dataesr/scientific-paragraphs-categorization huggingface dataset:
Along with the various prioritization approaches described in this report, especially the CLIP-seq analysis that identified direct targets of Celf1 (in addition to other parameters such as, lens-enriched expression in iSyTE, preferential expression in epithelial or fiber cells, etc. ), the microarray data identifies high-confidence candidates in the lens for future studies. These analyses show that upon Celf1 deficiency, a cohort of cataract-linked genes are misexpressed (e. g. , the crystallins Cryab, Cryba2, Cryba4, Crybb1, Crybb2, Cryga, Crygb, Crygc and Crygd, the connexins Gjb6 and Gja3, the membrane protein Bfsp1, the extracellular matrix associated peroxidase Pxdn, and the post-transcriptional regulator Tdrd7), in addition to alterations in distinct pathways, thus indicating that multiple factors likely contribute to the manifestation of the cataract defect.
3, 12 , 22 Figure 9. 12229 Figure 9. Gene ontology (GO) and pathway analysis on Celf1 cKO lens DEGs that are also identified in CLIP-seq dataset. The top significant GO terms enriched in (A) reduced DEGs, (B) elevated DEGs, and (C) all DEGs that are also identified in CELF1 cross-linked immunoprecipitation followed by RNA-sequencing (CLIP-seq) data on the human cell line (Hela cells).
Chemistry: General remarks Infrared spectra were recorded on a Perkin-Elmer spectrometer 100 Fourier Transform infrared spectrometer equipped with a universal ATR accessory. Mass spectra were acquired on a Bruker micrOTOF Q II spectrometer. 1 H and 13 C NMR spectra were recorded at 298 K on a Bruker AVANCE 400 spectrometer using standard pulse sequences. Proto-deutero solvent signals were used as internal references (CD 3 OD: δ H 3. 31, δ C 49. 00). For 1 H NMR, the data are quoted as position (δ), relative integral, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, dt = doublet of triplets, td = triplet of doublets, tt = triplet of triplets, ddd = doublet of doublet of doublets, m = multiplet, br = broad), coupling constant (J, Hz) and assignment to the atom. The 13 C NMR data are quoted as position (δ), coupling constant (J CF , Hz) and assignment to the atom.
min -  until 272°C,+10°C. min -  until 310°C and 7 min à 310°C. The transfer line was maintained at 300°C and the ion source at 200°C. Ionization was performed by electron impact at 70 eV and the MS acquisition was carried out after a solvent delay of 5 min in full scan mode at 7 spectra. s -1 over the m/z range 45-700. MS Spectra were processed with the software "GCMS Solutions" supplied by Shimadzu to adjust retention times between each run using a mixture of alkanes (C7 to C40, Sigma-Aldrich). Peak identity was established according to their retention time and mass fragmentation spectra with respect to authentic standards derivatized (Table  S1 ), and by reference to mass spectra of derivatives in the US National Institute of Standards and Technology database and in the Golm metabolome database.
All mass isotopologue raw areas were subjected to correction for the contribution of naturally occurring isotopes of all elements except the carbon arising from the metabolite backbone using the IsoCor v2. 1. 4 package of Python (https://github. com/MetaSys-LISBP/ IsoCor) in low resolution mode  (Millard et al. , 2019). In addition, unlabeled chemical standards, Arabidopsis seedlings and B. napus leaves were additionally corrected for the contribution of naturally occurring isotopes of the carbon arising from the metabolite backbone (giving a residual molecular 13 C enrichment of 0 for molecules labeled at natural 13 C abundance). 13 C-PT samples were not concerned by this additional correction since they held fully controlled 12 C/ 13 C patterns at all positions. A correction method dedicated to IsoCor was specifically created for the TMS-derivative fragment described in this study (Table  1 ), i.
e. by considering the contribution of all atoms added by the derivatization on the isotopic measurement of the monitored fragments (chemical separation of Workflow used in this study. A GC-MS method was built with abundant molecular ions deriving from TMS-derivatives of organic and amino acids that contained a large number of informative carbons. Then this method was evaluated by using: i) chemical standards and tailor-made 13 C-standards that had a predictable CID using E. coli as a metabolic factory ( 13 C-PT); ii) unlabeled and 13 C-labeled plant samples. all atoms arising from the metabolite and the derivative). All files required to run this method on IsoCor are available in the supplementary material of this article (Supplementary Files) and all information will be updated indefinitely in the following INRAE dataverse  (Dellero and Filangi, 2021).
