dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogenetic Analysis To comment on the phylogenetic position of our M. algicola OT strain with respect to the other strains, a molecular phylogeny of 16S rRNA gene sequences was performed using sequences from different Marinobacter species. The dataset comprises 56 nucleotide sequences from GenBank including the M. algicola OT sequence (MT023716), for a total of 1415 positions after multiple alignment using the ClustalW algorithm in MEGA X version 10. 1. 7 software (available at https://www. megasoftware. net/, accessed on 9 August 2021)  [36]. A tree was constructed using a GTR + I (invariable sites proportion) + G (discrete gamma distribution) model selected using the 'Find Best DNA Models' option in MEGA X version 10. 1. 7 software (available at https://www. megasoftware. net/, accessed on 9 August 2021) [36] and the maximum likelihood (ML) method using 100 bootstrap replicates (BP).
In Silico Genomic Screening of O. tauri Phycosphere Sequences and Complete Marinobacter Genomes Whole-genome sequencing data of 19 O. tauri mutation accumulation line sets were used for genomic screening. These 19 O. tauri non-axenic culture lines (containing O. tauri and all bacterial communities from its phycosphere) were the result of a previous extinctiondilution experiment of 378 days, which corresponded to approximately 512 generations per line with 27 points of extinction dilution to one cell  [41]. These lines were shown to exclusively exhibit M. algicola cultivable species at the end point  [25]. To detect whether the genomes of the remaining bacteria present in the 19 non-axenic O. tauri line cultures possessed genes of interest, we aligned the raw reads against the target gene sequences (detailed in the following sections) using Burrows-Wheeler Aligner (BWA, http://bio-bwa.
sourceforge. net, accessed on 26 July 2018) with standard parameters  [42]  and treated the resulting bam files with SAMtools (http://www. htslib. org, accessed on 26 July 2018) to obtain the coverage of these genes  [43]. We performed BLASTP of translated sequences of interest against the reference proteomes of the 21 available and complete reference genomes and proteomes of Marinobacter species, including the M. algicola DG893 strain, the closest strain to date to M. algicola OT, which were also used for screening (all accession numbers are noticed in Table  2 ).
Searching for Methionine Synthases Genes We searched for evidence of methionine synthesis by M. algicola by screening the different genomic datasets. We focused on the metH methionine synthase gene (locus_tag = 'MDG893_RS02235', NZ_ABCP01000002) and the metE methionine synthase gene (locus_tag = 'MDG893_RS14865', NZ_ABCP01000027) identified from the M. algicola DG893 annotated genome (PRJNA19321).
Searching for Quorum-Sensing Genes We sought evidence of QS-associated genes in the different databases. We focused on the reference QS genes from Vibrio species including luxI (AY275714) from V. fischeri  [44] , luxR (DQ108980) from V. harveyi  [45] , luxS (AY391122) from V. alginolyticus, luxM (DQ987706) from V. splendidus  [46] , vanM (KT258634) and ainS (AY277634) from V. fischeri.
In Silico Protein Analysis In addition to genomic analysis, the presence of potential AI synthase and LuxRlike receptors in the species M. algicola was examined in the InterPro Database v69. 0 (https://www. ebi. ac. uk/interpro/, accessed on 9 August 2021)  [47]  with the queries 'IPR001690-autoinducer synthase', 'IPR000792-Transcription regulator LuxR, C-terminal' and 'IPR005143 Transcription factor LuxR-like, autoinducer-binding domain'. Once protein sequences were retrieved, protein domains were then identified using SMART 7 software (online resource, http://smart. embl. de/, accessed on 9 August 2021) [48] and aligned using the ClustalW algorithm under MEGA X version 10. 1. 7 software (available at https: //www. megasoftware. net/, accessed on 9 August 2021)  [36]  with Vibrio fischeri LuxR and Agrobacterium TraR sequences to check for potential conserved amino-acids.
A prediction of ligand binding on LuxR proteins was performed to test whether the identified LuxR proteins of M. algicola could effectively be involved in QS. The ligands were identified using COACH-D software (online resource, https://yanglab. nankai. edu. cn/COACH-D/, accessed on 9 August 2021) available in the I-TASSER version 5. 1 package (online resource, https://zhanglab. dcmb. med. umich. edu/I-TASSER/download/, accessed on 9 August 2021)  [49].
