dataesr/scientific-paragraphs-categorization huggingface dataset:
Interestingly, the rORF of CxNV1 S2 may not encode a functional protein  [82]. Nevertheless, the function of the secondary genome segment of AejapNV1 and CxNV1 remains unknown, and future studies are needed to elucidate its role and evolutionary origin. These narnavirus secondary segments belong to the dark matter of metagenomics, since sequence similarity methods, such as local alignments, were not able to associate the AejapNV1 S2 sequence to the CxNV1 S2 reference in GenBank. Even the application of the powerful tool AlphaFold  [59]  to predict tertiary structures and infer protein function, was limited by the lack of similar sequences to ORFs in AejapNV1 S2. AlphaFold relies on initial alignments to protein sequence and structure databases, such as Uniref90 and the Protein Data Bank, to acquire atomic tridimensional data and perform structural assessments  [59].
japonicus. Infection with these likely ISVs might add yet another complex variable to the risk assessment of arbovirus outbreaks caused by Ae. japonicus, and future studies are needed to dissect the role of the virome in arbovirus transmission. Tertiary protein structure predictions for segment 2 ORFs of AejapNV1 and CxNV1. AlphaFold per-residue confidence estimation (pLDDT) and calculated models are shown for segment 2 ORFs of AejapNV1 and CxNV1 (GenBank MW226856. 1). In (A) is shown the AejapNV1 segment 2 fORF, in (B) its rORF; in (C) the CxNV1 segment 2 fORF and in (D) its rORF. A1, B1, C1, and D1 show the pLDDT values of the five calculated models for each ORF. A2, B2, C2, and D2 show the five estimated output models superposed. Confidence ranking values for all models can be found in Suppl.
Acknowledgements We thank  Marleen Abma-Henkens  for her assistance with Ae. japonicus collection in the field,  Pieter Rouweler  and other members of the insect rearing group from the  Laboratory of Entomology from Wageningen University & Research  for maintaining the Cx. pipiens colony,  Giel Göertz  for his contributions during the start of the project,  Monique van Oers  for her continued interest in the project, and  Eric Snijder ,  Andrew Firth ,  Nina Lukhovitskaya  and  Katherine Brown  for fruitful scientific discussions. We also thank  Isaque J. S. de Faria  and all members of  Marques Laboratory , who contributed with suggestions and discussions and  Rune Hartmann  for his insights about tertiary structure predictions.
Funding This study was supported by the  European Union 's  Horizon 2020 Research and Innovation Programme  (project: ZIKAlliance) under grant number  734548. SRA was also supported by the  ZonMw  project  ZikaRisk ("Risk of Zika virus introductions for the Netherlands "), project number  522003001. The work of the  Interdisciplinary Thematic Institute IMCBio , as part of the  ITI 2021-2028 program  of the  University of Strasbourg ,  CNRS  and  Inserm , was supported by  IdEx Unistra  ( ANR-10-IDEX-0002 ), by  SFRI-STRAT ' US  project ( ANR 20-SFRI-0012 ), and  EUR   IMCBio  (IMCBio  ANR-17-EURE-0023 ) under the framework of the  French Investments for the Future Program as well as from the previous Labex NetRNA  ( ANR-10-LABX-0036 ). This work has also been supported by grants from  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)  to JTM (grant  CNPq /AWS 032/2019 , process  440027/2020-9 );  Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG) ;  Institute for Advanced Studies of the University of Strasbourg  ( USIAS fellowship   2019 ) to JTM;  Google Latin American Research Award  ( LARA 2019-2020 ) to JTM and JPPA.
This work was also supported by  Investissement d'Avenir Programs  ( ANR-10-LABX-0036  and  ANR-11-EQPX-0022 ) to JTM. JTM is a CNPq Research Fellow. JPPA was also supported with a PHD fellowship from  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Brasil (CAPES). This study was financed in part by the  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Brasil (CAPES) -Finance Code   001  to JTM. The funders had no role in the design of the study, the collection, analysis or interpretation of the data, or the writing of the manuscript.
Supplementary Figure 6. 6 japonicus. Infection with these likely ISVs might add yet another complex variable to the risk assessment of arbovirus outbreaks caused by Ae. japonicus, and future studies are needed to dissect the role of the virome in arbovirus transmission. Tertiary protein structure predictions for segment 2 ORFs of AejapNV1 and CxNV1. AlphaFold per-residue confidence estimation (pLDDT) and calculated models are shown for segment 2 ORFs of AejapNV1 and CxNV1 (GenBank MW226856. 1). In (A) is shown the AejapNV1 segment 2 fORF, in (B) its rORF; in (C) the CxNV1 segment 2 fORF and in (D) its rORF. A1, B1, C1, and D1 show the pLDDT values of the five calculated models for each ORF. A2, B2, C2, and D2 show the five estimated output models superposed. Confidence ranking values for all models can be found in Suppl.