The method is publicly available and can also be run directly from GC-MS source files using a Galaxy Workflow URL available at the previously mentionned INRAE dataverse. For this purpose, each raw GC-MS dataset should contain a column "Name" for the fragments considered and a column "Area". The name of each fragment must be written exactly as specified in the GCMS example file (an example file is provided in the Supplementary Material and in the (3TMS) C18H35NO3Si3 397 TMS-CO2 117 C14H26NOSi2 280 2-3-4-5-6-7-8-9 Valine(2TMS) C11H27NO2Si2 261 TMS-CO2 117 C7H18NSi 144 2-3-4-5 Valine(2TMS) C11H27NO2Si2 261 C3H7 43 C9H20NO2Si2 218 1-2 a-Alanine(2TMS) C9H23NO2Si2 233 TMS-CO2 117 C5H14NSi 116 2-3 b-Alanine(3TMS) C12H31NO2Si3 305 CH3 15 C11H28NO2Si3 290 1-2-3 previously mentionned INRAE dataverse.
2. 7Statistical analysis Statistical comparisons were performed using either confidence intervals (comparison of a group of value against one reference value), a Student-test (comparison of 2 groups of values) or an ANOVA followed by a post-hoc Tukey-HSD test (comparison of 3 or more groups of values) with a level of p-value<0. 05 by using the publicly available Rstudio software and dedicated packages  (RStudio Team, 2016).
A B FIGURE 4 Dynamics of U-13 C-pyruvate incorporation in Brassica napus leaf discs exposed to light or dark conditions. (A), Mean fractional 13 C enrichment and (B), Metabolite pool sizes. Mean fractional 13 C enrichment were monitored with GC-MS, while absolute quantification of organic and amino acids was performed respectively with GC-FID and HPLC-UV. The results are presented as the mean ± SD of four independent biological replicates. Statistical differences between dark and light conditions are denoted with asterisks according to a Student test (*, p-value<0. 05; **, p-value<0. 01; ***, p-value<0. 001). The complete dataset is available in Tables  S2, S3. Supplementary statistics (ANOVA and post-hoc Tukey-HSD tests) are available in Tables  S4, S5. A B C FIGURE 5 Fractional 13 C enrichment at the isotopologue level for TCA-cycle derived metabolites.
(A), Metabolic network considered based on the 13 Clabeling strategy. (B), Light conditions and (C), Dark conditions. The M0 isotopologue was not represented in the graphs to facilitate the visualization of low-enriched isotopologues. The results are presented as the mean ± SD of four independent biological replicates. The complete dataset is available in Table  S2. In the proposed network, the second "turn" reflected the commitment of a molecule that has already experienced all reactions of the TCA cycle to another round of reactions (Orange and blue labels to compare acetyl-CoA-derived labeling from 1 st and 2 nd "turn"). Note that M0 istopologues of all metabolites will still continue to produce M0 istopologues at an important rate after a "turn" of the TCA cycle, given the 13 C-enrichment for acetyl-CoA active pool.
We also detected a significant abundance of an m/z 246 (siliconium ion) in the fragmentation spectra of Valine_2TMS, which seems to support this hypothesis for the contamination (Figure  S2 ). The third bias concerned the very high level of M1 isotopologue detected for Threonine_3TMS_C2C4. In its fragmentation spectra, we also found a M1 isotopologue contamination for the peak m/z 291, an important fragment for the identification of Threonine_3TMS by GC-MS (Figure  S2 , NIST database). Thus, this contamination could be due to: i) a co-elution of a contaminant chemically similar to threonine; ii) a strong analytical isotopic effect. The use of GC coupled to highresolution MS may help to resolve this analytical issue. Besides this, we could not evaluate Succinate_2TMS_C1C4 with our workflow, due to a previously reported E.
, 2021). However, another experiment (Arabidopsis leaf discs, 20 mM U-13 C-pyruvate, up to 8 hours in the dark) showed similar results but only observed M2 isotopologues for citrate, glutamate and succinate and not the M1 and M3 isotopologues that were observed in our experiments (complete dataset available on request from the authors)  (Le et al. , 2021). Against these observations for Arabidopsis, it is evident that the important commitment of TCA cycle-derived malate towards another "turn" of the TCA cycle is specific to B. napus (Figure  8 ). Therefore, part of the discrepancies between our results and previous works may also be explained by the use of different plant species. Since the non-cyclic nature of the TCA cycle in the light was mostly explained by the need to sustain de novo nitrogen assimilation  (Gauthier et al.