Most Abundant Lipid Degradation Genes Putative Organism Origin Uniprot Accession Number fadB Fatty acid degradation alpha subunit Pseudomonas putida F8FUP1 fadA 3-ketoacyl-CoA thiolase Pseudomonas putida F8FUP2 3. 6. Attempts to Detect AI-1 or AI-2 from M. algicola OT by Experimentation or Genomic Screening We evaluated the production of AHLs by M. algicola OT using sensor strains. The M. algicola OT strain did not produce type 1 (Figure  S1A ) or type 2 (Figure  S1B ) auto-inducers. However, genes coding for proteins involved in QS, mainly luxI, luxS and hdtS, were present with relatively high coverage in O. tauri phycosphere cultures. These genes belong to taxonomically distinct bacteria (Table  S1 ) and were all present in O. tauri RCC4221 culture at very low abundance rate  [25]. However, complete screening of available Marinobacter genomes did not identify any homologues of the luxI, luxS, luxM, vanM, ainS or hdtS QS genes involved in AI synthesis.
Nevertheless, LuxR receptor homologues were retrieved in 13 out of 21 Marinobacter genomes, including M. algicola DG893 (Table  S2 ). INTERPRO and SMART analysis of the Marinobacter LuxR protein sequences confirmed that all of them harbour the typical LuxR DNA-binding helix-turn-helix (HTH) domain at their C-terminal region. In the N-terminal region, eight sequences presented a signal transduction response regulator domain (IPR001789), three presented a Malt-like TPR region (IPR041617) and two presented N terminal domains that were not affiliated with any known type of protein domain. However, none of them presented the AI-binding domain (IPR005143), which was confirmed by a COACH-based analysis and alignment of LuxR sequences with the Vibrio fischeri and Agrobacterium LuxR sequences (personnal observation).
Participants Seventeen male recreational runners aged 19 to 52, without previous medical history, current medications or physical difficulties were tested. Participants were informed of the possible testing risks and institutionally approved consent was given. Approval for the research was granted by the University of Derby, UK (LSREC_1415_02) and followed the principles of the Declaration of Helsinki. Runners did not consume caffeine, alcohol or any stimulant for the 24 h before testing. There was no tobacco usage. Background data for each participant including, age, body weight, and training volume in hours per week are presented in Table  1  and were also published in an earlier work  [27]. Testing was performed in the afternoon and at least 3 h after food (with no set diet). No intense activity was performed the day prior to the test.
Exercise Protocol A motorized treadmill (Woodway, Birmingham, UK) was used for an incremental maximal cardiopulmonary exercise test for all runners. The treadmill was set for the Bruce protocol with increases in speed and inclination from 2. 7 km/h at ten percent grade, increasing by 1. 3 km/h and two percent grade every 3 min until exhaustion. A fan was used for cooling. Room temperature was approximately 24 • C for all tests. Gas Exchange Testing and Calculation of the AnTGas exchange kinetics were recorded continuously using a breath to breath metabolic cart (Metalyzer; Cortex Biophysik GmbH, Leipzig, Germany), with a Polar H7 (Polar Electro Oy, Kempele, Finland) wirelessly paired to the Metalyzer cart for the purpose of HR recording concurrent with gas exchange data. Heart rate corresponded to each reported breath to breath data point.
Assessment of the VO 2 over time relationship was performed to determine any significant plateau of the VO 2 curve for estimation of VO 2 linearity. VT2 associated HR was determined by Oxynet  [32, 33] , a convolutional neural network previously shown to have excellent agreement (average mean absolute error = 6. 1%, r = 0. 99) with manually derived results especially in individuals with medium to high aerobic fitness levels. Raw gas exchange data were uploaded to the Oxynet web app (http://oxynetresearch. promfacility. eu (accessed on 20 February 2021)) followed by a download of results.
RR Measurements and Calculation of DFA a1 Derived Threshold Each participant's ECG/RR times series was recorded with a 3-lead ECG (MP36; Biopac Systems Ltd. , Essen, Germany) with a sampling rate of 1000 Hz. Electrodes were placed in the CM5 distribution after appropriate skin cleaning. MP36 test data were saved as acq files. ECG data for each participant were imported into Kubios HRV Software (Version 3. 4. 3, Biosignal Analysis and Medical Imaging Group, Department of Physics, University of Kuopio, Kuopio, Finland). Kubios preprocessing settings were set to the default values including the RR detrending method which was kept at "Smoothn priors" (Lambda = 500). For DFA a1 estimation, the root mean square fluctuation of the integrated and detrended data is measured in observation windows of different sizes.
