dataesr/scientific-paragraphs-categorization huggingface dataset:
A. Data collection and preprocessing The Instagram API allows for the collection of all the meta-data and comments of photos on a maximal 5 km radius around a given geographical coordinate. To define points of interest, for countries we use a worldwide database of geographical locations with more than 500 inhabitants. For cities we simply define a dense enough grid that guarantees that the entire territory is covered, given the 5 km radius around each point. We then query the API for all photo meta-data within the maximal radius around each point. Given the possibility of overlap for locations close to each other, we perform further data processing to remove duplicates and associate each photo with the closest known location.
Network partitions We employ the well-known Louvain method 6 -a de facto gold standard in network community detection, widely used for the high quality of its results at a low computational cost -as implemented in the igraph software package  12, 37. Optimal community detection, like many clustering problems, is probably NP-hard  16. The Louvain method is thus an approximation algorithm. It is also non-deterministic. To both achieve higher quality partitions and increase the stability of partitions across scales, we perform 100 runs of Louvain for each graph, and choose the result that attains the highest modularity. Another common approach is to consider all the outcomes of a large number of runs, and visualise the partitions in a way that assigns visual weights to boundaries in proportion to the number of times they appear  34.
ACKNOWLEDGEMENTS This paper has been partially supported by grants " Phantomgrenzen" and "Algodiv"  ( ANR-15-CE38-0001 ), funded respectively by the  BMBF (German Federal Ministry for Education and Research)  and by the  ANR (French National Agency of Research). We warmly thank  Béatrice von Hirschhausen ,  Sabine von Löwis  and  Karin Casanova  for useful discussions and remarks. We are also grateful for constructive anonymous review comments.
Acknowledgements. This work was supported by grants from  AFM  ( Association Française contre les Myopathies ,  14199 ) to AN, from  Telethon-Italy  ( GUP13013 ) and  Eurobiobank network  ( QLRT2001-027769 ) to CA, from  AFM-Telethon  ( 19524 ),  Leducq  and  ERC (European Research Council ,  282310-MyoPHAGY ) to MS. We acknowledge the  Telethon Genetic Biobank  and the  Eurobiobank Networks  for providing patients' muscle biopsies. We thank  Dr. C Settembre  ( Telethon Institute for Genetics and Medicine, Naples, Italy ) for providing the anti-P-TFEB antibody and the  Sanofi-Genzyme Corporation (Modena, Italy)  for the anti-GAA antibody. We thank  Drs P Codogno  and  E Morel  for their support and for sharing reagents.
Negative and positive controls were included in each assay. The success of amplification was confirmed by electrophoresis on a 1. 5% agarose gel. Purification of PCR products was performed using NucleoFast 96 PCR plates (Macherey-Nagel EURL, Hoerdt, France) as per the manufacturer's instructions. The amplicons were sequenced using the Big Dye Terminator Cycle Sequencing Kit (Perkin Elmer Applied Biosystems, Foster City, CA) with an ABI automated sequencer (Applied Biosystems). The electropherograms which were obtained were assembled and edited using ChromasPro software (ChromasPro 1. 7, Technelysium Pty Ltd. , Tewantin, Australia) and compared with those available in the GenBank database by NCBI BLAST (http://blast. ncbi. nlm. nih. gov/Blast. cgi).
Data analysis For the head lice cytb sequences obtained in this study, unique haplotypes were defined using DnaSPv5. 10 and compared with all the reference cytb haplotypes as described previously  [12]. All obtained sequences of Rickettsia and Anaplasmataceae species were analyzed using BLAST (www. ncbi. nlm. nih. gov/blast/Blast. cgi) and compared to sequences in the GenBank database. For C. burnetii, all the sequences obtained from the three spacers were compared with those reported in the reference database available on the website (http://ifr48. timone. univ-mrs. fr/ MST_Coxiella/mst). Sequences of three spacers from all available genotypes were concatenated and aligned using CLUSTAL W for multisequence alignment implemented in MEGA software version 6. 06  [44]. A maximum-likelihood method was used to infer the phylogenetic analyses and tree reconstruction was performed using MEGA software version 6.
aeschlimannii based on a BLAST search, sharing 99, 65% (1,154 of 1,158 base positions in common) and 99, 74% (1,155 of 1,158 base positions in common) similarity with a reference strain of R. aeschlimannii isolate Crimea-4 (GenBank number KU961540), respectively. These results were also confirmed by a specific qPCR for R. aeschlimannii  [39]. The phylogenetic position of this Rickettsia is given in Fig 3. The partial nucleotide sequence of the gltA gene obtained in this study was deposited in the GenBank under accession number: KY937991-KY937992. For Anaplasmataceae, the 23S-based qPCR screening showed 15 out of 600 (2. 5%) head lice, collected from 11 of 117 (9. 4%) individuals, contained DNA of the Anaplasmataceae species. Conventional PCR and sequencing using specific Ehrlichia genus-primers targeting a 590-bps fragment of groEL gene showed that 14 of the 15 lice tested were positive for Ehrlichia.
