dataesr/scientific-paragraphs-categorization huggingface dataset:
In addition, some peptides released during digestion can specifically increase mucin secretions (threonine-rich proteins)  (Plaisancié et al. , 2013). There were no data in the literature on the digestibility of plant-based protein foods. Common understanding is that proteins in plant food feature lower digestibility than that in animal products, but evidence is lacking to support this for protein-rich plant foods that are commercially available. Indeed, most digestibility measurements have been performed on plant protein isolates, or raw materials. This study is the first to characterise the true ileal digestibility (TID) of proteins in seitan, tofu, and soya milk; foods commonly consumed by humans. We found that their TIDs were high: 98, 95, and 92%, respectively. Although slightly higher, these values are consistent with those seen for wheat protein isolates (93%)  (De Vrese et al.
Data pre-processing Both photometric and spectral calibrations of the Ralph instrument were conducted before the launch of the spacecraft and completed with in-flight calibrations with respect to stars. An additional ''flatfield'' calibration was performed, based on a rapid scan of Pluto's surface in the cross-track direction (as opposed to the in-track direction which is the nominal orientation of the instrument when collecting observations). Each pixel of the 256 pixels array thus covers almost the same part of the surface. The overall calibration of LEISA data is based on a combination of those ground-based and in-flight stellar calibrations, spectral smile corrections, and flat fielding. Nonetheless, some calibration issues remain in New Horizons data. The LEISA reflectance values are overestimated by an amount of 26% and should therefore be scaled down accordingly  (Protopapa et al.
, 2020). Several scans of Pluto's surface by the LEISA instrument were conducted, and data cubes were reconstructed with the Integrated Software for Imagers and Spectrometers (ISIS) software from the United States Geological Survey (USGS). Two of the close-encounter data cubes were calibrated, and projected onto LORRI Pluto-sized spherical data map (orthographic projection at same observation geometry). Sharp geological features identifiable in both LORRI and LEISA data were finally used for slight mismatch corrections in LEISA data projection, with respect to the higher resolution LORRI base map. Together, the two calibrated LEISA data cubes cover the whole visible disc of the planet. In this work, we used the same calibrated data cube covering Cthulhu region as in  Schmitt et al. (2017).
This data cube does not consist of raw data but follows from a Principal Component Analysis (PCA), described in more details in  Schmitt et al. (2017). This postprocessing step aims at identifying the main surface components, as well as mapping their distribution, and removing most of the instrumental effects and noise. The result of the PCA was that the first nine Principal Components account for almost 95% of the variance, demonstrating the good quality of LEISA data. Reduced-noise data cubes were reconstructed from a PCA inversion, by assuming that the first Principal Components account for the major part of the variance. Using these reduced-noise data cubes instead of the raw ones allows for a sharper analysis of New Horizons spectra collected over the Cthulhu region. The LEISA data from the reconstructed cube covering Cthulhu region were scaled down by 26% to correct the calibration issues previously mentioned.
A precise and reliable value for the uncertainty of this calibration factor is hard to determine. We however used 7% as a conservative estimate for MVIC data error bars. This value is based on the comparison of two independent calibration methods for MVIC data in  Howett et al. (2017). Discrepancies in the correction factor are limited to 3%-7%, such that 7% seemed a reasonable upper limit for the uncertainty value. Finally, MVIC data were corrected to LEISA geometry, following the method presented in  Protopapa et al. (2020). New Horizons reflectance spectra. The light and dark blue curves correspond to New Horizons LEISA spectra collected over H 2 O-rich and H 2 O-poor eastern regions of Cthulhu, respectively. They are retrieved from the reconstructed data cube described in Section 2. 2.
Cthulhu spectra To identify the red dark material covering Cthulhu, New Horizons spectra collected over this specific region were extracted from the data cube described above. The main focus of this study is on the core of the Cthulhu region, where the dark organic material is supposed to be the most concentrated. A spatial average was then computed over several pixels which were identified as the end-member of the red material in  Schmitt et al. (2017). Using the averaged spectrum as a reference for comparison with laboratory reflectance measurements allows to further reduce the pixel-to-pixel noise of the New Horizons spectrum. The MVIC data and LEISA reflectance spectrum of the red material's end-member are reproduced in Fig. 1. In addition to the dark material end-member spectrum, we also used an average spectrum collected in the eastern periphery of Cthulhu.
