dataesr/scientific-paragraphs-categorization huggingface dataset:
59 Additionally, Arnold reported a homoleptic U(III) aryloxide complex, U(O-2,6-t Bu 2 C 6 H 3 ) 3 , 60 which upon reaction with CO also formed an ethynediolate. 61 The Liddle group isolated an ethynediolate through the reaction of U(III) ligated with the sterically encumbering Tren  DMSB   63  To our knowledge, the only report of further functionalization of a uranium ethynediolate complex, through addition of a substrate, is a structure in the Cambridge Crystallographic Database Centre, [{(2,6-t Bu 2 C 6 H 3 O) 3 U} 2 (m 2 -OC(H)]C(BC 8 H 15 )O)], by Mansell and Arnold in which hydroboration occurs across the CC triple bond. 64 ] [67]  Herein, we describe the use of two metallocene aryloxide uranium(III) complexes, [(C 5 Me 5 ) 2 (    69  Treatment of 1 atm of CO to 1 in hexamethyldisiloxane has a colour change from dark green to brown, eq 1.
Flame speed determination The most used method to evaluate flame speed for ammonia combustion available in the literature is by using a closed spherical vessel with Schlieren  [18] [19] [20]  and by vertical tube with direct imaging  [21] [22]. Han et al. [23]  used the heat-flux burner method to provide the flame speed data whereas Ronney et al. [24]  provided the flame speed at microgravity in a closed spherical vessel with thermocouples. When the spherical flame method is used, stretch effects must be considered. The unstretched laminar flame speed is obtained by applying the continuity equation to the burning velocity and the flame ball expansion. For this calculation, the thin flame approximation is imposed i. e. it is assumed that the radii of the unburnt gases and burnt gases at the flame front are the same.
For each nucleophile, the rate data measured with [1]0 = 1 M (10 equivalents with respect to 2) were again in agreement with a first order decay (see Tables S8-S11 and Figures S6-S9 for details), yielding the rate constants collected in Table  1. Quite remarkably, a strong electronic effect was observed, since p-CF3C6H4SH reacted 120 times faster than its methoxy-substituted analogue. A plot of log(kX/kH) as a function of   X gave a Hammett correlation with an excellent linear fit (R 2 = 0. 995), see Figure  2. A rather high positive electronic effect ( = 2. 38) was observed, which suggests a build-up of negative charge on the thiolate anion at the transition state level. The activation parameters were determined on the basis of the rate constants determined at four different temperatures, using p-MeOC6H4SH (1b) as the nucleophile.
Tissue iron staining and quantitative iron measurement. Left lateral lobes (LLL), right lateral lobes (RLL), medium lobes (ML) and caudate lobes (CL) of the liver from three mice per genotype were fixed in 4% buffered formalin and subsequently embedded in paraffin. Following deparaffinization, tissue sections were subjected to staining using Perls Prussian blue stain to visualize nonheme iron, followed by counterstaining with nuclear fast red. The slides were observed under a light microscope and images were captured or scanned using a Pannoramic 250 Flash II (3DHISTECH). Subsequent analysis was performed utilizing a Pannoramic Viewer software. Due to the size of certain lobes, quantitative assessments of nonheme iron in hepatic lobes were conducted by pooling each specific lobes from three mice per genotype (pooled lobes: 3xLLL, 3xRLL, 3xML or 3xCL).
Histology and immunohistofluorescence analysis Following fixation and embedding in paraffin, each lobe (LLL, RLL, ML, and CL) was prepared for tissue sectioning. Following blocking with BSA 1% and 10% heat inactivated goat serum for 30 min at room temperature, deparaffinized liver sections were incubated with primary antibodies for 1hr. After three washes with PBS containing 0. 5% BSA, the sections were incubated with Alexa conjugated secondary antibodies for an additional one hour at room temperature. Once mounted, sections were visualized using an epifluorescence microscope LEICA DM-IRM, a Zeiss confocal fluorescent microscope or a Pannoramic 250 Flash II (3DHISTECH) scanner. Image acquisition was performed using either ARCHIMED-PRO (Microvision Instruments), Zeiss LSM Image Browser softwares or the Pannoramic Viewer software.