Comparison with the GenBank database sequences showed that 11/14 of these sequences form new genotypes closely related to not officially recognized species E. mineirensis UFMG-EV (GenBank number JX629806) with 98. 26-98. 6% similarities. These new genotypes, referred to here as E. aff. mineirensis, together with E. mineirensis are clustered within the clade of E. canis, as shown in the phylogenetic tree (Fig  4 ). For three of the 14 remaining sequences, BLAST analysis showed a homology score of under 93% which means that these sequences are likely to be a potential undescribed new species. The closest officially recognized species is E. ewingii (GenBank number AF195273) with 90. 4% identity. These three sequences have one to two SNP between them. In the phylogenetic tree (Fig 4 ), the sequences of this potential new Ehrlichia sp.
aff. mineirensis showed an infection rate of 1. 8% (11/600) of the total number of lice tested, Ehrlichia sp. "Mali" showed an infection rate of 0. 5% (3/600) lice tested and Anaplasma sp. "Mali" showed an infection rate of 0. 5% (2/600) lice tested, including one coinfection E. aff. mineirensis/Anaplasma sp. "Mali". The partial nucleotide sequence of the groEl gene of Ehrlichia and rpoB gene of Anaplasma obtained in this study were deposited in the GenBank under the accession numbers KY937978-KY937986.
Blood meal identification in head lice We also performed blood meal analysis in the 29 head lice specimens which were positive for at least one pathogen tested. As expected, DNA from human blood was detected in all lice tested. Thus, 25 of the 29 obtained sequences showed 100% identity, while the remaining four sequences showed 99. 83-99. 65% similarities with the 16S ribosomal RNA of Homo sapiens mitochondrial sequences available in the Genbank database.
shows that this newly found genotype is mostly related to MST genotypes 6 and 7. As reported in the reference database (http://ifr48. timone. univmrs. fr/mst/coxiella_burnetii/strains. html), genotype 7 was detected in human blood from France and Russia, and genotype 6 was detected in ticks from Senegal and clinical human samples (heart valve and human sera) from France, with no available epidemiological data. Rickettsial species are transmitted by hematophagous arthropods, which contain several agents of human disease  [60]. R. prowazekii, a member of the typhus group, is the only known species naturally associated with human lice, in which the body louse is the natural vector and the head louse has been proposed as an additional vector, demonstrated only under laboratory conditions  [1, 24].
Introduction The current International Temperature Scale of 1990 (ITS-90) is defined by means of platinum resistance thermometers calibrated at specified temperature fixed-points and by using interpolation procedures at temperatures between the triple point of hydrogen (13. 8033 K) and the freezing point of silver (961. 78 °C)  [1]. Above the triple point of water, metal melting or freezing transitions are used as calibration points for Standard Platinum Resistance Thermometers (SPRTs). In the temperature range between the freezing temperatures of aluminium and silver, special High Temperature Standard Platinum Resistance Thermometers (HTSPRTs) are used to realize the ITS-90  [2]. Within the scope of the EuraThermal project, LabView software was developed that enables recording and graphical representation of instrument readings, regardless of the quantities measured by an instrument.
As soon as the new readings were taken from the instrument, software triggers start of subroutines for calculations, and graphical representation of the results and the loop starts again. As the Project participants work in the field of temperature measurements, software is currently supporting the calculations related to temperature measurement. In this case, the temperature is calculated based on the resistance readings obtained by using thermometry resistance bridges (for platinum resistance thermometers) or voltage readings obtained by using millivoltmeter (for thermocouples). The calculation subroutine is accessed from the main logging loop immediately after a new reading is taken from the instrument. Based on this reading and characteristic of the temperature sensor (or sensors if the scanneris used), the temperature is calculated and stored to the appropriate position in the data storage variable.