This is crucial to retrieve tholins' optical properties from their reflectance measurements for modelling purposes (see Section 5. 5). The reflectance measurements were conducted under incidence angles of 0 • , 30 • , and 60 • , and emergence angles ranging from -70 • to 70 • with a step of 10 •. Some additional measurements were carried out under vacuum and with progressive heating of the samples (up to 100 • C), to verify that the observed absorption features were not caused by adsorbed water. All data are made available through the GhoSST database in SSHADE infrastructure of solid spectroscopy: https://doi. org/10. 26302 /SSHADE/EXPERIMENT_BS_20201201_001  (Fayolle et al. , 2018).
Fitting the model to the New Horizons observations We tried to reproduce New Horizons spectra using the models presented in Sections 4. 1 and 4. 2. The surface was modelled as a mixture between H 2 O ice, hydrocarbon-rich ices (e. g. C 2 H 6 , CH 3 OH), CH 4 ice and tholins, as analogues for the dark material covering Cthulhu region. Except for the tholins, optical constants found in the literature were used for the other chemical components: H 2 O-ice:  Grundy et al. (2018) ; CH 4 -ice: Grundy  et al. (2002); C 2 H 6 -ice: Quirico  and Schmitt (1997);   CH 3 OH-ice:  Trotta (1996)  and  Cook et al. (2019). Most of these data are available online in the GhoSST database of the SSHADE infrastructure (www. sshade. eu). For simplification purposes, the single scattering phase function of Cthulhu's surface was assumed to be isotropic and independent of wavelength (i.
Discussion Because of the remaining discrepancies between the modelled surface spectra and New Horizons data (see Section 6. 2), we cannot yet draw any firm conclusion about the surface's composition and properties in Cthulhu region, and in particular about the exact chemical nature of the red material. Reliable information about the surface can indeed only be derived from Hapke model's parameters when both the photometric level and spectral features are properly fitted. Especially, as previously highlighted, the simulated spectra for H 2 Opoor terrains still display tholins absorption features which are absent in LEISA observations. Assuming that the presence of these features is not only due to experimental limitations discussed in Section 6. 1. 2, three possible explanations are discussed here.
A mix of tholins and CH 4 , H 2 O, CH 3 OH, and C 2 H 6 ices was assumed and two different surface models were tested (intimate mixing between all refractory species and condensation of icy species around core tholins particles, respectively). 1%CH 4 tholins overall led to significantly better fits than 5%CH 4 tholins. Especially, they better match the MVIC data in the visible and the average photometric level in the near-infrared. This indicates that slightly changing the composition of our Pluto tholins might improve the fit with respect to New Horizons data. Still, our optimisation algorithm failed to fit the three MVIC data points perfectly, even with 1%CH 4 tholins. This misfit in the visible needs to be investigated further, especially since reproducing the strong red slope that Cthulhu's spectra exhibit is key to unravel the composition and origin of the dark red material covering this region of Pluto.
New Horizons data collected over the H 2 O-rich region of Cthulhu are easier to reproduce with our surface reflectance model than H 2 Opoor region' spectra. The strong H 2 O absorption bands dominate the near-infrared part of the H 2 O-rich region' spectrum and hide the absorption bands clearly visible in the tholins spectra. On the other hand, the four absorption features of Pluto tholins appear in the simulated spectra of H 2 O-poor region, while they are absent in New Horizons data. The presence of the tholins bands in the modelled spectra prevented the optimisation algorithm from reproducing the near-infrared features of the New Horizons spectrum. It is therefore crucial to understand which phenomena could explain such an attenuation of the spectral contrast before concluding about how representative tholins are of the dark red organic material on Pluto.
A. 3. Tabulated results of the Hapke model inversion This appendix provides the tabulated values for the single scattering albedo  and phase function  obtained after performing the inversion of the Hapke model as described in Appendix A. 1. Results are reported for both 5%CH 4 and 1%CH 4 tholins, in Tables A. 1 and A. 2 for  and  , respectively. Table  A. 3 contains the optical constants extracted from the single scattering albedo, as described in Appendix A. Again, it must be highlighted that those parameters are determined in a purely numerical way. They need to be used carefully, keeping in mind the inherent lack of physical meaning behind the least-squares inversion of our models. These data are also available through the GhoSST database in SSHADE infrastructure of solid spectroscopy: https://doi.