Acknowledgments P2M2 ( Metabolic Profiling & Metabolomics Platform ,  Le Rheu , France, www. 6. inrae. fr/p2m2/)and its staff members are gratefully acknowledged for access to mass spectrometry facilities and for supporting the methodological developments required for this study. We thank  MetaToul (Metabolomics & Fluxomics Facitilies, Toulouse, France , www. metatoul. fr)for technical support and access to NMR facilities. We are grateful to  Nathalie Marnet  and  Mathieu Aubert  for technical assistance in the quantification of amino acid content and  Pierre Millard  and  Floriant Bellvert  for fruitful scientific discussions.
Galectin-3C could increase the anticancer activity of bortezomib in human multiple myeloma cells  (290). G3-C12 oligopeptide is a frequently used galectin-3-CRD domain blocker, which inhibited lung metastasis in a mouse model of breast cancer  (288). The protective effects of G3-C12 were improved in combined therapy with N-(2-hydroxypropyl) methacrylamide (HPMA) compound and 5-FU. G3-G12-HPMA complex strongly improved the anti-tumor activity of 5-FU in nude mice bearing tumor of human PC-3 cancer cells  (289). GM-CT-01 (DAVANAT) is a modified vegetal galactomannan oligomer that strongly binds the dimer interface of galectin-1 and galectin-3  (318). GM-CT-01 enhances the infiltration of T cells into the tumor microenvironment and induces IFNγ synthesis  (319). GM-CT-01 was administered in combination with 5-FU in patients with metastatic solid cancers that failed initial therapy (NCT00388700).
In clinical trial phase II, 70% of the patients were stabilized at the highest DAVANAT dose level, 46% of patients experienced an increase in life expectancy, and merely 41% of patients developed serious adverse effects, compared to the best standard of care. Food Drug Administration (FDA) approval was given to progress to clinical trial phase III studies, although this was not followed up as of now  (320). Multiple factors led to the withdrawal of two further clinical trial phase II studies using GM-CT-01 therapy (NCT00388700 and NCT00386516). The vaccine form of GM-CT-01 is currently in clinical trial phase II, injecting patients with diffuse melanoma (NCT01723813). GR-MD-02 (Belapectin) binds galectin-3 and preclinical settings could improve liver function by reducing collagen deposition, fibrosis in non-alcoholic steatohepatitis (NASH), and cirrhosis  (321).
Furthermore, MCP function was also studied in cardiovascular and renal diseases. MCP could inhibit aldosterone-induced cardiac and renal fibrosis and improve cardio-renal dysfunction  (326). MCP could prevent fibrosis in rodents with heart failure and hyperaldosteronism and inhibit obesity-associated adipose tissue inflammation and differentiation of adipocytes and atherosclerotic plaque progression  (327) (328) (329). Additionally, MCP reduced myocardial injury after ischemic reperfusion  (330). A derivative of MCP, PectaSol-MCP was evaluated in clinical trial phase II (NCT01681823) regarding its capability to improve prostatespecific antigen (PSA) kinetics in men with increased PSA levels and biochemically relapsed prostate cancer, PSA progression was inhibited in 58% of patients. PSA doubling time, a prognostic marker predicting the development of metastasis, lengthened in 75% of patients versus baseline indicating a reduced risk of metastatic spread  (331).
However, the major limitation of this study was the lack of a placebo arm, which, given the perceived positivity of PectaSol-MCP, was not conducted. GCS-100 is an MCP-derived polysaccharide and was used to study galectin-3-mediated pro-tumorigenic effects. GCS-100 could induce apoptosis in multiple myeloma cells, which displayed strong resistance to doxorubicin, melafalan, bortezomib, and dexamethasone  (295). GCS-100 treatment together with a BH3-mimetic also induced apoptosis in acute myeloma cells and interestingly these effects were associated with the induction of P53  (296). Although GCS-100 was well tolerated by patients in clinical trial phase II, partial response and stable disease were observed in patients with recurrent chronic lymphocytic leukemia (NCT00514696). TD139 binds the CRD domain of galectin-3 with a strong antiinflammatory and anti-fibrotic potential in mouse models of lung injury and fibrosis  (332, 333).