Preliminary validation of the calculation subroutine The calculation subroutines related to measurements with thermocouples and platinum resistance thermometers are validated in Laboratory for process measurement (Croatia). The validation consisted of a comparison of the temperatures calculated using the software with those calculated by using other means. As the first calculation reference, the additional software is used, which was successfully validated in the process of laboratory accreditation. Those results were additionally confirmed by using the Excel based calculations as the validation reference. The comparison was performed for SPRTs calibrated according to the ITS-90in the following subranges: -189. 3442 °C to 0. 01 °C, -38. 8344 °C to 29. 7646 °C and 0. 01 °C to 961. 78 °C with the temperature step of 10 °C.
The uncertainty evaluation module For the primary calibrations of HTSPRTs and Au/Pt thermocouples, the additional module was added to the software, enabling the user to automatically calculate the calibration uncertainty and generate the related uncertainty budget in the Excel format. To enable the module, the user is required to set the appropriate calibration type in the software and start measurement recording procedure. After the measurements are finished, the type A uncertainty is automatically calculated. All other uncertainties, related to the primary standard (fixed point cell) and equipment used (i. e. resistance bridge, millivoltmeter, calibration furnace,etc. ) are derived from the database, containing the relevant uncertainty components. In this way, the user has the option to specify the equipment used and the software will add the related uncertainty components to the editable fields, whose values can be changed if required in particular situation.
Conclusion The new software described is currently under test in the Laboratory for Process Measurement and will be used for the intercomparison of primary realizations of the fixed points of silver according to the ITS-90 temperature scale in the scope of the EMPIR project Eura-Thermal. The testing will be performed with the thermocouples connected to the high precision multimeter as well as with the standard platinum resistance thermometer connected to the thermometry resistance bridge. It is planned to use the same software in other laboratories participating in the intercomparison. In this way, the software will be verified through the intercomparison results. In order to avoid biases of the results that could be potentially caused by the software itself, several laboratories will still use their already validated data acquisition techniques.
The analysis only included sounds produced by the vocal tract; thus, sounds like snorts (i. e. exhalation of air from the nostrils) were not analysed. We used the same call types previously described by  Muñoz et al. (2011)  for wild and captive Mediterranean monk seals, and we identified new call types not described previously. Acoustic analyses were performed only on goodquality vocalizations; we selected calls with low background noise and no overlap with other vocalizing animals. In general, this meant that selected calls showed a signal-to-noise ratio (SNR) greater than 30 dB, information from the spectrogram and its amplitude scale. Using Avisoft SAS Lab Pro v. 5. 207 (R. Specht, Avisoft Bioacoustics) we measured the following 11 variables: total duration of the call (DUR; ms), frequency value of the 1 st peak (F max1 ; Hz), fundamental frequency (F o ; Hz), frequency excursion (F exc ; Hz), quartiles (Q25, Q50 and Q75; Hz), energy below 1500 Hz (E1500; %), and lastly the frequency bandwidth within which the energy falls within 12 dB of the first peak (BDW; Hz), which we calculated as the difference between its maximum and minimum values (BDW min , BDW max ; Hz).
Acknowledgements. We thank  Marianna Psaradellis  for her assistance in the field work. This study was conducted in accordance with the guidelines of the research permits ( 92705/770/09-03-05  and  86286/340/31-01-07 ) issued by the  Hellenic Ministry of Rural Development and Food. Financial support was provided in Greece partially by a research and conservation grant of the  Marine Mammal Commission of the USA and The Mohamed bin Zayed Species Conservation Fund.
2003 ) and rotational  (Corson et al. 2003)  grazing. Hern andez-Arrieta et al. (2000)  adapted the original TAMU model to simulate R. microplus in rotational grazing systems in Venezuela. Later,  Corson et al. (2004)  built a new simulation model (BoopMod) to predict influences of hourly microclimate, habitat heterogeneity, and within-pasture cattle movement. By this time, Sutherst (1998) had voiced concern: "The present situation, with parasitologists each doing their own thing in terms of developing and using software tools, is like the tower of Babel. " It was a call for development of more generic approaches using common scientific terms and computer languages to facilitate communication and collaboration in the research and management of vector-borne diseases.
Introduction Recent progress in X-ray crystallography has yielded more than hundred thousand protein structures deposited in the Protein Data Bank. As such, current trends in structural biology are increasingly focusing on more complicated macromolecular complexes, which remain difficult to analyze using traditional approaches. A recently developed approach for dealing with such complex and often huge systems is integrating the atomic coordinates of individual building blocks determined by X-ray crystallography and/or NMR spectroscopy into a low-resolution three-dimensional (3D) map as a template provided typically by cryo-electron microscopy  [1]. This integrative approach has successfully resulted in 3D structure models of biomolecular assemblies such as HIV capsid assemblies and the DNA telomerase complex  [2, 3].