The data are then plotted against the size of the window on a log-log scale  [34]. The scaling exponent represents the slope of the line, which relates (log) fluctuation to (log) window size. DFA a1 window width was set to 4 ≤ n ≤ 16 beats. Visual inspection of the entire test recording was done to determine sample quality, noise, arrhythmia, and missing beat artifact. As mentioned above, two participants with excessive atrial ectopy were excluded from analysis. The RR series of the included participants was then corrected by the Kubios "automatic method"  [35]  and relevant HRV results exported as text files for further analysis. Percent artifact occurring during threshold interpretation segments was below 5%. The following procedure was used to indicate at what level of running intensity HR the DFA a1 would cross a value of 0.
Materials and Methods 2. 1. Data Mining, Gene Model, SRA Verification, and Functional Annotation of Genes with Sister (Stw)Introns in Species of Hypoxylaceae Intervening sequences with high sequence similarity were collected from the genome of Hypoxylon sp. CO27-5 (GenBank Master Accession number MDCL00000000) upon BLASTN screening at the National Center for Biotechnology Information (NCBI, Bethesda, MD, USA), using the available online tools  [23]. The (D1,2) stwintron we previously identified in the gene for a well-conserved mitochondrial carrier (named HCOc017A) (see Results Section 3. 1) was the query sequence. The coding sequences (ATG-stop) of the genes harbouring sister (stw)introns were mined by TBLASTN screening of the Whole Genome Shotgun contigs (WGS) database at NCBI. The genome master accession numbers of the nine fungi in which sister (stw)introns were encountered are listed and referenced in Table  1.
Because the splinter still contains the external intron of the stwintron and thus is not a splicing end product, its read count is generally (considerably) lower than that for the fully spliced RNA. SRAs that confirm sister (stw)introns and their predicted stwintron splicing intermediate in the three species mentioned above are listed in Supplementary Table  S1. Contemporary automated annotation software does not recognise stwintrons, particularly not (D1,2) stwintrons that start with the noncanonical 5 -GGU (or occasionally, 5 -GGC) at the 5 -splice site. We did not use the results of automated annotation ("Models" or "mRNA" at the nr/nt database), nor did we use deduced protein databases to collect proteins. After translation of our predicted mRNAs, we functionally annotated most of the genes carrying sister (stw)introns with one or more protein domains categorised in the Protein Families (Pfam) database  [31].
Other Informatics Methods Multiple sequence Alignment with Fast Fourier Transform (MAFFT: version 7) was used for multiple sequence alignments  [32]. To compare two or three intronic sequences across their entire span, Clustal Omega alignments were performed  [33]. For the tree of the 37 mitochondrial carrier proteins, the alignment was trimmed with Block Mapping and Gathering with Entropy (BMGE: version 1. 12)  [34]. The maximum likelihood phylogenies of the Hypoxylon sp. CO27-5 sister (stw)introns and of the mitochondrial carrier protein were inferred using PhyML with Smart Model Selection (version 3. 0)  [35]. Branch support was estimated as detailed in the respective Figure legends. Trees were drawn with FigTree (version 1. 4. 3: http://tree. bio. ed. ac. uk/software/figtree, accessed on 4 October 2016) and further annotated with Adobe Illustrator (Adobe Inc.
KG, Düren, Germany), then cloned in pGEM-T Easy (pGEM-T Easy Vector System I, Promega Corporation, Madison, WI, USA). Plasmid DNA was isolated using the NucleoSpin Plasmid EasyPure kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Three independent clones were sequenced over both strands using universal primers hybridising to the vector (Eurofins Genomics, Ebersberg, Germany) or gene-specific oligonucleotide primers where appropriate. cDNA and splinter sequences from Hypoxylon sp. CO27-5 were deposited at GenBank under accession numbers MW490712-MW490722, MW498245-MW498262 and MW530466-MW530509.
Results 3. 1. Identification of a New (D1,2) Stwintron in the Gene for a Mitochondrial Carrier Protein in Two Allied Hypoxylon While investigating the intron-exon structure of a gene for a well-conserved, 339 amino acid-long mitochondrial carrier in Aspergillus nidulans (A. nidulans GenBank AACD01000130, CDS coordinates start-stop: 208790-210069, unpublished work) with comparative genomics, we noticed an archetypal (D1,2) stwintron in the orthologue gene in the Hypoxylon sp. CO27-5 and EC38 genome sequences, absent from all other fungi assessed. When the CO27-5 genome was back screened with the stwintron's sequence (BLASTN), dozens of full length and partial hits were uncovered, suggesting that this new (D1,2) stwintron is part of a set of structurally related intervening sequences. In all, we identified with a simple BLASTN search 23 (D1,2) stwintrons in Hypoxylon sp.