Another anti-Tim-3 antibody, LY3321367 also presented a safety profile and modest antitumor activity or in combination with LY300054, an anti-PD-L1 antibody  (309). Similar combinations were also developed using MBG453, anti-Tim-3 antibody and spartalizumab, an anti-PD1 antibody, which presented better outcome and antitumor activity as compared to monotherapy  (310). LYT-200 is an IgG4 monoclonal antibody, designed to inhibit the activity of galectin-9. It was given orphan drug designation by the FDA and it is tested in an open-label, uncontrolled, multicenter phase 1/2 study with a dose escalation phase and a cohort expansion phase in patients with relapsed/refractory metastatic solid tumors, including PDAC, colorectal cancer, and cholangiocarcinoma (NCT04666688). The study was posted in 2020 and is currently in its recruiting stage.
9, [19] [20] [21] [23] [24] [25] [26] [27]  In particular, studies demonstrated that some PHD2 mutations induce a subtle loss of function, sometimes very close to the wild-type protein. 26  This article describes a collaborative study of 34 novel genetic variants (in addition to 5 previously described  16, 19, [28] [29] [30] [31] [32] [33]  ) identified in the EGLN1 gene using next-generation sequencing panels. The study includes data from sequencing of a total of 2,160 patients with hereditary or idiopathic erythrocytosis recruited in seven European countries. Forty-seven cases carrying genetic variants in PHD2 were identified. We performed comprehensive in silico and functional studies to decipher their potential causal role in the disease pathogenesis.
In silico analyses The MobiDetails annotation platform  34  was used for the interpretation of DNA variations (frequencies in the control population, prediction of the impact of missense variants and analysis of splicing with the Splicing Prediction Pipeline (SPiP)) and for the localization of the mutated amino acids on the three-dimensional protein structure (AlphaFold Protein Structure Database). The localization of the affected amino acids on the two-dimensional structure was analyzed using the MetaDome website. 35  The UK Biobank resource was used to analyze the hematologic parameters of the carriers of EGLN1 genetic variants.
A B (Online Supplementary Figure  S1A , left panel) and the missense variants described in this study (right panel) on the Protein's Tolerance Landscape. The variants were distributed throughout the protein, with no particular hotspot of mutations. The majority of the amino acids targeted by the genetic variations in the present study are expected to have a moderate impact (orange on the scale). Only three are expected to be highly intolerant (red on the scale): D50H, V210del, and Y329H (scores are detailed in Online Supplementary Table  S3 ). The targeted amino acids on the three-dimensional structure were localized using the AlphaFold Protein Structure Database through the Mobi-Details website (Figure  2B ). PHD2 has two main domains: a N-terminal MYND-type zinc finger domain and a C-terminal prolyl hydroxylase domain with the double-stranded β-helix core fold supported by surrounding α-helices (in blue in Figure  2B ).
For each variant, the scores of individual and meta-predictors were plotted on a graph to allow their classification into three categories: probably damaging, possibly damaging/ tolerated, or benign (Figure  3A ). These analyses showed that all identified variants had elevated scores, with the exception of variants P77L, A96V, Q157R, K255E and D419H (which are mainly located outside the main domains in the three-dimensional structure). We analyzed the UK Biobank database, a large-scale biomedical database containing in-depth genetic and health information from half a million participants from the United Kingdom. We selected the PHD2 variants identified in the literature and this study (Figure  3B ) and/or other variants associated with elevated hematocrit and hemoglobin levels (Online Supplementary Figure  S4 ).
Functional studies of PHD2 variants using luciferase reporter tests The effect of the genetic variants on PHD2 activity was assessed using a reporter assay for HIF transcriptional activity. The HIF-2α subunit was co-expressed with a luciferase gene driven by HRE (Figure  4A ). The activity of accumulated luciferase was quantified 24 h after transfection. The addition of wild-type PHD2 causes a dose-dependent suppression of HIF2-mediated induction of the reporter gene. When immunoblotted to monitor expression of the PHD2 protein, W334R and W389R proteins accumulated at levels below that of the wild-type protein for equivalent amounts of transfected plasmid (data not shown). To account for this effect, the amounts of transfected plasmid were adjusted to yield equivalent amounts of protein. We observed an inhibitory activity comparable to the wild-type for W334R, G349S and G349C variants, as well as for the previously published P200Q and R371H  26  variants.
Study of the impact of variants on splicing using a minigene assay Since some of the genetic variants studied do not seem to have a major impact on the function or the stability of PHD2 proteins, we attempted to test their impact on splicing. The potential effects of some PHD2 variants on splicing were analyzed using Alamut Visual ® , an exploration software application for genomic variation (Online Supplementary Figure  S7A ). These analyses showed a potential impact on splicing protein binding in all cases, except for the c. 1165T>C, p. W389R, which was used as a control to study exon 4 splicing. In silico analysis using the SPiP site via MobiDetails, was more restrictive and showed only three deleterious splicing variants (c. 891+1G>A, c. 1152C>T, p. Y384Y, and c. 1216+1G>T) (Online Supplementary Figure  S7B ).
