dataesr/scientific-paragraphs-categorization huggingface dataset:
Flow cytometry Harvested cells were fixed in 2% paraformaldehyde in dPBS for 10 minutes at room temperature and then washed and stored in dPBS. Cells were incubated in blocking buffer for 15 min at 4uC, followed by 30 minute incubation at 4uC with primary antibodies against CD14, CD45, CD73, CD105 (Millipore Chemicon) or corresponding isotype controls (Invitrogen/Molecular Probes) in blocking buffer. After a brief wash, cells were incubated with 1:800 dilution of corresponding secondary antibodies for 30 minutes at 4uC in the dark. For each sample, 30,000 events were acquired using BD FACS Calibur Flow Cytometer (BD Biosciences). Histogram overlay subtraction analysis using the BD Cell Quest Pro software (BD Biosciences) was performed to calculate the percent of marker positive cells.
58); hence the data sets were pooled for the tests on normality and skewness. To investigate the relationship between peak frequency and body size/condition, only the new data set from this study was used (n = 90) as some measurements from previously published data  [22, 23]  were not available (e. g. not collected). From the present study, a total of 90 individuals (75 females and 15 males) captured during the mating season (2 nd -24 th September 2010) were recorded in a screened tent while animals were hanging around 1 m from the detector. Recordings were made from stationary individuals to obtain a measure of peak frequency not altered by Doppler shift  [23]. Echolocation calls were recorded with a D1000X ultrasound detector (Pettersson Elektronik AB, Uppsala, Sweden; 65 dB between 30 and 120 kHz) with a sampling rate of 384 kHz.
Given that peak frequency measured over many calls from the same individual showed limited variation compared to the range of frequency used in the species  [23] , we measured ten good signal-to-noise ratio calls to determine an individual's peak frequency, which was then considered as the arithmetic mean of these ten calls. Following this procedure, the peak frequency of each individual was estimated with precision (mean standard error = 0. 018 kHz). Measurements were done with the package Seewave  [26]  v. 1. 6. 5 in R  [27]  v. 3. 0. 2. The 'fpeaks' function was used to search for the peak frequency in the frequency spectrum over the entire call (FFT size: 2048; window type: Hanning) provided by the 'spec' function. The following mass and size characteristics were measured by the same person (IB) for each individual; capture weight, forearm length, and head-body length (from the tip of the snout to the anus, ventrally).
The 'scaled mass index' (SMI), the predicted body mass when the head-body length is standardised, was used as a measure of body condition  [28]  with males and females treated separately. Adult and sub-adult individuals were treated together as sub-adults R. mehelyi have been shown to reach their adult size in August in Bulgaria  [29]. The SMI was calculated in R using custom written scripts and following equation 2 in Peig & Green  [28]. Mass and size characteristics from 266 individuals (male: 169; females: 97) captured in Northern Bulgaria were used to precisely estimate the scaling component b SMA necessary to calculate the SMI. As there was no significant correlation between the logarithm of body weight and the logarithm of forearm length (data not shown), the SMI was only calculated with captured weight as the body mass variable and head-body length as the linear body measurement.
Files for adult males with low or high frequency were standardised with on average the same number of calls (mean = 29. 2 calls/file). In total, the data set comprised 702 different calls. A custom written Matlab routine (The MathWorks Inc. ) drew from these two sets of files at random and played back one second files alternating between the two speakers until each speaker had played back 100 files. The speakers were connected to the computer running Matlab via a two output PCMCIA card (DAQ TM -6062E, National Instruments). Playback files were normalized such that the loudest call had an amplitude of about 60 dB sound pressure level at the perch of the test bat. This amplitude mimics echolocation calls of a bat hanging or passing at a few meters' distance  [31]. The frequency response of the combined recording and playback system was flat (63 dB).
Permutation test For each animal, we counted the number of landings in the high and in the low frequency compartments. We tested the null hypothesis that the number of landings in the two compartments was equally likely. The test was carried out by comparing the difference in the average number of landings in the high and in the low frequency compartment for the observed data set versus the null distribution estimated from 99999 data sets where the number of landings in the high and low frequency compartment were randomly permuted and individuals were drawn with replacement. The test was implemented in R via a custom written script.
