dataesr/scientific-paragraphs-categorization huggingface dataset:
Data collection Baseline clinical data and neonatal comorbidities were retrospectively retrieved from patients' medical records. Nutritional intakes were prospectively collected from our local computerized physician order entry system. The following maternal details were obtained: singleton or multiple pregnancy, preeclampsia, clinical chorioamnionitis, antenatal steroid therapy initiated (at least two injections), and vaginal or cesarean birth. At birth, baseline clinical data included: gestational age, gender, anthropometric measurements (weight, length, HC) and surfactant replacement therapy. The presence of comorbidities associated with prematurity were collected such as mechanical ventilation duration, bronchopulmonary dysplasia defined as ventilatory or oxygen requirement at 36 weeks' PMA, PDA confirmed by echocardiography requiring ibuprofen or surgical ligation, NEC defined as a stage 2A or more according to Bell's modified classification, and retinopathy of prematurity (ROP) defined as a stage 2 or more according to international classification.
Both energy and protein are necessary to promote net lean tissue accretion and produce normal rates of growth including head growth  [24] , impacting body composition to adulthood if energy intakes are insufficient during the initial hospital stay  [25] , with a short leeway since excessive intakes are implicated in promoting overweight and central adiposity  [26]. The optimal energy to protein ratio to maximize protein accretion whilst minimizing metabolic harm stay unknown. Furthermore, neonatal comorbidities seem to strongly influence nutritional intakes in early life and their impact was hardly controlled in this study. In addition to the limitations already described, this investigation has the potential bias inherent in observational uncontrolled study. Outcome data reported here were collected retrospectively and some data, such as the primary outcome, were provided by the parents.
Funding: This work was financially supported by the  GRATITUDE  project ( Ref. FP7-KBBE 2011. 2. 5-02/289843/2012 ) and by  FCT-Fundação para a Ciência e a Tecnologia  through the project  UID/Multi/50016/2013. Dr. Clara Piccirillo  thanks  FCT  for the Grant  SFRH/BPD/86483/2012.
Results Description of study population. In total, 370 women were enrolled from seven European countries, Spain (ESP), France (FRA), Italy (ITA), Norway (NOR), Portugal (PRT), Romania (ROU) and Sweden (SWE) based on the eligibility criteria (Fig. 1 , Table  1 ). 226 mothers completed the study. HMO data were available for N = 239, 290, 261, 243, 234, 224 individuals at 2 (0-3) d, 17 ± 3 d, 30 ± 3 d, 60 ± 5 d, 90 ± 5 d, and 120 ± 5 d (visits V1-V6), respectively. The main reasons for drop-outs were: Without explanation (37 women), agalactorrhea (50 women) and other reasons such as feeding infant with infant formula for more than 7 consecutive days, deciding to withdraw from the study or stopping breastfeeding to return to work (57 women) (Fig. 1 , Supplementary Table  1 ). Maternal characteristics are summarized in Table  1.
We observed several HMOs related with maternal parity, however with differences between PP and MP mothers of relatively small magnitude and only seen at single timepoints during early lactation (day 2 and 17). In our dataset, although not withstanding FDR correction for multiple comparisons, PP women showed lower concentrations of several HMOs, namely 3FL, 6′GL, LNFP-II and LNFP-V, while they had higher concentrations of other HMOs such as DSLNT and LNnT, compared to MP women. A recent publication from Azad and colleagues  24  using data from the CHILD cohort is the only other study that has investigated the associations between parity and HMOs. They observed lower levels of LNnT, LNT and higher levels of 3FL in PP compared to MP women, contrary to what we observed. Theirs was a predominantly Caucasian population (73%) similar to ours, although HM samples were collected at 3-4 months postpartum and not earlier in lactation, when we observed most differences.