B. 2. Selection of the optimisation algorithm To conduct the optimisation process, we used the PAGMO toolbox developed by the Advanced Concepts Team (ACT) at ESA, which offers a wide range of optimisation algorithms (in C++). The documentation can be accessed at https://esa. github. io/pagmo2/. As mentioned in Section 4. 3, the performance of several global optimisation algorithms was assessed in terms of convergence and computational efficiency for our particular optimisation problem. The simple genetic algorithm, differential algorithm, predator-swarm algorithm, and artificial bee colony were tested. Those are all population-based evolutionary algorithms. Except for the artificial bee colony algorithm, the other ones all achieved convergence (verified by reconducting the optimisation process with different random seeds).
Acknowledgements This work was supported by  NASA 's New Horizons Project. M. Fayolle ,  E. Quirico ,  B. Schmitt ,  L. Gabosova  and  O. Poch  acknowledge the  Centre National d'Etudes Spatiales (CNES)  for its financial support through  its ''Systeme Solaire'' program  (it is based on observations with RALPH embarked on New Horizons) and the  ANR Project CLASSY. O. P. acknowledges funding from the  Centre National d'Etudes Spatiales (CNES)  and the  European Research Council  under grant  SOLARYS (77169 ). T. G. Thanks and PNP for their financial support. N. C and L. J thank the  European Research Council  for funding via the  ERC   PrimChem  project (grant agreement No. 636829 ). We would like to thank the two anonymous reviewers for their careful reading and useful feedback, which significantly contributed to improve the quality of our manuscript.
Search Strategy We conducted a comprehensive review of the sexual dysfunction in men with benign prostatic hyperplasia (BPH) with a specific focus on ejaculatory disorder. PubMed Medline, Cochrane, and Scopus databases were used in September 2020. The search strategy was unrestricted and used explored MeSH (medical subject heading) terms such as: "Prostatic Hyperplasia", "lower urinary tract symptoms", "sexual dysfunction", and "ejaculatory dysfunction".
Inclusion Criteria A review protocol guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist was established following inclusion criteria for article selection: publications had to be written in English or French language, including prospective and retrospective trials providing data on physiopathology, epidemiology, evaluation and therapeutic management of ejaculatory dysfunction related to BPH. Abstracts were read by authors (FP, ID, UP, NC). Article quality was assessed on clinical interest and on the quality of the described cohorts. Regarding the impact of surgical treatments, we considered all the existing techniques (TURP, endoscopic or open enucleation of the prostate) without excluding new techniques currently under evaluation. We also included trials assessing non-surgical invasive treatment such as prostatic arteries embolization.
Data Management From the selected articles, the number of patients, the study design (prospective or retrospective), and the methodology to assess postoperative outcomes were extracted and analyzed. Finally, the postoperative outcomes were assessed. The quality and the heterogeneity of the included studies were evaluated based on the demographic characteristics of the population (number of patients and inclusion criteria), the study design (prospective or retrospective), and the methodology used to assess postoperative outcomes (functional, ejaculatory status).
RESULTS The A. fumigatus gene spfA is induced by ER stress in a UPR-dependent manner. A search of the A. fumigatus genome database using the Saccharomyces cerevisiae P5 ATPase Spf1 protein as the query identified the uncharacterized protein Afu3g13790 (SpfA) as the closest homolog (52% identity and 68% similarity). A comparison of A. fumigatus SpfA with known protein signatures using InterPro 84. 0  (35)  revealed SpfA to be a member of P-type ATPase subfamily V (IPR006544). P5 ATPases are further divided into two subfamilies: P5A-type ATPases localize to the ER membrane, whereas P5B-type ATPases are vacuolar or lysosomal membrane-associated proteins  (24, 36). An alignment of SpfA with other species homologs of Spf1 revealed conservation of the 12 predicted transmembrane domains, including the extended N-terminal domain (NTD) preceding the A domain that is shared with the P5A ATPase class (see Fig.