Upon examining the collective dataset, a clear correlation emerges between the detected level of hepcidin expression (mRNA) in the mouse models and the spatial distribution of Perls staining (indicative of iron levels) within the liver (Fig. S5 ). In instances where mice displayed extremely low hepcidin levels [Group D: Bmp6 KO (male), Hamp KO, Hjv KO (male), Bmp6 KO / B2m KO, Bmp6 KO / Tfr2 KO, and Bmp6 KO / B2m KO / Trf2 KO], iron deposition predominantly occurred in the centrilobular regions, aligning with the observations in this study (particularly evident in young Bmp6 KO mice). In these mice, the notably diminished hepcidin levels exert dual positive impacts on both systemic (macrophages, duodenum) and local (hepatic) Fpn expression, consequently contributing to the redistribution of iron from periportal hepatocytes to hepatocytes encircling the central veins (Fig.
Acknowledgements We wish to thank the staff of the  INRAE Infectiology of Fishes and Rodents Facility  ( IERP-UE907 , Jouy-en-Josas Research Center, France) where animal experiments have been performed. IERP Facility belongs to the  National Distributed Research Infrastructure for the Control of Animal and Zoonotic Emerging Infectious Diseases through In Vivo Investigation. This work was funded by  Agence Nationale de la Recherche  [ ANR-11-LABX-0021-01 ];  Conseil Ré gional de Bourgogne, Franche-Comté  [ PARI grant ];  FEDER  ( European Regional Development Fund).
Biological Data Tryptase was assayed from a blood sample placed into EDTA K2 Vacutainer ® tubes (Becton Dickinson, Franklin Lakes, NJ, USA) during a systematic check-up (at 12 h of life (H12) for premature newborns and on Day 3 (D3) for the Guthrie test for full-term newborns. It was assayed using a fluoroenzymatic technique (immunoCAP method) at the biochemistry laboratory of Clermont-Ferrand University Hospital. The fecal calprotectin assay was also performed by the biochemistry laboratory on a meconium sample weighing at least 1 g by immunofluorescence using a Liaison XL Dia analyzer (Diasorin, Italy).
R 2 was calculated. The sample size was estimated in order to assess whether tryptase and calprotectin levels were influenced by BT: premature vs. full-term newborns. With at least 100 infants per group, a minimal difference effect size of 0. 5 could be highlighted between groups with a two-sided type I error rate of 5% and a statistical power greater than 90%. Statistical analyses were performed using Medcalc (version 19. 1, Medcalc Software) and GraphPad prism (version 8. 0. 1). All statistical tests were conducted for a two-sided type I error rate of 0. 05.
| Microcomputed tomography (µCT) The bone structures of the spine and femur from 6-and 19-month-old male and female mice were analyzed using µCT. The spines and femurs were dissected and fixed with 70% ethanol. The spines were scanned using the SkyScan-1276 X-ray µCT system (Bruker) at 60 kV and 57 µA. Data series were reconstructed using SkyScan NRecon software (Bruker). The trabecular bones of the lumbar spine (L4) were analyzed between endplates using 200 slices, each 9 µm thick. Trabecular morphometric parameters were analyzed with SkyScan CT Analyzer (CTAn) software (Bruker). The femurs were scanned using the ScanXmate-L090T X-ray µCT system (Comscan) at 60 kV and 120 µA. Data series were reconstructed using ConeCTexpress software (Comscan). The cortical bones of femurs were analyzed with TRI/3D-BON (TRI) software (RATOC Systems).