All methods were performed in accordance with the relevant local and institutional guidelines and regulations. The participants provided a written informed consent form to participate in the study after receiving explanations and having read and understood the purpose and the objectives of the study in their respective local languages. The study was registered at www. clinicaltrials. gov with the identifier NCT01894893. Pregnant women were recruited before delivery, generally during the last trimester of pregnancy. Inclusion criteria for this study were: (i) pregnant women between ages of 18 and 40 years; (ii) ppBMI between 19 and 29, inclusive; (iii) intention to breastfeed at least until 4 mo post-partum and (iv) agreed to the study protocol and signed informed consent form. Exclusion criteria for this study were: (i) currently participating in another trial; (ii) presenting conditions that contraindicate breastfeeding; (iii) medical conditions or on medications for conditions such as metabolic and cardiovascular abnormalities; (iv) dietary problems such as anorexia or bulimia and (v) subjects not able to comply to the study procedures.
Dedicated, trained and certified research nurses and assistants collected all data for this study. Maternal data included: demography, anthropometry, medical history, history of dietary supplements, three-day food diaries. Infant data included: demography, anthropometry, history of medication use, body composition (one centre in France and one in Sweden), infant HM intake diary (three centres in France only). Standardized human milk sampling. HM sampling was standardized for all subjects. Milk was collected at 11h00 ± 2h00 using an electric breast pump (Medela Symphony, Switzerland). For each mother, HM was collected from the same breast for the entire study and mothers were requested to empty the breast manually in the previous feed. This collected single full breast milk samples were mixed and an aliquot of 5-10 mL for the first time point and 10-40 mL HM for all other time points was collected.
Acknowledgements We kindly acknowledge all study participants for participation, the study teams at each site for excellent help with study conduct, especially  Maria Gorett Silva ,  Thameur Rakza  and  Almerinda Barroso Pereira  as well as  Maurice Beaumont ,  Amélie Goyer  and  Emilie Ba  for their support in study and data management,  Marco Meschiari ,  Neotron Spa  for technical help with sample analysis, and  Armin Alaedini  and  Irma Silva Zolezzi  for support and critical review of the manuscript.
Data analysis Calcium mobilization traces were raw data obtained from single wells. Changes in fluorescence (ΔF) were calculated as the peak fluorescence minus baseline fluorescence  (Lei et al. 2015). The calcium mobilization was quantified as the percentage of change (ΔF) relative to baseline (F). Each data point for bar graphs and dose-dependent responses was averaged from triplicates (mean ± 20 ----+ --- - - - - - - - - - - - - - - - - - CuSO 4 20 ----+ --- - - - - - - - - - - - - - - - - - MgCl 2 20 ----+ --- - - - - - - - - - - - - - - - - - SD). Calcium mobilization traces and bar graphs along with dosedependent plots were all generated by GraphPad Prism 7. Analysis of variance with Dunnett's multiple comparisons test was used for statistical analysis. *P < 0. 05.
Molecular modeling of TAS2R7 The 3D structure of the human TAS2R7 was obtained by comparative modeling using Modeller 9. 19  (Sali and Blundell 1993)  based on the crystal structure of the 5-HT 2C serotonin receptor, PDB identifier 6BQG  (Peng et al. 2018 ) (Supplementary Figure  S1 ). The best homology model according to the DOPE score has been energy minimized using AMBER  (Case et al. 2005 ) and the AMBER ff14SB force field  (Maier et al. 2015)  parameter prior to structural validation with PROCHECK. Electrostatic potential was calculated with the APBS program  (Baker et al. 2001). To obtain accurate electrostatic properties, we used the 2-step focusing technique and a grid spacing lower than 0. 5 Å in each space dimension. The molecular surface was generated using a water probe with a radius of 1.
4 Å. The dielectric constant of the protein and the solvent was fixed to 2 and 80, respectively. The protonation states of titratable residues were predicted at pH 6. 5 through the H++ server  (Gordon et al. 2005). Cromolyn was docked within the TAS2R7 binding cavity using Autodock Vina  (Trott and Olson 2010). The Zn 2+ cation was manually docked into the TAS2R7 model. The cation-receptor complex was energy minimized with the AMBER software using 500 steps of the steepest descent optimization followed by 1000 steps of conjugate gradient optimization with positional restraints of 50 kcal/mol/Å on backbone heavy atoms.