In total, we obtained 209,567 reads. After quality checks, 87,811 and 33,504 could be attributed to R. euryale and R. mehelyi respectively based on the MID-tag. Reads that contained perfect dinucleotide, trinucleotide, and tetranucleotide tandem repeats that were at least 12 bp in length were extracted using a Perl script as detailed in Castoe et al. [35]. Reads with microsatellites containing flanking regions with high quality priming sites (referred to as PAL, 'potentially amplifiable loci'  [35] ) were submitted in batches to a locally installed Primer 3 program  [36]. This primer pair design process was automated via a Perl script detailed in Castoe et al. [35]  using the same primer design criteria, except the melting temperatures that were set between 58-62uC (optimal at 60uC) and the amplicon length that was set to different values in separate runs (105-125; 180-220; 280-320; 380-420; 480-520).
Running the script with different length enabled selection of loci with amplicon lengths that would not overlap, facilitating multiplexing of a maximum of loci. Outputs from primer 3 were summarised with custom written R scripts and a total of 51 primer pairs were selected based on the number of repeats (favouring repeats numbers. 10 whenever possible) and repeats type (26 tetranucleotides, 12 trinucleotides and 13 dinucleotides) (GenBank accession No. KC908111-KC911274). The 102 primers were screened in the program Autodimer v. 1  [37]  for non-specific interactions. To evaluate amplification success and select polymorphic loci among those 51 loci, two individuals from each species (R. mehelyi and R. euryale) were screened with unlabelled primers in a 10 mL simplex reaction as in Puechmaille et al.
Relatedness estimates Males with high reproductive success will sire more offspring and have more relatives in a colony, hence their average relatedness with other members of the colony will be high. The situation is different for females as irrespective of their frequency, each female can have a maximum of one offspring per year, hence we expect a much weaker correlation (if any) between peak frequency and average relatedness in females. To provide evidence that females indeed choose their mate according to peak frequency, we investigated the relationship between mean relatedness and peak frequency. Relatedness between individual pairs within colonies was first estimated in the program Coancestry  [43]  using the Wang moment estimator  [44]. For groups showing a significant correlation between the relatedness estimate and peak frequency (males in El Haouariya), we verified that the significant relationship was not sensitive to the relatedness estimator used.
Acknowledgments This paper is dedicated to the memory of PD  Dr. Bjo ¨rn Siemers , head of the  Sensory Ecology Group in Seewiesen , who passed away on May 23 rd 2012. Our deepest thanks go to him for his support, encouragement, kindness and humour, which he shared with all who knew him. We acknowledge  Markus Schuller  and  Daniela Schmieder  for their help with setting up the mate choice experiment,  Diethard Tautz  for and  Heinke Buhtz  for assistance. The comments of  Egoitz Salsamendi ,  John Altringham  and an anonymous reviewer helped to improve a previous version of this manuscript.
Studies on tropical livestock have focused on sheep  (Paul et al. , 2003) , goats  (Mandal et al. , 2005)  and cattle  (Paul et al. , 2004)  under the same condition with local breeds. However, to our knowledge, there is no recent work that has focused on the requirements of ruminants in tropical regions using a large database in order to take into account the maximum diversity of animal genotypes and dietary systems. The objective of this study was to determine energy and protein requirements of growing ruminants in tropical and warm countries by running a meta-analysis on a large database built from independent studies.
Data collection A literature survey was conducted taking data from various international scientific reviews, easily accessible regional reviews, reports and theses. Publications were selected to include several major criteria: (1) chemical composition of the diet; (2) data on animal performances; and (3) if possible, data on in vivo digestibility and nitrogen balance. In total, 589 publications representing 2225 different dietary treatments from feeding trials were used in the present study. In addition, another database containing published results on energy and protein requirements obtained via different methods (the calorimetric method, the slaughter method and meta-analysis of feeding trials) has been analysed in order to compare the results in our study (see Tables  1  and 2 ). The calorimetric method is conducted in respiration chambers to measure gas exchange, fasting heat production and energy loss via urine and methane with animals fed at maintenance level.