GenBank accession number Forward primer Reverse primer p16 ink4a (Cdkn2a) NM_009877 5′-ATGGAGTCCGCTGCAGACAGAC TG-3′ 5′-CGTTGCCCATCATCACCTGAATCGG -3′ p21 cip1 (Cdkn1a) NM_007669 5′-GAACATCTCAGGGCCGAAAA-3′ 5′-TGCGCTTGGAGTGATAGAAATC-3′ Glb1 NM_009752 5′-GCCTATTGGAATGGTGCCAAC -3′ 5′-GGATACCCAGAGCTTCAGCC-3′ Lamin b1 NM_010721 5′-GCTGCTGCTCAATTATGCCAA-3′ 5′-TAACTGCTTTTTGGCGGCAG-3′ Nupr1 NM_019738 5′-AGGACCTAGGCCTGCTTGAT-3′ 5′-CTCTGCTTCTTGCTCCCATC-3′ Rankl (Tnfsf11) NM_011613 5′-CAGCATCGCTCTGTTCCTGTA-3′ 5′-CTGCGTTTTCATGGAGTCTCA-3′ Mmp13 NM_008607 5′-CTGGACCAAACTATGGTGGG-3′ 5′-GGTCCTTGGAGTGATCCAGA-3′ Gapdh NM_001289726 5′-TGCACCACCAACTGCTTAG-3′ 5′-GGATGCAGGGATGATGTTC-3′ Ccl5 NM_013653. 3 5′-GCCCACGTCAAGGAGTATTTCT-3′ 5′-ACAAACACGACTGCAAGATTGG-3′ Il-1β NM_008361. 4 5′-CCTTCCAGGATGAGGACATGA-3′ 5′-TGAGTCACAGAGGATGGGCTC-3′ Sost NM_024449 5′-TCAGGAATGATGCCACAGAG-3′ 5′-CAGGAAGCGGGTGTAGTG-3′ Phex NM_011077 5′-GAAAGGGGACCAACCGAGG-3′ 5′-AACTTAGGAGACCTTGACTCACT-3′ Dmp1 NM_001359013 5′-AAGCTAGCCCAGAGGGACAGG CAA-3′ 5′-TTATCGGCGCCGGTCCCCGTAC-3′ Slx1b NM_029420 5′-CACAGAGGAGGAAGAGGATTTG-3′ 5′-GAGAGAAGCAGGAAAGGTACAG-3′ Cystm1 NM_001368637 5′-CCATACCCACCTTATCCACAAC-3′ 5′-GGTCGTCTCTTCTTTGGTCTTC-3′ Gdpd3 NM_024228 5′-CCCTCTCCTGTACTTTGTTCTG-3′ 5′-CTGGGCCATGGAATTCTCTAC-3′ Gli4 NM_177001 5′-ATGTGGTCGTGGCTTTAGTG-3′ 5′-TTGATGGAACTGTGGTGTGAG-3′ Tacc2 NM_206856 5′-ACGGGAAGTGGTGGAAATG-3′ 5′-CTGTACAGTTTGGTGGGAGATG-3′ Igfbp6 NM_008344 5′-GAAGAATCCACGGACCTCTG-3′ 5′-CCTCTGAGGTCACAGTTTGG-3′ HtrA1 NM_019564 5′-TTGCTGATGTGGTGGAGAAG-3′ 5′-CAATCAGTCCATCCTCCGATAC-3′ HtrA2 NM_019752 5′-TCAAACCAAGGAGCCTCTTC-3′ 5′-TACCAGATGTGATCGTGTTCTG-3′ HtrA3 NM_030127 5′-TCATCAATTACGGGAACTCAGG-3′ 5′-CAGAGAGGAAGCGTGTGATG-3′ HtrA4 NM_001081187 5′-ACCTGGGTCTTCGAATGCTG-3′ 5′-GGTTGCCCGTTTATGCTGAC-3′ NUPR1 NM_001042483 5′-CTTGGTTACAGGAGGTGGAG-3′ 5′-CAGTCCCGTCTCTATTGCTG-3′ HTRA1 NM_002775 5′-CCCTGCCGTGGTTCATATC-3′ 5′-TTGTCACGATCAGTCCATCTTC-3′ GAPDH NM_002046 5′-GAGTCAACGGATTTGGTCGT-3′ 5′-TTGATTTTGGAGGGATCTCG-3′ Abbreviations: HTRA1, high temperature requirement A 1; NUPR1, nuclear protein 1; RT-qPCR, RT-quantitative PCR.
After 1 week of culture, the cells were lysed and analyzed by RT-qPCR or western blot analysis. Graph on the bottom panel show quantifications of pSMAD1/5/9 versus SMAD1. Relative expression levels were analyzed using ImageJ. Data are presented as mean ± SD (n = 3). Means were compared using one-way ANOVA, followed by Tukey's post hoc test, in (a, c, d) and using Student's t-test in (b, e). *p < 0. 05, **p < 0. 01, ***p < 0. 001. ANOVA, analysis of variance; HTRA1,high temperature requirement A 1; NUPR1,nuclear protein 1; RT-qPCR, RT-quantitative PCR; SD, standard deviation; TGF, transforming growth factor; WT, wild-type. F I G U R E 4 Expression of cellular senescence markers was reduced in osteocytes of 19-month-old Nupr1-KO male mice. (a) p16, ink4a p21, cip1 Rankl, Mmp13, Glb1, and Lamin b1 expression in osteocytes of 6-and 19-month-old WT male mice (n = 5).