CO27-5, which are highly similar in sequence over the complete width. An alignment is shown in Figure  2. The BLASTN query stwintron is named HCOc017A, where HCO refers to the fungus Hypoxylon sp. strain CO27-5, c017 refers to the sequence contig in which it occurs (i. e. , GenBank MDCL01000017), and the terminal capital letter (here, A) identifies the individual stwintron(s) in that contig.
We have termed these 23 stwintrons sister stwintrons to reflect their similarity and the likelihood of common ancestry. They are located in 22 different contigs, scattered throughout the genome (Supplementary Table  S1 : sheet CO27-5). One sister stwintron (HCOc224-179) is split over two non-overlapping CO27-5 sequence contigs due to an assembly artefact: we have determined its full-length sequence (GenBank accession number MW477887). Repetitive sequence elements that correspond to functional intronic sequences are called "introners"  [39]  and have been reported in a number of organisms in different eukaryotic kingdoms, including in fungal taxa  [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] , but the proliferation of complex intervening sequences, e. g. , stwintrons, has never been described before.
Experimental Identification of Sister Stwintrons We have verified the typical two-step splicing of the predicted stwintrons and their splicing intermediate using the available RNA SRAs (Sequence Read Archive) at NCBI. In parallel, we have sought to experimentally confirm both the stwintron splicing intermediates and the complete (D1,2)s by targeted RT-PCR and cDNA sequencing using specific oligonucleotide primers (detailed in the Materials and Methods section). See Supplementary Table  S1  for SRA evidence and GenBank accession numbers. By these complementary means, we could confirm the two-step excision for 31 out of 36 predicted stwintrons. The transcripts of the genes in which four of the remaining predicted (D1,2) stwintrons are located could not be amplified by RT-PCR, implying that these genes are not expressed under the growth conditions used to generate template RNA (see Materials and Methods section).
In Hypoxylon sp. CO27-5, putative POLQ-like helicase mRNA and protein are extant (named HelQ; see GenBank accession numbers MW530496 and MW530509). In Hypoxylaceae, this clearly identifiable helicase gene includes a (D1,2) stwintron (albeit not a sister stwintron). The transition of a (D1,2) stwintron to a canonical intron implies that the 5 -donor G 1 of the external intron of the stwintron becomes exonic, and secondary mutations being required to restore the reading frame of the mature mRNA. In this case, (HECc034A), secondary mutations adjacent to either intron-exon junction resulted in a transversion of the exonised G 1 into a T with a concomitant shift in intron position, by which the Thr codon (A|CC) split by the phase-one stwintron (CO27-5) is changed to an Ile codon (AT|C) split by the phase-two canonical intron (EC38), with the loss of one of the exonic Cs directly downstream the ancestral stwintron.
The 33 highly similar sister (stw)intron RNAs in Hypoxylon sp. CO27-5 could not be assigned to any known RNA family in the Rfam database (version 14. 3: 3446 families)  [57] , which contains highly structured, self-splicing RNAs as well as intron-born, small nucleolar RNAs (aka, snoRNAs). They also do not bear primary sequence similarity to any described family of fungal introner-like sequences in Dothideomycete species of the Capnodiales order  [42, [44] [45] [46] 48, 50]. The expression data (SRAs/RT-PCR) strongly suggest that terminal symmetry-including the intronic 10-nt palindrome (5 -WTTCTAGAAA)-is not necessary for (stw)intron removal by the U2 spliceosome (see Supplementary Table  S1 ). A remarkable feature of the TIRs in the Hypoxylon sister (stw)introns is that frequently, the three invariant nucleotides involved in the two transesterification reactions of U2 excision-the 5 -terminal donor G, the lariat branch point A, and the 3 -terminal acceptor G-are not base pairing in the predicted hairpin structure in single-stranded (ss) RNA (not shown).