Solution scattering measurements SANS experiments were performed using the D22 instrument installed at the Institut Laue-Langevin (ILL), Grenoble, France (Table  S1 ). The SANS intensities were observed with 6. 0 Å neutrons and two sample-to-detector distances of 5. 6 m and 1. 4 m: the covered q-ranges are 0. 01-0. 55 Å -1. The temperature was maintained at 25 °C in the irradiation. The observed SANS intensity was corrected for background, empty cell and buffer scatterings, and transmission factors and subsequently converted to the absolute scale by GRASP software using incident beam flux (http://www. ill. eu/instruments-support/instrumentsgroups/groups/lss/grasp/home/). For all SANS measurements, we used 99. 8% D 2 O (ISOTEC) containing 50 mM Tris-HCl, pH 8. 0, and 150 mM NaCl as the solvent to reduce the incoherent scattering and obtain high statistical data in the higher q-range.
We measured the SANS of non-deuterated Fc (14 μM, 0. 73 mg/ml) and 75%-deuterated sFcγRIIIb (31 μM, 0. 70 mg/ml) as well as their 1:1 mixture at each concentration of 16 μM (0. 83 mg/ml of Fc plus 0. 36 mg/ml of sFcγRIIIb). As reference, 75%-deuterated sFcγRIIIb (31 μM) under identical solution conditions was also subjected to small-angle X-ray scattering (SAXS) measurement with BL15A2 at Photon Factory, KEK, Tsukuba, Japan. SANS profiles were calculated from atomic coordinates deposited in the Protein Data Bank (PDB) with Debye functions, taking into account the deuteration ratios of both solvent-exchangeable and nonexchangeable hydrogens, as well as the excluding volume of the protein(s) (Table  S2 ) (for more detail, refer to Supplementary Method in Supplementary Materials).
Acknowledgements We thank  Dr. Susumu Uchiyama  ( Osaka University ) for useful discussion. This work was supported by grants ( JP16H00766  and  JP15H02042  to M. S. , and  JP25102001 ,  JP25102008 ,  JP15K21708 , and  JP15H02491  to K. K. , and  JP17H05893  to S. Y. ) from the  Ministry of Culture, Sports, Science and Technology (MEXT) of Japan , by the  Okazaki   ORION  project, and by the  Joint Studies Program in the Okazaki BIO-NEXT project  of the  Okazaki Institute for Integrative Bioscience. The SANS experiments at ILL were performed under proposal No. 8-03-884  and the SAXS experiments at BL15A2 were also performed under proposal No. 2015G658.
Statistical analysis The analysis of survival rates was performed using the STATA v. 11 software (Stata Corp. , College Station, TX). The median follow-up of the series was calculated according to the inverse Kaplan-Meier method  [12] , with the deaths being censored  [13]. OS, LC, PFS and MFS were calculated using the Kaplan-Meier method. OS was based on the date of first histological diagnosis to the date of analysis or time to death. LC, PFS and MFS were based on the date of the start of the tomotherapy.
Dosimetric data collection All dosimetric data were collected according to the International Commission on Radiation Units and Measurements, ICRU 83 criteria  [14]. For the PTVs, the conformity indices (CoI) of the 95% (CoI 95% ) and 98% (CoI 98% ) isodoses (volume of 95% or 98% isodose divided by PTV volume, respectively), and the homogeneity indices (HI = (D 2% -D 98% )/D 50% , where D x% is the dose covering x% of the PTV volume) were recorded. For the OARs, we noted the maximal doses to the spinal cord, medullary canal, cauda equina, sacral nerve roots, rectum, bladder and bowels (including small intestine and colon). Healthy tissue was the volume defined by the external contour excluding the PTVs and we calculated and collected its average dose (in Gy) and integral dose (in J). Dosimetric data were collected in the same way for tomotherapy plans and for proton therapy plans.