ACKNOWLEDGMENTS We would like to thank  Dr. Hiroshi Miyamoto  for providing the experimental devices, and Editage for English language editing. A part of this work was supported by " Advanced Research Infrastructure for Materials and Nanotechnology in Japan (ARIM) " of the  Ministry of Education, Culture, Sports, Science and Technology (MEXT)  (grant number  JPMXP1222KU1008 ). We are grateful to  Dr. Fumiyuki Toshimitsu  and  Yuriko Kakita  of  Kyushu University  for their helpful support with the Raman microscopy. This work was supported by the  Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) (C)  ( 18K09034 ,  19K09553 , and  22K09360 ).
This study analyzed the correlations between the acute and habitual intake of dietary tyrosols, their main food sources, and 24 h urine excretions of tyrosol (Tyr) and hydroxytyrosol (OHTyr) in participants from the European Prospective Investigation into Cancer and Nutrition study (EPIC). Participants (n = 419) were healthy men and women aged from 34 to 73 years from 8 EPIC centers belonging to France, Italy, and Germany. Acute and habitual dietary data were collected using a standardized 24 h dietary recall software and validated country-specific dietary questionnaires, respectively. The intake of 13 dietary tyrosols was estimated using the Phenol-Explorer database. Excretions of Tyr and OHTyr in a single 24 h urine sample were analyzed using tandem mass spectrometry. Urinary excretions of Tyr, OHTyr, and their sum (Tyr + OHTyr) correlated more strongly with their corresponding acute (rho partial ~0.
In addition, tyrosols can exert important biological effects on human health, having antioxidant, anti-inflammatory, antiatherogenic, cardioprotective, anticancer, neuroprotective, antidiabetic, and antiobesity effects, among others  [8, 10]. In fact, in vitro studies have demonstrated that OHTyr possesses a higher antioxidant capacity than Tyr due to the lack of a catechol group (-OH) in the latter  [11]. However, evidence from epidemiological studies is lacking, probably because of the difficulty in accurately estimating tyrosol exposures. Currently, the estimation of tyrosol intake is based on either the combined use of self-reported questionnaires and (poly)phenol food composition databases  [4, 12]  or the quantification of Tyr and OHTyr in biological fluids  [13, 14]. To date, however, these methods have hardly been used together to evaluate the potential use of systemic (poly)phenol excretions as biomarkers of their dietary intake, especially in large populations  [15].
Samples and Analytical Method The current EPIC substudy includes a convenience subsample (i. e. , participants with a single 24 h dietary recall (24-HDR) and 24 h urine samples collected the same day), composed of 419 women and men, aged between 34 and 73 years, and recruited from 8 EPIC centers (i. e. , Paris, Florence, Varese, Ragusa, Turin, Naples, Heidelberg, and Potsdam). It should be noted that the participants from Paris and Naples centers were all women. Participants' data from Greece were not available for the current study and were therefore excluded compared to previous EPIC studies  [19]. Collection, storage, and analysis of urine samples were carried out as previously described  [20]. Briefly, urine samples were collected over a 24 h period, submitted to the EPIC center the same day as the 24-HDR interview, and stored at -20 • C using boric acid as a preservative.
Dietary and Lifestyle Information Data on the acute and habitual intake of foods were collected using a single 24-HDR  [21] , and a quantitative or semi-quantitative dietary questionnaire (DQ)  [17, 18] , respectively. The 24-HDR was administered in a face-to-face interview using the standardized software EPIC-Soft (renamed GloboDiet)  [21]. The DQs were developed and validated in each EPIC center/country  [17]. The average time interval between the collection of the 24-HDR and the DQ varied between one and three years  [22]. The dietary intakes of the following 13 tyrosols were estimated using the Phenol-Explorer database  [23] : Tyr, OHTyr, Tyr acetate (p-HPEA-AC), OHTyr acetate (3,4-DHPEA-AC), oleuropein, oleuropein aglycone, oleuropein-aglycone mono-aldehyde (3,4-DHPEA-EA), oleuropein-aglycone di-aldehyde (3,4-DHPEA-EDA), ligstroside, ligstroside aglycone, ligstroside-aglycone mono-aldehyde (p-HPEA-EA), ligstroside-aglycone di-aldehyde (p-HPEA-EDA), and oleoside 11-methyl ester.