Estimations, calculations and encoding The most important parameters considered were growth, physiological stage, duration of observations, intake, digestibility and nitrogen balance. In addition, equations were applied to provide consistency and conventional expressions for certain variables. Thus, MEI per kg of LW (MEI/LW, kcal/kg LW) was predicted from digestible organic matter intake per LW (DOMI/ LW, g/kg LW) by the regression equation obtained on the 'RUMENER' database containing only calorimetric measurements on sheep, goats and cattle  (Sauvant et al. , 2011). The slope of 4. 03 (MEI/DOMI) is similar to the value of 4. 45 kcal ME/g total digestible nutrients (TDN) suggested by the NRC  (2001). MEI/LW = -2. 03 + 4. 03 DOMI/LW (n = 975, R 2 = 0. 99, r. s. d. = 11. 3) For the assessment of requirements in terms of metabolisable protein (MP), the French protein digestible in the intestine (PDI) system was applied using global and robust equations for prediction based on dietary CP and digestible organic matter (OMD) taken from the INRA feed tables.
Statistical analyses Inter-publication regressions of nutrient intake on ADG were calculated. Moreover, to test simultaneously the influences of species and genotypes on the intercept (maintenance requirements) and the slope (growth performance), analyses of variance and covariance were applied to the parameters. These meta-analyses were performed following the recommendations of  Sauvant et al. (2008)  using Minitab software (Minitab ® 15. 1. 30. 0. , 2007). Outliers were removed when their normalised residues were >3.
Moreover, the effect of age is not well studied, but some findings with ruminants indicated decreasing requirements with age  (Luo et al. , 2004a). Energy requirement for maintenance and growth A limit of this work is that ME, in all probability, is not the energy type best suited to assessing the actual energy value of feeds and fibre-rich diets. Most European energy systems are effectively built on the proposals of  Van Es (1972)  showing that the efficiency of conversion (k) of ME to NE was closely and positively linked to the ratio Q = ME/GE, or dietary ME/kg DM, which is closely linked to OMD. Consequently, for cell wall-rich low-ME/kg DM diets, which are more frequent when observations are closer to low performance levels in our database, the difference between ME and NE is more important.
e. distance, area, circle radius etc. ?)  [15]  we used segments of the track, the length of which defines the scale. Centered on each dive, we selected a segment that measured two, six and twelve kilometers in total length. These three scales were chosen empirically based on careful observations of the tracks. Segments of two kilometers typically encompass localized foraging patterns at the diving site, such as a succession of loops. Segments of six kilometers encompass medium scale movements that could be described as ''hopping between potential diving sites''. Segments of 12 km are long enough to describe relocations from a foraging area to another one. It is important to note that these values are adapted to our dataset and cannot be generalized. In order to test the sensitivity of these values on the final results, we replicated the analysis using some variations in these numbers (1,5, 10 km, and 2,8, 20 km).
The wind data were derived from the Cross-Calibrated Multi-Platform Ocean Surface Wind Vector L3. 0 First-Look Analyses: http://podaac. jpl. nasa. gov/dataset/CCMP_MEASURES_ ATLAS_L4_OW_L3_0_WIND_VECTORS_FLK. Documentation can be found at: "ftp://podaac-ftp. jpl. nasa. gov/allData/ccmp/L3. 0/docs/ccmp_ users_guide. pdf". Wind data were available at 6 hours intervals. The wind data was chosen in time and space to correspond to the position of the birds after 1 hour at sea (2 thirds of the data collection period). The wind data associated with each of the three foraging situations were stable in time, and the data obtained were likely to have been a true reflection of foraging conditions. Data analysis was performed using Matlab (R2010a, The MathWorks, Natick, MA, USA). This study was carried out in strict accordance with the recommendations from the South-African National Parks (SAN-Parks).