[32]  have demonstrated that osteosynthesis material can introduce uncertainties of up to 1 cm in proton range. Finally, osteosynthesis material complicates the delineation of volumes because of artifacts in the planning CT. The clinical characteristics of our patients were comparable to those stated in the literature  [1, 2]. Symptoms were dominated by pain, similar to other series  [33]. We recorded partial or total pain alleviation in the available data. However, some data were missing as pain was not always reported. Vesical-sphincterian dysfunctions were not aggravated by HT. In the majority of cases, HT was delivered without interruption due to toxicity. Only six cases of Grade 3 toxicity were recorded. In our cohort, we did not observe any Grade 4 or 5 toxicity, radiation myelitis or radiation neuropathy (including the roots of cauda equina).
These findings were consistent with our earlier data showing that the proangiogenic effect of CDCs was endoglin dependent. In addition, any direct contribution of CDCs from CAG-eGFP donor mice to the vessels of the wild-type recipient hearts was investigated using anti-GFP immunostaining. Direct contribution of GFP-labeled CDCs to these vessels was rarely observed, confirming the pro-angiogenic effect of CDCs were a result of paracrine mechanisms (Figures  S2B  and S2C ). Heart function was measured using cardiac magnetic resonance imaging (MRI) at 1 week and again at 4 weeks following MI, but the pro-angiogenic effect of CDCs was insufficient to promote significant rescue of cardiac function, in line with the large infarct size used in this study (Figure  S3 ). Left ventricular mass, ejection fraction, and end-diastolic and systolic volumes at 1 week and at 4 weeks following MI were similar in both CDC-treated and CDCuntreated mice, irrespective of the presence of endoglin (Figure  S3 ).
As endoglin acts as a co-receptor for bone morphogenetic protein 9 (BMP9), BMP10, TGFb1, and TGFb3 ligands  (Castonguay et al. , 2011; Cheifetz et al. , 1992; Scharpfenecker et al. , 2007) , we used a separate group of wild-type C57BL/6 mice (without CDCs) to examine the relative levels of these ligands in infarcted myocardium, as well as in serum, during the first week after MI. This time period was chosen as it corresponds to the period immediately after CDC injection, when the ligands would be available to interact with endoglin-expressing CDCs, before CDCs are cleared from the recipient heart tissue. Neither BMP9 nor BMP10 were detected by qPCR in the left ventricular tissue either before or after MI (data not shown). In contrast, qPCR revealed dynamic changes in expression of TGFb1 and TGFb3 in the left ventricular tissue following MI, reaching a peak at day 5 for TGFb1 and at day 7 for TGFb3 (Figure  S4 ), similar to previously published data  (Christia et al.
, 2016; Li et al. , 2009). If improved functional outcomes are not reproducible in a standardized pre-clinical model, translation of any benefit to patients becomes even more challenging. Indeed, a recent meta-analysis of 1,871 individual patient datasets from 28 studies of acute MI patients found that intracoronary cell therapy provided no beneficial effect on left ventricular function  (Gyongyosi et al. , 2015). It is critical, therefore, that pre-clinical studies are reproducible to help improve the translatability of pre-clinical findings  (Jones et al. , 2015)  and to determine the essential factors responsible for beneficial outcomes in cardiac stem cell therapy. CDCs and MSCs are currently in clinical trials for a range of cardiac myopathies  (Golpanian et al. , 2016) , and consistency of cell preparation/culture techniques is critical for their efficacy.
001. (B) Healing of the HUVEC scratch-wound assay is reduced in the presence of Eng KO CM. CM collected after pre-treatment of Eng KO CDCs with 2 ng/mL BMP9 for 24 hr restored the pro-migratory capacity of Eng KO CM. In contrast, pre-treatment with ALK5 inhibitor (SB431542) had no effect. Data are plotted as mean ± SEM from three independent experiments; *p < 0. 05, **p < 0. 01. analyzed using an LSRII flow cytometer and FACSDiva software (BD Biosciences). Positive cells were defined as the percentage of the cell population stained by more than 99. 7% of isotypematched antibody. To prepare CM, we cultured CDCs in serum-free IMDM for 48 hr. For specific experiments, ALK5 inhibitor (SB431542, Sigma) or BMP9 (Peprotech) were added to CDCs for 24 hr and washed away with PBS prior to 48 hr of culture in fresh serum-free medium to prepare CM.
2D Matrigel Angiogenesis Assay HMEC-1 cells were cultured on growth factor reduced (GFR) Matrigel in H-medium without EGF. Either CM or IMDM medium was added to H-medium to a final concentration of 20%. Tubule formation was imaged after 18 hr using an Axiovert200 inverted microscope fitted with an AxioCamHR digital camera. Total tubule length was quantified using NeuronJ plugin software.