Despite the fact that spfA gene deletion is a very different type of ER stress compared to treatment with agents that cause acute protein unfolding, 47% of the genes that were upregulated by DTT and TM in the core UPR data set were also upregulated in the DspfA mutant, suggesting that the absence of spfA creates an environment of ER stress that necessitates UPR intervention. Genes that were downregulated in the DspfA mutant were largely associated with the metabolism of carbohydrates, amino acids, nitrogen, and sulfur (Fig. 2 ), suggestive of a need for broad metabolic rewiring when spfA is absent. In addition, there was downregulation of genes that encode abundantly secreted proteins, which is a type of ER stress response that relieves pressure on the secretory pathway during stress  (7).
The site-specific integration of the spfA-mrfp1 construct was verified by PCR (data not shown). The coexpression of both SpfA-mRFP1 and SrcA-eGFP was confirmed by epifluorescence microscopy (Fig. 1A ). To create an spfA gene knockout construct, the left and right arms flanking the spfA open reading frame were PCR amplified with primer pairs 1386/1387 and 1388/1389, respectively, and assembled with the cme R -b-rec and pUC19L fragments mentioned above, resulting in vector p706. To obtain a DspfA mutant strain (772), cultures of the parental strain KU80 (399) were transformed with the FspI-linearized p706 plasmid. In the same manner, the DspfA/DsrcA double mutant (756) was created by transforming a DsrcA strain (402) with FspI-linearized p706. Confirmation of all genotypes was performed by PCR (Fig.
Confirmation of complemented genotypes was performed by PCR analysis (Fig. S3 ). Bright-field and fluorescence microscopy. Approximately 1 Â 10 3 conidia of strain 826 expressing SpfA-mRFP1 and SrcA-eGFP (Table  S1 ) were first pipetted onto glass coverslips in petri dishes filled with liquid AMM and incubated for 17 h at 30°C without agitation. For live-cell imaging, the samples were then mounted onto glass carriers and analyzed using an Olympus BX51 microscope equipped with a 100Â/1. 35 oil immersion objective. Bright-field and fluorescence images of germlings were captured with a Diagnostic Instruments RTKE fluorescence imaging camera adjusted for brightness, contrast, and color with the open-source program Fiji (https://fiji. sc/). Real-time quantitative PCR analysis. Cultures were grown in YG medium to facilitate comparisons with a previously published data set of ER stress response genes that was obtained using this medium  (8).
Melting curves were generated to verify the specificity of the reactions, and the primer efficiencies (between 95 and 105%) were determined with cDNA standard curves. The results are presented as fold changes in transcript levels in comparison to samples from the parental strain or untreated controls. RNA sequencing and analysis. Cultures were grown in YG medium to facilitate comparisons with a previously published data set of ER stress response genes that was obtained using this medium  (8). A Direct-zol RNA MiniPrep kit (Zymo Research) was used for RNA isolation, and RNA integrity was confirmed using an Agilent 2100 Bioanalyzer instrument prior to submission for RNA sequencing (data not shown). Library preparation was performed using the NEBNext Ultra II directional RNA library prep kit for RNA-Seq.
Poly(A) RNA-Seq was carried out in the Genomics, Epigenomics, and Sequencing Core (GESC) at the University of Cincinnati using a NextSeq 550 system (Illumina). After adapter trimming and quality control, fastq files of each sample were merged before data analysis. Gene expression analysis was carried out using the A. fumigatus Af293 reference genome and annotation tracks from FungiDB (release 51) in CLC Genomics Workbench (Qiagen). Expression values were estimated as transcripts per million (TPM). Differential expression for RNA-Seq was calculated between the control and mutant strains using TMM (trimmed mean of M values) as the normalization method. Downstream analysis was performed using FungiDB  (62)  and FungiFun2  (39). Analysis of cell wall monosaccharide composition. Cultures were grown in YG medium to facilitate a comparison with the RNA-Seq data generated in this study.
Cell wall analysis was performed as previously described  (9). Flasks containing 50 ml of liquid YG medium were inoculated with 1 Â 10 8 conidia and incubated for 24 h at 37°C under constant shaking (150 rpm). Mycelia were collected by filtration and subjected to cell wall carbohydrate analysis as previously described  (7). The composition of the monosaccharides identified in the alkali-soluble (AS) and alkali-insoluble (AI) fractions was calculated for each strain from three independent cultures. Analysis of sterol composition. Cultures were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) medium to facilitate comparisons with data from a previously published sterol analysis of the S. cerevisiae Dspf1 mutant using this medium  (25). A total of 1 Â 10 7 conidia were inoculated into 5 ml of YPD medium in a 50-ml conical tube and incubated at 37°C for 24 h with gentle shaking (200 rpm).