Except for preliminary experiments (see below), only the major dimeric form has been studied and is described here. http://dx. doi. org/10. 17504/protocols. io. vgye3xw. Matrix-Assisted Laser Desorption/Ionization-Time of flight mass spectrometry (MALDI-TOF). For protein identification after SDS-PAGE, bands of interest were cut, submitted to trypsynolysis and analyzed using MALDI-TOF/TOF 5800 (AB Sciex) (SICaPS platform, IMAGIF). Comparison to NCBI database sequences using Mascot confirmed that the purified protein was ZitR protein from lactococcal strain MG1363 (UniProtKB/Swiss-Prot A2RNS2) (data not shown). http://dx. doi. org/10. 17504/protocols. io. vgze3x6. Fluorescence-based Thermal Shift Assay (TSA). Thermal stability of fully purified ZitR MG protein was calculated by induced thermal denaturation using a Q-PCR ABI Prism 7900HT (CTPF platform, IMAGIF).
D-10-camphorsulfonic acid was used to calibrate the SRCD signal using the CDtool software  [22]. Spectra were obtained using calcium fluoride circular cells (Hellma) of 50 μm path length. They were loaded with ZitR MG protein (8 μg) in 20 mM Tris-HCl (pH 7. 0), 50 mM NaCl and 100 μM ZnSO 4 buffer. Acquisitions at 1 nm step per second between 170 to 305 nm were recorded in triplicates. Averaged spectra were corrected with respect to the baseline by buffer subtraction and set to zero in the 300-305 nm region (S2 Fig). Standard circular dichroism (CD) measurements were carried out at 20 ˚C on a JASCO J-810 spectropolarimeter. Temperature was controlled by a Peltier (Jasco PFD423S/L) (biophysics platform, LEBS/IMAGIF). Spectra from 185 to 260 nm were obtained using a 100 μm path length suprasil quartz cell (Hellma) containing ZitR MG protein (400 μg) in 20 mM Tris-HCl (pH 7.
0), 50 mM NaCl and 100 μM ZnSO 4 buffer. All data processing was performed using CDtool software and secondary structure prediction of ZitR MG protein was carried out on Dichroweb server (http://dichroweb. cryst. bbk. ac. uk) using all available algorithms (CON-TINLL, SELCON3, CDSSTR and K2D3) and all sets of proteins (database 1-7, SP175, SMP180)  [23, 24]  http://dx. doi. org/10. 17504/protocols. io. vg4e3yw.
Isothermal Titration Calorimetry (ITC) was performed on a Microcal ITC200 (GE Healthcare) (calorimetry platform, IBBMC/IMAGIF). Purified ZitR MG protein was dialyzed against a 20 mM Tris-HCl (pH 7. 0), 150 mM NaCl and 100 μM ZnSO 4 buffer. Duplicate titration of approximately 20 μM ZitR MG protein, while stirring at 1000 rpm, was carried out by 20 injections of 2 μl of each dsDNA at 270 μM in the same buffer as the protein. The heat generated by DNA dilution was determined from the peaks measured after full saturation of the protein. Experimental data were fitted to the theoretical titration curves using the Origin software (Ori-ginLab, Northampton, MA) according to the relationship between the heats generated by each injection. The following values were calculated: ΔH cal , enthalpy change in kcal.
Holo-ZitR MG structure determination Holo-ZitR MG protein was subjected to crystallization assays using spare matrix screens in a robotic system (Nano-Robot Cartesian) (crystallography platform, LEBS/IMAGIF). In preliminary experiments, crystals were first obtained using ZitR MG tetrameric form by vapor diffusion in 0. 2 M ammonium acetate, 0. 1 M sodium citrate tribasic dihydrate (pH 5. 6) and 30% polyethyleneglycol 4,000. They diffracted to a resolution of less than 6 Å. These crystals belong to P4 1 space group with cell parameters of a = b = 129 Å; c = 88 Å; α = β = γ = 90˚. Crystallization conditions were then optimized using the dimeric form. X-ray data were collected at the zinc peak absorption edge up to 3. 7 Å resolution on the PROXIMA-1 beamline at SOLEIL synchrotron. After data processing by XDS  [25] , molecular replacement with coordinates of different MarR proteins was unsuccessful.