Total tyrosol intake was calculated as the sum of all individual compounds; total daily energy intake was estimated using the EPIC standardized nutrient database  [24]. The acute and habitual intakes of six foods/food groups (i. e. , olives, olive oil, wine (including its red and white subtypes), and beer) with tyrosols content in Phenol-Explorer were used to calculate their correlations with urinary Tyr and OHTyr. Notably, data on the habitual intake of olives, and red and white wine were not available in all EPIC centers due to the differences in the specific DQs used in each center  [17]. For example, data on olive intakes were only collected in Paris and Ragusa; red wine in Florence, Varese, Ragusa, and Turin; and white wine in Florence, Varese, Turin, Heidelberg, and Potsdam. Other lifestyle information such as smoking status and physical activity was collected via standardized questionnaires at recruitment  [18].
Italy had the highest median acute and habitual intakes of total tyrosols with 30. 4 and 15. 9 mg/d, respectively, followed by France (11. 3 and 8. 74 mg/d, respectively), and Germany (2. 95 and 2. 71 mg/d, respectively). The acute and habitual intakes of olive oil and wine were higher in Italy, while the acute and habitual intakes of beer were higher in Germany. a Number of participants with available data of the intake for the corresponding compound or food; b number of participants reporting a null intake of the corresponding compound or food (i. e. , non-consumers); c statistical significance from a Mann-Whitney test; d data on habitual intake of olives was only reported in Paris (France) and Ragusa (Italy) centers; e data on habitual intake of red wine was only reported in Florence (Italy), Varese (Italy), Ragusa (Italy), and Turin (Italy); f data on habitual intake of white wine was only reported in Florence (Italy), Varese (Italy), Turin (Italy), Heidelberg (Germany), and Potsdam (Germany).
The main limitations of our study are related to the use of both self-reported questionnaires and the Phenol-Explorer database. In general, although self-reported dietary questionnaires are still a practical and affordable way to record individuals' habitual diet, they may also introduce bias into the tyrosol intake assessment as a result of random and systemic measurement errors and may also restrict the variety of food items available in every study. However, it is worth mentioning that the dietary questionnaires used in this study were standardized or validated for the EPIC population. In addition, the lack of complete data on the habitual intake of specific tyrosol food sources may not only hamper the comparisons of correlations for their acute and habitual intakes of these foods with the urinary excretion of tyrosols but also may influence the estimation of the habitual intake of dietary tyrosols and their subsequent correlations with urinary tyrosols.
Acknowledgments: The authors thank  Bertrand Hémon  for his valuable help with the EPIC database and all the participants from the  EPIC study. We also thank the  University Paris-Saclay , the  University of Versailles Saint-Quentin-en-Yvelines (UVSQ) ,  Institut National de la Santé et de la Recherche Médicale (INSERM) ,  Gustave Roussy , and  Centre de Recherche en Epidémiologie et Santé des Populations (CESP), Villejuif, France.
The CAZy database implemented subfamily classifications based on phylogenies for families GH5 (3), GH13 (4), GH30  (5) , and many polysaccharide lyases  (6) (7) (8) (9)  or on Sequence Similarity Networks (SSNs) for families GH16  (10)  and GH43  (11). The SSN method allows the analysis of very large datasets that could not reliably produce multiple sequence alignments and phylogenies. The GH family 31 (GH31) is a large family with more than 20,000 sequences (by December 2022) from GenBank reported on CAZy website (www. cazy. org). Among these, only 130 proteins have been characterized, which exhibit activity on a variety of α-glycoside substrates and which have been linked to fifteen distinct enzyme commission (EC) numbers (Table  1 ). One of the most common enzyme activities in family GH31 is α-glucosidase (EC 3.