TAFA4 alone provided significant reversal of injury-induced pain hypersensitivity, as shown by the significant increase in mechanical threshold. IT administration of RAP alone had no effect, whereas its co-administration with TAFA4 abolished TAFA4-mediated reversal of mechanical hypersensitivity in a dose-dependent manner (Figure  3E ). Given that TAFA4 interacts with at least LRP1 and LRP1b, these data demonstrate that the antihypersensitive effect of TAFA4 requires functional RAP-sensitive LRPs. (E) Acute anti-hypersensitive effect of IT administration of TAFA4 alone (170 nmol), RAP alone (160 pmol), or TAFA4 in combination with decreasing amounts of RAP on day 7 after SNI (left) and on day 1 following paw incision (right). IT injection of BSA had no effect on injury-induced mechanical hypersensitivity in either of the pain models.
In contrast, TAFA4 immunostaining on SC sections required special conditions, as described in the STAR methods section. TAFA4 is expressed in a subset of DRG neurons, and, as expected for C-LTMRs, TAFA4 + central terminals project into LIIi, just beneath IB4 + fibers (Figures  S3B  and S3C ). TAFA4 labeling was abolished in both types of samples from TAFA4-null mice, demonstrating the specificity of the anti-TAFA4 antibody. We used this tool in combination with qRT-PCR, to determine whether SNI affected TAFA4 expression at the transcriptional, translational, or trafficking levels. We first identified the lumbar DRGs affected by the nerve lesion by injecting the cholera toxin B subunit (CTb) into the footpad of the hind paw. Under these conditions, CTb retrogradely labeled myelinated sensory neuron cell bodies located in lumbar 4 and 5 (L4 and L5) DRGs but not in L3, L2, or L1 DRGs (Figure  6A ; data not shown).
LRP1 is a large (600 kDa) cell surface receptor with a broad spectrum of functions. In the context of pain, it may regulate the cellular microenvironment of the injured or inflamed nervous system through endocytosis of various extracellular mediators or by facilitating endocytosis of other transmembrane receptors involved in cell signaling (Gonias and Campana, 2014). Deletion of the LRP1 gene in Schwann cells leads to prolonged partial sciatic nerve ligation (PNL)induced mechanical hypersensitivity  (Orita et al. , 2013) , whereas deletion of this gene in microglia prevents development of PNLinduced mechanical allodynia by impairing microglial activation  (Brifault et al. , 2019). Consistent with these findings, we also found that deletion of microglial LRP1 prevents SNI-induced microglial activation and strongly decreases paw incision-induced mechanical hypersensitivity (data not shown).
Immunofluorescence Slides were washed for 5 minutes (min) in PBS, incubated for 1 h at room temperature with a blocking solution (10% normal donkey serum, 1% BSA, 0. 4% Triton X-100, in PBS), and then overnight at 4 C with primary antibodies in the same blocking solution. For TAFA4 immunostaining, saturation, and incubations with the primary and secondary antibodies were performed in 3% BSA with no serum or detergents. Images were acquired with a Zeiss AxioImager M2 fluorescence microscope or a Zeiss LSM 780 confocal microscope, with a 20x, 25x or 63x objective and appropriate excitation wavelengths and emission filters. Laser power and acquisition settings were kept constant between image acquisitions for different conditions. Images were analyzed with ImageJ software. Cell surface binding assay RAW264.
Cells were incubated with the blocking solution (10% normal donkey serum, 1% BSA, 0. 4% Triton X-100, in PBS) for 1 hour and then overnight at 4 C with anti-LRP1 antibody (1:500, Abcam, ab92544) in the same blocking solution. Cells were incubated with Alexa Fluor-conjugated secondary antibodies (1:500, Invitrogen, A32790) for 1 hour, washed with PBS (3 times, for 5 min each) and mounted on slides with Immu-Mount (#99904402, Thermo Fisher Scientific). Images were acquired with a Zeiss LSM 780 confocal microscope with a 63x objective and appropriate excitation wavelengths and emission filters. Laser power and acquisition settings were kept constant between image acquisitions for different conditions. Images were analyzed with ZEN and ImageJ software. The images shown are representative of cells from three independent experiments.