated from these standard curves using RotorGene software. Expression of S6 ribosomal proteins as internal controls was analyzed at the same time. For each sample, the ratio between the relative amount of each specific transcript and S6 was calculated to compensate variations in the quantity and quality of starting mRNA.
Acknowledgments The authors would like to extend their thanks to  Muriel Quignard-Lopes ,  Camille Pana ,  Julie Jaulin  and  Catherine Le Berre-Scoul  for their participation in the experiments. The authors also thank  Dr. Y Urade  who kindly provided AT-56, specific L-PGDS inhibitor. This work was supported by grants from the  INSERM (Institut national de la Santé et de la Recherche Médicale) ,  Nantes University , and the  Centre Hospitalier Universitaire (CHU) of Nantes.
Data collection Data collected included patient age and gender, duration of symptoms prior to admission, results of clinical, radiological and laboratory findings, results of clinical and radiological follow-up 6 weeks after hospital discharge, and the definitive diagnosis. Weight-bearing status was determined from the clinical examination, and delay between limp onset and presentation was recorded in days. Fever was defined as an oral temperature >38. 5 °C. The values of ANA, ASO and RF were interpreted according to our laboratory references, i. e. , greater than 6 U/ml for RF, 1:80 for ANA, and above 200 U/ml for ASO. At ultrasonography, the presence and amount of articular effusion was reported in mm of space between the femoral neck and the joint capsule.
In total, 417 hospitalisation episodes for hip pain without a definite diagnosis at the emergency room were collected. Among this group, the diagnosis of TSH was subsequently confirmed in 383 (91. 8%) cases. After admission on the ward, one patient presented clinical and biological parameters (CRP of 51 mg/l and WBC count of 24. 0 x 10 3 /mm 3 ) compatible with septic arthritis, and was treated accordingly despite negative hip joint aspiration. One patient had Lyme arthritis diagnosed on positive Lyme's serology, and the remaining 32 patients had a hip pain or limp of unknown origin defined as irritable hips of unknown origin with a negative ultrasound for hip effusion (table  1 ). Among these 32 cases of irritable hip of unknown origin, full recovery was observed at follow-up. Demographic data of patients who underwent the specific protocol are shown in table  1.
In fact, ultrasound served mainly to confirm the localisation of symptoms to the hip and to detect the presence of effusion. In the present study, a hip ultrasound was performed in all children presenting with suspicion of TSH. A hip effusion was present in 92% of cases. All negative ultrasound cases were treated as TSH and had ANA = antinuclear antibodies; RF = rheumatoid factor; SD = standard deviation *The two patients diagnosed with septic arthritis and Lyme disease were excluded from data analysis.
As for Sgr II, isolating the stars in these CMD features (orange box in the central CMD panel) highlights the stellar overdensity in the spatial distribution shown in the right-most panel. As for Sgr II, we identify a potential blue straggler in green. Due to the absence of any HB star, 14  we cannot reliably break the distance-age-metallicity degeneracy with the PS1 data alone. Consequently, we explored isochrones of different ages and metallicities, located at varying distances. The best fit is provided by the PARSEC isochrone shown in Figure  1 ; it has an age of 12 Gyr and [Fe/H] = -2. 2 and is located at a distance modulus of 16. 9 ± 0. 3 but we caution the reader on the reliability of this particular isochrone that needs to be confirmed from deeper data.