3 ). The active site is located within the catalytic domain and exists as either a pocket or a cleft. The active site contains two aspartic acids (Asp/D) that act as nucleophile and general acid/base catalyst for hydrolases and transglycosidases, or nucleophile/general base and general acid for lyases. Each structural representative contains four domains: an N-terminal domain, a catalytic domain, and proximal and distal C-terminal domains. These four domains are the active module for all GH31 members (GH31 module). Certain GH31 proteins contain extra domains such as carbohydrate binding modules (CBMs). We provide hereafter an overview of principal features of each GH31 subfamily. Upon selection of 10 -125 as the most appropriate SSN Evalue, the RaxML platform  (22)  was used to obtain a phylogenetic tree to assess the evolutionary relationships among GH31 subfamilies.
The structure of members of GH31_1 contains four major domains and two subdomains. The structural representative α-glucosidase from sugar beet (Protein Data Bank, PDB 3W37) has a long loop in the N-terminal domain that is a part of the active site pocket within the (α/β) 8 barrel catalytic domain. This subfamily contains several human glycosidases including α-glucosidase A (GAA, lysosomal), α-glucosidase II (GANAB), maltase-glucoamylase, and sucrase-isomaltase (SI). Maltase-glucoamylase and SI both duplicated GH31_1 modules with all four modules individually exhibiting exoglucosidase activities against linear α-1,4-linked maltose substrates but different preferences for oligosaccharides substrates with various lengths  (26). The N-terminal GH31 domain of SI also has activity for the α-1,6-linkages of starch, and the Cterminal domain of SI has activity for the α-1,2-linkage of.
α-galactosidase Taxonomical diversity: MUL, multiple kingdoms; PDB code: a selected structural representative for each subfamily for superposition and comparison among subfamilies, the number in brackets indicates the total number of characterized structures for each subfamily. Colors used in column 1 are the same as those for Table  2. sucrose  (27). The human hydrolases have an extra domain, an N-terminal trefoil type-p domain, which is a secondary substrate-binding domain (Fig. S2 )  (26, 28, 29).
GH31_3 This large subfamily contains mainly bacterial sequences and some fungi and archaea. However, this may reflect sampling bias as the CAZy database contains mostly bacterial genomes (>15,000), with fewer archaeal (459), fungal (259), metazoan  (29) , and plant  (23). Most bacterial members of this subfamily belong to gram-negative Gammaproteobacteria (>70% of Bacteria); the rest are mostly from the Terrabacteria taxon (Firmicutes and Actinobacteria). Just two activities are described for members of this subfamily, namely α-xylosidase (3. 2. 1. 177) from five bacterial and fungal proteins and α-glucosidase (3. 2. 1. 20) for a single Bacteriodetes protein. There are subfamily structural representatives for an α-xylosidase and an α-glucosidase, with only slight differences between them. The α-glucosidase is a monomeric enzyme, and the active site is a cleft that binds small, linear maltooligosaccharides  (30).
GH31_18 This is the only family GH31 subfamily with members active on a 2-acetamido sugar, namely exo-acting protein α-N-acetylgalactosaminidase (3. 2. 1. 217) (19). The subfamily spans several kingdoms but consists mainly of bacterial sequences from several phyla (mostly Firmicutes, Bacteroidetes, Actinobacteria, and Gammaproteobacteria) and just a few metazoan members. The cohesion of this subfamily is evidenced by its early emergence at low stringency (E <10 -60 ) and it does not disaggregate even at E = 10 -140. In the 3D structure (PDB: 6M76) from Enterococcus faecalis, an extra subdomain is present in the catalytic domain that includes a short α-helix and an antiparallel β-sheet  (47). There is a conformational change of the active site between the ligand-free (open) and ligand-bound (closed) forms (  47 ), which has not been observed in other GH31 subfamily members, and may be connected to the unique exo-acting N-acetylgalactosaminidase activity of this subfamily.
Unclassified sequences The SSN classification scheme leaves only 1% of GH31 modules unclassified into subfamilies (for a detailed description of the minimum threshold for defining a family, see Experimental procedures). Most of the unclassified modules are singletons that do not share similarities to any other family member. There are several small clusters of proteins that lack the minimum number of proteins to define a subfamily and do not contain characterized members. It is expected that these groups may integrate subfamilies or become new subfamilies as more sequences are deposited and curated into the CAZy database.