3, allowing one mismatch. Size profiles of small RNAs matching reference sequences and 5' nt base preference were calculated using in-house Perl v5. 16. 3, BioPerl library v1. 6. 924 and R v4. 0. 5 scripts (https://github. com/JPbio/small_RNA_MetaVir/). Plots were generated in R using ggplot2 v3. 3. 5 package. For manual curation of putative viral contigs, top five BLAST and DIAMOND hits were analyzed to rule out the similarity to other organisms; ORF organization and small RNA profiles (size distribution and coverage) were analyzed to differentiate exogenous from endogenous viruses and check for inconsistencies. Contigs containing truncated ORFs and.
, 1996; Yang et al. , 1998). Each ecotin monomer inhibits its respective target via binding at two different surface contact sites: a primary and a secondary site  (McGrath et al. , 1994; Yang et al. , 1998). This 1:1 stoichiometric configuration of two ecotin monomers for two protease units is unique among all the known structures and mechanisms of serine-protease inhibitor complexes (Figure  1A ;  Yang et al. , 1998). Therefore, ecotin does not belong to one of the already established serpin families and has been classified in the MEROPS database as inhibitor family I11, clan IN  (Rawlings et al. , 2018). Interestingly, ecotin does not target endogenous E. coli proteases, and is therefore unlikely to be involved in the regulation of protease activity in this organism  (Eggers et al. , 2004).
(A) More than six hundred species are present throughout the Tree of Life and encode at least one ecotin homolog. Protein sequences were extracted from InterPro (query: IPR036198) and validated as belonging to the same orthogroup with eggNOG-Mapper (E-value: 0. 0001, minimum bit score: 60, % identity >40, query coverage >20%;  Blum et al. , 2021; Cantalapiedra et al. , 2021). Orthology assignments were double checked in EggNOG database using EggNOG OGs. Remaining protein sequences were checked by the presence of ecotin domains as predicted by Pfam using eggNOG-Mapper  (Mistry et al. , 2021). One sequence for each species was retained, after which they were further aligned based on their amino acid sequence using MUSCLE  (Edgar, 2004 ) in MEGA11 (Tamura et al. , 2021). (A) Among Bacteria, the class of Proteobacteria (502 species) represents the majority of ecotin-expressing species.
Note that this analysis is not comprehensive and homologs may have been missed due to biases in database representation and/or search parameters. (B) Among the Eukaryotes, both the Trypanosoma and Leishmania species, belonging to the Kinetoplastida class, contain over 10 species that are causative agents of several and widespread infectious diseases. The figure was made using KronaTools 2. 7. 1  (Ondov et al. , 2011). (C) Unrooted phylogenetic tree of ecotin orthologs. Only one representative sequence per identified EggNOG OG was retained. Sequences were aligned based on their amino acid sequences using MUSCLE  (Edgar, 2004)   Frontiers in 04 frontiersin. org paralogs, named ISP1, ISP2 and ISP3  (Eschenlauer et al. , 2009; Morrison et al. , 2012). In L. major, ISP1 is located on the same transcription unit upstream to ISP2 and ISP3  (Eschenlauer et al.
Funding AC acknowledges support from the Flemish Fonds Wetenschappelijk Onderzoek under grant G017717N. AC also acknowledges support from the French National Research Agency under grant agreement ANR-19-TERC-0004-01 and from the French Laboratory of Excellence project "TULIP" (ANR-10-LABX-41; ANR-11-IDEX-0002-02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
HPLC/MS-MS Analysis High-performance liquid chromatography was performed using an Agilent 1290 Infinity. The analytical column was a ZorbaxSB-C18 column (2. 1 mm, 50 mm, 1. 8 µm) (Agilent Technologies) maintained at 40 • C. The mobile phases consisted of water, acetonitrile, and formic acid (75:25:0. 1; v/v/v) (A) or (0:100:0. 1, v/v) (B). The linear gradient was as follows: 0% B at 0 min, 85% B at 8. 5 min, 100% B at 9. 5 min, 100% B at 10. 5 min, and 0% B at 12 min. The flow rate was 0. 35 mL/min and the injection volume was 5 µL. The HPLC system was coupled on-line to an Agilent 6460 triple quadrupole MS (Agilent Technologies). Electrospray ionization was performed in negative ion mode. Analyses were performed in selected reaction monitoring detection mode. Peak detection, integration, and quantitative analysis were conducted using Mass Hunter Quantitative analysis software (Agilent Technologies) via correlation with the IS response.
Acknowledgments The authors are grateful to Guillaume Martin for several insightful comments. They thank the Center for Interdisciplinary Research in Biology (CIRB, Collège de France) for funding, as well as the MESRI (French Minister of Research) and the Polytechnique for the PhD scholarship of JG. [1] Sören Abel, Pia Schulz Zur Wiesch, Brigid M. Davis, and Matthew K. Waldor. Analysis of bottlenecks in experimental models of infection. PLOS Pathogens, 11(6):e1004823, jun 2015. 13.