ZitR MG protein is a stable Zn(II)-bound dimer able to bind its DNA operator site We produced a recombinant, untagged form of ZitR MG protein (145 amino acids, 16. 3 kDa) in E. coli, purified it in the presence of Zn(II) as previously described  [16] , and analyzed its secondary structure. CD spectra demonstrated that purified ZitR MG contained a majority of helices (73. 7%) and a few strands (11%). This is in agreement with ZitR MG protein being predicted to contain six α-helices and two antiparallel β-hairpins per protomer, as all other MarR superfamily members  [7, 9]. We also determined the oligomeric state of purified ZitR MG by SEC-MALS. Its molar mass was found to be 32. 1 ± 0. 3 kDa (S1 Fig) as expected for a dimer. The protein hydrodynamic radius was found to be 2. 3 ± 0. 1 nm (data not shown) denoting a globular protein.
These results confirm that purified ZitR MG protein is complexed to divalent (metallic) cations  [16]  whose binding is required for protein stability. ZitR MG protein has been found to be very unstable in the presence of EDTA, so that its apo-form could not be further characterized. We also verified whether purified ZitR MG protein could bind DNA as expected  [16]. Purified ZitR MG has previously been shown to be able to bind two imperfect TTAACYRGTTAA   [30]. We noticed that several lactococcal proteins are erroneously annotated as 'AdcR' in gene/protein databases, as they share a higher homology level with ZitR proteins than to the prototypal AdcR protein from S. pneumoniae  [13, 18, 19]. We therefore renamed them as ZitR proteins. The following sequences are shown: i) ZitR from L. lactis subsp.
lactis subsp. lactis strain NCDO 2118 (gb |AII13676. 1|) and subsp. lactis bv. diacetylactis (gb |KZK11188. 1|), not shown; iii) ZitR ('AdcR') from L. piscium (Lpis) strains MKFS47 (gb |CEN27435. 1|) and iv) CNCM I-4031 (gb |SCA91076. 1|); v) ZitR ('AdcR') from L. raffinolactis (Lraf) strain 4877 (gb |CCK19333. 1|); vi) ZitR ('AdcR') from L. garvieae (Lgar) strains DCC43 (gb |EKF52529. 1|) and vii) 122061 (gb |BAV02535. 1|), which is identical to the protein from strain M14 (gb |CEF51164. 1|), not shown; viii) ZitR ('AdcR') from Lactococcus sp. (Lsp) strain DD01 (gb |KXT61547. 1|); ix) the prototypal AdcR protein [13, 18]  from S. pneumoniae (Spne) strain D39 (gb |Q04I02. 1|, PDB: 3TGN [13] ); and finally x) AdcR protein from S. pyogenes strain MGAS315 (gb |AAM78676. 1|), or serotype M3 (PDB: 5JLU [20] ).
Acknowledgments This work was supported by the  French Infrastructure for Integrated Structural Biology (FRISBI) ,  ANR-10-INSB-05-01. The structure data from this publication have been deposited in the PDB database https://www. rcsb. org/and assigned the accession number  6FI9. This work has benefitted from the facilities and expertise of the  IMAGIF Structural and Proteomic Biology Pole at the Research Center of Gif  (https://www. imagif. cnrs. fr):crystallization, SICaPS, biophysics, CTPF and calorimetry (now I2BC); as well as the PROXIMA-1, PROX-IMA-2A and DISCO beamlines at SOLEIL synchrotron (http://www. synchrotron-soleil. fr). We thank  Herman Van Tilbeurgh  (I2BC at Orsay),  Nicolas Leulliot  and  Benjamin Dray  ( LCRB at Paris ), for initial crystallization assays;  Frank Wien  (SOLEIL synchrotron) for SRCD experiments;  Julie Me  ´netrey (I2BC at  Gif ) for discussion and  Joni Frederick  ( I2BC at Gif ) for English corrections.