In addition, the study of databases such as the UK Biobank has been very useful for the classification of benign variants (A96V, C127S, Q157H, Q157R). Examination of the clinical data showed that complications are rare in patients carrying EGLN1 mutations (in the present study, only 1 patient with portal vein thrombosis). Notably, clinical data from all the families described in the literature and in the present study (N=72 and N=47, respectively) showed that tumor development can be considered a very rare event (only 2 cases of paraganglioma  20, 21  and 1 case of pheochromocytoma  42  ) and may, therefore, be associated with additional genetic events. However, given the demonstrated role of PHD2 in the pathogenesis of pseudo-hypoxic pheochromocytoma,  43  it is essential to medically monitor the occurrence of a possible tumor.
This result paves a new way to fine-tune the hypoxia pathway which regulates expression and splicing of its different players. In conclusion, our study provides an example of a comprehensive approach to classification of genetic variants that could be applied to many rare hematologic diseases. Here, we demonstrated the importance of collaborating and combining results from different diagnostic centers dedicated to rare diseases. In silico studies with analysis of databases such as the UK Biobank may also facilitate classification, especially of non-pathogenic variants. We have shown the importance of performing a wide range of functional analyses and of studying finer regulatory mechanisms of the gene, such as the splicing studied here, whose complexity remains to be explored. Finally, accurate classification is essential in order to make the most appropriate diagnosis in patients and thus ensure proper follow-up and treatment.
Acknowledgments The present research has been conducted using the  UK Biobank  resource under application number 49823. We are most grateful to the  Bioinformatics Core Facility of Nantes BiRD , member of  Biogenouest ,  Institut Français de Bioinformatique (IFB)  ( ANR-11-INBS-0013 ) for the use of its resources and for its technical support. We thank  Thomas Besnard  for minigene expertise,  Morgane Taligot  for technical assistance and  Dr Emmanuelle Verger  for expertise in next-generation sequencing analysis.
Gly719Ala variant was detected, an amplification curve was observed but variants were not formally identified because the amount of amplifiable DNA present in the cartridge (EGFR total Cq was 25. 7 cycles) was low. In this third case, the sample-in comprised 5% neoplastic cells, which was also below the study testing requirements (i. e. , at least 10% neoplastic cells). In the remaining two cases, which included one Ex19del (deletion 24) and one Ex20ins (InsG), no amplification curve was observed with the Idylla ™ EGFR Mutation Test; total Cq values (27. 6 and 25. 7 cycles, respectively) confirmed that low amounts of amplifiable DNA were present in the cartridges. The deletion 24 had a COSMIC database prevalence of 0. 02%. Overall, the 10 discordant negative cases had a mean EGFR total Cq value of 24.
Discordant-by-design cases Thirteen cases of discordance by design occurred across seven different sites; 10 used amplicon-based NGS as the reference method, two used Sanger sequencing and one used hybrid capture NGS (Figure  2 ; Supplementary Table  S3 ). Five of 13 variants were described in the COSMIC database and occurred as the following base changes (variant; prevalence in NSCLC, %): c. 2127_2129del (p. Glu709_Thr710delinsAsp; 0. 35%), c. 2125G>A (p. Glu709Lys; 0. 12%), c. 2311_2319dup (p. Asn771_His773dup; 0. 24%), c. 2224G>A (p. Val742Ile; 0. 03%) and c. 2239_2240delinsCC (p. Leu747Pro; 0. 29%). All 13 cases had a 'no variant' result with the Idylla ™ EGFR Mutation Test with a mean (±SD) EGFR total Cq value of 23. 2 ± 3. 5 cycles.
Search strategy We created and conducted the search strategy with input from all the authors and a medical librarian (E. U. from the E. M. Uleryk Consulting). We searched the following databases from inception to April 5, 2022: MEDLINE and Embase (OvidSP); Scopus (Elsevier); Web of Science (Clarivate), and Cochrane Library (Wiley). We used a combination of controlled vocabulary (MeSH [Medical Subject Headings] and Emtree terms] and keywords with various synonyms for the following concepts: "multiple myeloma" AND ("frailty" or "geriatric assessment"). We limited the search strategy to English language studies. The full search strategy for each database is available in Supplementary Table  S1. We also did a manual search of (1) bibliographies of any included trials or relevant review articles, (2) ongoing clinical trials (clinicaltrial.