obs. ). As collisions rarely happen, but can be fatal  [18] , looping pattern could represent an anti-collision strategy, and may suggest the presence of a high density of aerial predators. With video data available for only about 10% of the foraging trips, we were limited in associating movement patterns to the respective foraging contexts. It is important to note that the first 10% of these tracks were mostly associated with locating foraging zones and the beginning of foraging phases in some cases. From a methodological standpoint, we propose that 90 minutes of camera autonomy is required to enable foraging phases to be recorded for Cape gannets and other similar study species. The results from the extrapolation of the foraging contexts from the first 10% to the remaining 90% of the trip using the classification tree need to be interpreted carefully, because the foraging phases were determined as short low-speed periods, without certainty about dive occurrence.
Patients Two groups of patients are tested in this study, the first with a triple negative breast cancer profile and the second with a non triple negative breast cancer profile (Luminal A, Luminal B, and HER-2). Formalin-fixed, paraffin-embedded (FFPE) tissue files were drawn from the department of pathological anatomy of Salah Azaiez Institute of Tunis. We managed to recover 30 FFPE tissues for each group of patients with their corresponding normal tissues. Three 10 mm cores were obtained from both the tumor and the normal tissue. Essential information includes stage, grade, lymph nodes metastasis and distant metastasis along with data on ER, PR and HER-2 tumor expression and the genico-obstetric history of patients were collected from the Salah Azaiez Institute data base. For tumor tissue sampling, a great effort was made to avoid any adjacent normal tissue and to isolate areas of tissue containing.
Statistical analysis Normality of the data distribution was checked by Kolmogorov-Smirnov test. Differences in the expression levels between breast tumor and normal tissue were measured using the Mann-Whitney U test. The association between miRNA expression and clinical features were analyzed via the Spearman's correlation test. Numerical values are expressed as the mean 6 standard deviation (SD). Statistical significance was set at the 95% level (p,0. 05). All statistical analyses were performed with SPSS 20 (SPSS, IBM) software.
Clinical outcome The subjects of our study consisted in 60 patients with primary breast carcinoma. These cases were divided into two groups: 30 patients with triple negative breast carcinoma and 30 patients with non triple negative breast cancer profile including 16 cases with the Luminal A subtype, 10 with the Luminal B subtype and 4 with the HER-2 subtype. Data concerning the expression of the three markers (ER, PR and HER-2) by routine immunohistochemistry along with clinical and personal information were collected from the archive of the Salah Azaiez Institute data base. We first compared the two studied groups in terms of the clinical data including age at diagnosis, histological breast cancer type, lymph node metastases, distant metastases, grade and stage, along with genico-obstetric information including age of first menstruation, age at first pregnancy, number of completed pregnancy, breastfeeding, contraceptive pills and body mass index (Table  3 ).
Acknowledgments The authors would like to thank all persons who have so far contributed to the realization of this work in  Salah Azaiez Institute of Carcinology (Tunis, Tunisia), in the Laboratory of Genetic Immunology and Human Pathology (Tunis, Tunisia), in the Laboratory of Genetic and Molecular Diagnostic (Clermont-Ferrand, France ) and in the  Laboratory of Molecular Screening In The Treatment of Breast Cancer  ( Montreal, Canada ).
This paper provides an in-depth case study of the ink-jet printing (IJP)    technology that emerged from a mature industrial sector in the Castellon region (Spain)    in the first decade of 2000. We propose an analytical framework that combines the theoretical perspectives of Industrial Districts and Innovation Systems, and exploit a qualitative methodology that includes information from patent and scientific article databases, technical literature and 21 interviews. Our results show that IJP is a major innovation that breaks with the tradition of machinery innovations in this industry in Spain. We provide micro-level evidence of the complex external and internal relationships in the innovation process. Internal ties, trust relations and strong in-house R&D were the determinants of the IJP innovation.