Supplementary Materials: The following are available online at https://www. mdpi. com/article/ 10. 3390/jof7090710/s1. S1 : Contig identifiers, SRA reads, GenBank accession numbers, and more information about sister (stw)introns; Table  S2 : Oligonucleotide primers used; Table  S3 : SRA identifiers; text document S1: Fastas sister stwintrons CO-27-5; text document S2: Fastas derived canonical introns CO-27-5; text document S3: Fastas sister stwintrons E7406B; text document S4: Fastas sister stwintrons H. rubiginosum-Daldinia. Author Contributions: Conceptualisation, E. F. , M. F. and L. K. ; Methodology, E. F. and M. F. ; Software; Not applicable; Validation, E. F. , F. P. , N. Á. , C. S. , M. F. and L. K. ; Formal Analysis, E. F. , F. P. , N. Á. , C. S. , M. F. and L. K. ; Investigation, E.
Figure2. Alignment of 23 (D1,2) sister stwintrons from Hypoxylon sp. CO27-5. 23 (D1,2) stwintrons with high global sequence similarity were collected by BLASTN screening of the genome sequences of Hypoxylon sp. CO27-5 (GenBank MDCL00000000: 580 contigs) with the (D1,2) stwintron in a conserved mitochondrial carrier gene (stwintron HCOc017A) as the query. The sequence of stwintron HCOc224-179 and the gene harbouring it (duf636) was determined experimentally (GenBank Accession MW477887). The full-length intronic sequences were aligned by Multiple Sequence Alignment (MAFFT) using E-INS-i iterative refinement and the 20PAM scoring matrix without sequence trimming. The consensus line was annotated with IUPAC symbols for combinations of bases occurring on each of the 276 positions, except for the apparent insertions that had occurred in only one or two sequences.
Acknowledgments: E. F. received a  János Bolyai Research Scholarship  from the  Hungarian Academy of Science  ( BO/00093/18/8 ). F. P. and E. F. were supported by the  New National Excellence Program of the Hungarian Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund  (grants  ÚNKP-20-3-I-DE-40  and  ÚNKP-20-5-DE-13 , respectively). Funding for open access charge:  Hungarian National Research, Development and Innovation Fund  ( NN 128867 ).
PROTOCOL OF THE ASSESSMENT Technical description of the videoconference system The videoconference system (or telemedicine) tool was internally developed as a web-based platform, using common web-development technologies and libraries (JavaScript, Node. JS, HTML, etc). No Skype, Zoom or other existing videoconferencing systems were involved. A secured server allows connecting two clients (clinician and patient) through the two interfaces described in figure  1. Both clinician and patient connect to the platform through any existing web browsers (Chrome, Firefox, Safari, Edge) under any operating system that supports webRTC standard. WebRTC (https:// en. wikipedia. org/ wiki/ WebRTC) (Web Real-Time Communication) is a free, open-source project providing web browsers and mobile applications with real-time communication via simple application programming interfaces.
For practical reasons, we will use a laptop or a desktop with a minimum of 17-inch screen width. This will make the clinical tests' contents (images and text) visible for the patients. In addition, we will use a wide-angle camera, especially for the patient's side, in order to allow the clinician to see the upper body of the patient to be able to observe gestures. This is particularly important for some clinical tests, in which seeing the patient's hands is required. The videoconferencing communication requires a dedicated server to allow the transmission of different information between the two clients (clinician and patient). Servers to store different data (database, patients' information, videos, speech recordings, scores, etc); and to run the different services allowing the videoconferencing communication are mandatory.
All the servers will be hosted in dedicated and regulated infrastructure such as the ones of the clinical partners, and thus respect the legislation related to health data and privacy. The developed system is linked to third parties cloud infrastructures allowing speech and video analysis. For the planned clinical study, audio and video data will be stored on secured servers. The processing of these data is done according to the procedure explained under data processing. The use of speech and video analysis, in addition to providing potential digital biomarkers, helps in overcoming both the physical absence of the patient and the lack of sophisticated and complex observation devices (such as Pan-Tilt-Zoom 'PTZ' cameras). By providing the clinician with meaningful information about the patient's behaviours and state (comfort, fatigue, stress), the physical distance can be potentially compensated for.
DATA COLLECTION, MANAGEMENT AND ANALYSIS Data collection Data will be collected at the Hospital Center in Digne-les-Bains; the assessments will be performed remotely and face-to-face by clinicians from the Memory Clinic in Nice. For remote assessments, the videoconference software will record test scores, video and speech and store them on a dedicated secured server complying with healthcare data hosting regulations. Other clinical and neuropsychological data collected by the clinicians will follow the standard practice of the centre. Prior to initial participation in the study, each participant will consent on paper, or an alternate decisionmaker will consent and the participant will provide assent. Each individual (or dyad) will be given as much time as they need to review the consent form and decide whether they want to participate.