1|, gb |Q9CDU5|, PDB: 5YHX [21] ), which is identical to ZitR proteins from L. lactis subsp. lactis strain NCDO 2118 (gb |AII13676. 1|) and subsp. lactis bv. diacetylactis (gb |KZK11188. 1|), not shown; iii) ZitR ('AdcR') from L. piscium (Lpis) strains MKFS47 (gb |CEN27435. 1|) and iv) CNCM I-4031 (gb |SCA91076. 1|); v) ZitR ('AdcR') from L. raffinolactis (Lraf) strain 4877 (gb |CCK19333. 1|); vi) ZitR ('AdcR') from L. garvieae (Lgar) strains DCC43 (gb |EKF52529. 1|) and vii) 122061 (gb |BAV02535. 1|), which is identical to the protein from strain M14 (gb |CEF51164. 1|), not shown; viii) ZitR ('AdcR') from Lactococcus sp. (Lsp) strain DD01 (gb |KXT61547. 1|); ix) the prototypal AdcR protein [13, 18]  from S. pneumoniae (Spne) strain D39 (gb |Q04I02. 1|, PDB: 3TGN [13] ); and finally x) AdcR protein from S.
pyogenes strain MGAS315 (gb |AAM78676. 1|), or serotype M3 (PDB: 5JLU [20] ). Secondary structure elements of ZitR MG protein are displayed above its sequence: α-helices as medium squiggles and β-strands as arrows. ZitR MG residues shown here (see below) to belong to the dimerization interface or to the metal binding pocket (Fig 2)are respectively indicated by 'd' and 'z' characters below the sequences. Amino acids that appear in white characters in a red background are identical in all aligned proteins, while those in red characters and in blue frames are conserved in the majority of proteins.
4 µm step). Enlarged illustrations (Figures  2E, F , 3) correspond to 0. 4 and 0. 51 µmthick stacks, respectively. For cell density measurements, fluorescent immunostaining for SOM and SSTR2 performed on WT serial 40 µm coronal OB sections was imaged at constant light settings using a Lamina slide scanner (Perkin Elmer, ×20 objective) equipped with GFP and Cy3 filter sets. Each two-channel image was extracted using Pannoramic Viewer software and exported into Image J using Bio-Format importer plug-in. Six anterior anatomic levels (every 250 µm from Bregma 4. 25) were analyzed with Image J with a dedicated macro transforming SSTR2 and SOM staining into masks in order to count the labeled cells or area in each region of interest (GL, EPL and GCL). Data were averaged from three to four mice per level.
7 mm deep. One-hundred nanoliter of the injection solution (PRVBA2001 virus + fluorospheres) was injected at 20 nl/min and left in place for 15 min to ensure proper injection and diffusion. Injection sites were checked a posteriori using detection of fluorospheres. Mice were sacrificed 3-5 days post-injection in order to trace PRVBa2001 virus progression. Brains were then fixed as previously described and 2D reconstructions of serial anteroposterior coronal sections (50 µm thick, every 300 µm) were prepared and analyzed using Zeiss Axovision software on a Zeiss Imager M2 epifluorescence microscope (10× magnification). The neuroanatomical location of the positive labeled cells was determined using the mouse brain in stereotaxic coordinates atlas  (Paxinos and Franklin, 2008).
Statistical Analysis All results are expressed as mean ± standard error of the mean (SEM). The degree of statistical significance was calculated using STATVIEW software (SAS Institute, Cary, NC, USA). For SSTR2 distribution, two-way repeated-measures analysis of variance (r-m ANOVA) with cellular layer as an in-between factor and anteroposterior levels as a within-subjects factor with Bonferroni correction was used. Statistical analyses for behavioral data can be found in Supplementary data. Raw data of the habituation-dishabituation protocol were analyzed, respectively between H1 and H4 trials, H4 and C +1 trials and H5 and C +3 trials using two-way r-m ANOVA with the group as in-between subjects factor and trials as within-subjects factor. For multiple comparisons, a Bonferroni post hoc test was performed.