Specifically, we considered patents, scientific articles, and secondary documents such as organization reports and technical articles from the literature (Web of Science, Scopus, Ceramic abstracts, etc. ) and the information in patent databases (Esp@cenet, la Oficina Española de Patentes y Marcas (OEPM, Spain); PAJ and the Derwent Innovation Index) using the Matheo Patent software  (Breschi and Lissoni, 2004). We consulted the annual reports of Gold Alfa's Award of the Spanish Society of Ceramics and Glass (  2010 ), which is a prestigious annual award that has been presented at the CEVISAMA Fair since 1975 in recognition of the most important innovations in the sector. To obtain an in-depth understanding of the sector we conducted 21 interviews during January to July 2011, with the principal actors involved in the generation, development and diffusion of the IJP technology using an hermeneuticdialectic method where the interviewer played an active role, and interviewer and respondent shaped the interview 'content' together  (Jørgensen and Phillips, 2002).
ceramic decoration were conducted in 1980 by W. Roberts of British Ceram Research Ltd (UK). For some 10 years research focused on the adaptation and upgrading of ink properties, particularly flowability and conductivity, and testing of different printing methods and substrates. Developments in IJP technology as a new method of decoration on an industrial level appeared in 1997 in the Castellon region. To explore the history of this technology we ran database searches using some general keywords, such as inkjet, ceramic, tile, etc. , identifying documents related only to ceramic tile manufacture and rejecting applications for the design and manufacture of printed circuit boards, ceramic processing tools and fine ceramics, etc. (e. g. a patent registered in 1975 mentions the IJP technology in reporting a procedure for flexographic printing).
Patients meeting all eligibility criteria were invited to participate in an intervention study designed to help patients gain better control of their asthma. They were informed that we would be collecting pharmacy refill data but not that it was the primary outcome of interest. Consenting patients returned to the hospital within approximately 4 weeks to undergo baseline assessments with the study research assistant, which included completing a battery of self-report questionnaires and conducting pulmonary function testing (standard spirometry) (see "Measures" section for details). Following the completion of all baseline assessments, patients were randomized to MI or UC using a computer algorithm that generated a random code that was kept in a concealed envelope until opened by the study coordinator at the time of randomization as per the CONSORT guidelines.
MI intervention Patients randomized to MI underwent three to four individual 15-30 minute sessions over a 4-6 week period. The educator and the patient decided together that more than three (up to a maximum of five) sessions were needed to achieve therapeutic goals. In preparation for this pilot trial, an MI intervention manual that was adapted from Rollnick et al  34  for use with nonadherent asthmatics was developed. Data from focus groups including asthma patients, pulmonologists, and allied health professionals who treat asthmatics (eg, nurses, inhalotherapists) were incorporated to inform aspects of the intervention design and manual, including dose (session length, intervention duration), environment (where the intervention would be delivered and by whom), and format (individual/group, in-person/telephone) that was deemed most acceptable to key stakeholders (ie, patients, physicians, and allied health professionals who treat asthmatics).
Primary outcome: ICS adherence Baseline ICS adherence measures were taken for the 12-month period prior to study entry, and posttreatment measures were taken at 6 and 12 months postintervention. ICS adherence (primary outcome) was measured as a proportion according to the following equation: the number of treatment (prescription) days/182. 5 days (6 months adherence) and 365. 5 days (12 months adherence), respectively. Data were obtained by accessing the patients' pharmacologic chart at their community pharmacy. Secondary outcomes: self-reported adherence, asthma control, asthma-related quality of life, and asthma-related self-efficacy Self-reported medication adherence was measured using the Morisky scale. 45 This questionnaire includes four items that are rated on a 5-point Likert-type scale, where 5= never and 1= very often.
Statistical analyses Imputation of missing data Multiple imputation is recommended for studies with missing values that affect less than 60% of the sample. 60 In the present study, 14 patients (26%) had at least some missing data, so multiple imputation procedures were used. The imputation method used assumes that missing data are random, and includes all covariates that were included in the final analysis. We imputed data on cases who had missing data, producing five independent replicates of datasets. Finally, each filled-in dataset comprised 54 patients, which was the final sample size used for analyses in this study. Estimation for model coefficients was produced using PROC MINIANALYZE, which averages all estimates and adjusts standard errors according to Rubin's rule. 61 Details of the amount of missing data per variable are included in Table  1.