, 2002; Gastambide et al. , 2010). In the OB, SSTR4expressing cells surround glomeruli labeled by SSTR2-positive terminals suggesting a similar mechanism. The physiological conditions requiring SSTR4 activation remain obscure. One hypothesis would be that SSTR4 plays a role in the olfactory control of emotional behavior, since several studies have consistently reported anatomical, physiological and behavioral evidence that deleting sstr4 gene induces stress responses in mice  (Scheich et al. , 2016; Prévôt et al. , 2017). The local or extra-bulbar origin of the ligand targeting these receptors remains an open question since, no major SOM immunostaining was detected in the GL or OSNs, as previously reported  (Lepousez et al. , 2010a; De La Rosa-Prieto et al. , 2016). Only rare somata and parts of SOM neurites were occasionally labeled in the GL, in accordance to in situ hybridization data in the GL from Allen Brain Atlas 1.
ACKNOWLEDGMENTS The authors thank  Drs M. Alonso ,  G. Lepousez  and  S. Wagner  ( UMR3571   CNRS-Unité Perception et Mémoire, Institut Pasteur)  for olfactometer technical support,  Dr Yoshihara  ( RIKEN, Japan ),  Dr C. Adori  ( Karolinska Institute, Stockholm, Sweden ) and  Dr J. Diaz  ( CPN, Paris ) for providing Tbx21, secretagogin and Arl13b antibodies, respectively,  Dr D. de Saint Jan  ( INC, Strasbourg, France ) for providing Kv3. 1-EYFP brains,  Dr S. Schulz  ( Jena University, Germany ) for providing SSTR2 KO-lacZ KI brains. PRVBa2001 was generously provided by.
The experiment was implemented in MATLAB (the Mathworks Inc. ) using the Psychtoolbox-3  (Brainard, 1997; Kleiner et al. , 2007; Pelli, 1997). The experimental setup was similar to that in  Yoxon et al. (2019). For each trial, a home position (a blue circle with a 1. 5 cm diameter) would appear 1 cm above the bottom edge of the screen, along with two unfilled blue squares (2 cm per side) as placeholders for the target. The blue squares were 28 cm horizontally from each other and 25 cm diagonally from the home position. An image of a young adult male was used as the cue model, placed between the two target placeholders. The male extended his arms out with hands opened and facing upwards, placed directly beneath the two placeholders as if he was ready to catch or grab them (Figure  1  top). Every object was displayed against a light grey background.
Participants were informed of this nonpredictive gaze cue and were instructed to fixate on the male model prior to the target onset. Positions of the participants' index finger were recorded using Optotrak for 1,500 ms starting from the moment the target was presented. Participants were instructed to hold their finger at the target location until the 1,500 ms data collection window was completed. Given the two target locations (left and right) and two gaze directions (left and right), the target could either be cued (both the target location and gaze direction were the same) or uncued (the target location and gaze direction were opposite). Combined with three SOAs (100, 350, and 850 ms), there were 12 unique trial types (2 target locations × 2 gaze directions × 3 SOAs), which were treated as a block.
Trials within each block were presented in a random order. Each block was repeated for 16 times, resulting in 192 trials. The first block was used as training and was not included in the analysis. The entire experiment took about 45 min to complete. Data analysis. Data analysis was performed using a custom Python movement analysis package and was divided into the following steps. Spatial Calibration. Given the screen surface was at an approximately 20° angle, each trajectory was first rotated back to the transverse plane (Figure  2  Spatial Calibration). With the four reference screen corners ( , , , ) p p p p 1 2 3 4 and the scikit-spatial Python library  (Pedregosa et al. , 2011) , the surface norm, n , for the best-fitting plane was derived using singular value decomposition (see  Soderkvist (2021)  for detailed steps).