Search strategy and study selection A systematic review was performed in the electronic databases MEDLINE (PubMed), EMBASE, and Cochrane Library, with the following search terms: "ketogenic" AND ("refractory status epilepticus" OR "super refractory status epilepticus" OR "intensive care unit" OR "new onset refractory status epilepticus" OR "NORSE" OR "febrile infection related epilepsy syndrome" OR "FIRES"). The relevant studies have been selected with no date restriction, including children and adult patients. The reference lists of the included articles were also searched manually to find any additional eligible papers. The search was up to date as for the 2nd October 2022. The results of this systematic review were reported according to the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement  (14).
All study designs with individual details, including at least one patient of any age with SRSE in whom KD was started, have been included. Duplicate records were excluded. Reviews, meta-analyses, editorials, commentaries, and expert opinions were excluded. Titles and abstracts were screened for study eligibility, and full-text articles were reviewed by SM and PDL. Any disagreement was resolved by discussion with a third review author (RN). For each selected study, the following data were extracted on individual bases when available: age at SRSE onset, gender, previous history of epilepsy, etiology of SRSE, number of treatments (ASMs and anesthetic agents) prior to KD start, other treatments (i. e. , steroids) prior to start KD, the time lag from SRSE onset to KD initiation, fasting at KD initiation, KD ratio, time to achieve ketosis, KD efficacy to stop SRSE, time to SRSE resolution after KD initiation, length of KD, side effects, number of treatments at hospital discharge, time of follow-up, and outcomes.
Data analysis Demographic and SE characteristics were summarized by standard descriptive measures. The primary outcome was the responder rate, defined as clinical and electroencephalographic (EEG) resolution. Kaplan-Meier survival curves were generated for the time-to-KD response. As secondary outcomes, Cox proportional hazard models were created to assess the impact of the following factors on KD efficacy: age at SRSE onset, gender, previous history of epilepsy, etiology, the clinical presentation with NORSE/FIRES, number of treatments prior to KD, the time lag from SRSE onset to KD initiation, fasting at KD initiation, KD ratio, time to achieve ketosis from KD initiation, and side effects. A p-value ≤ 0. 05 was considered statistically significant. Data were analyzed using STATA/IC version 15 (StataCorp LLC, College Station, TX, USA).
7, 32    The essential oil was fractionated on a silica gel column with a hexanes/methylene chloride eluent system, and fractions 25-31 contained over 90% ascaridole [sum of ascaridole and isoascaridole in GC/FID is 93. 0%, and no isoascaridole signal is observed in nuclear magnetic resonance (NMR)]. This fraction was characterized to properly identify ascaridole as the main compound of the essential oil and of this fraction. Ascaridole characterization and structure confirmation were done by GC-MS, polarimetry, and NMR ( 1 H,  13  C, COSY, HSQC, HMBC, and DEPT) (see data below). The NMR spectra are presented in the Supporting Information. The experimental polar LRIs we observed for ascaridole are quite different from the reference in the NIST 14 library; no polar LRI was to be found in the Robert P.
The mass range was 50-500 Da. The ionization energy was 70 eV. Data acquisition, instrument control, and processing were achieved with Thermo Scientific software (Excalibur for instrument control and acquisition and QualBrowser for processing). Compounds were identified by comparing mass spectra and LRIs to GC-MS commercial spectral libraries (FFNSC 3 (Wiley),  40  Robert P. Adams' library,  39  NIST 14,  41  and ESO 2000  42  ). The alkane standard for LRI determination was a C7-C30 saturated alkane solution (Millipore Sigma, 49451-U) for both columns. C4-C24 even carbon numbered fatty acid ethyl esters (FAEEs) and fatty acid methyl esters (FAMEs) standards (Millipore Sigma, 49454-U and 49453-U) were also used for polar column analysis. LRIs were calculated using the equation by Van den Dool and Kratz.
79  The relative percentages of compounds in total extracts were calculated with data obtained from GC/FID analyses and peak integration without correction factors. The GC/FID instrument was a Trace GC Ultra (Thermo Scientific) with a TriPlus autosampler (Thermo Scientific). The column was DB-5MS, 30 m × 0. 25 mm × 0. 25 μm. The FID temperature was 300 °C [gas flows: air = 350 mL/min; H 2 = 35 mL/min; and N 2 (makeup) = 30 mL/min], and the injection port temperature was 170 °C. The temperature program and other settings were the same as used for non-polar phase GC-MS analysis. The analysis of fractions recovered from flash chromatography was performed as described above for the essential oil sample with the following changes: a Trace Ultra GC-MS was used with an ITQ 900 MS detector, with a gradient from 50 (5 min hold time) to 250 °C (5 min hold time) at a 10 °C/min rate.
00 (6H, d, J = 7 Hz), 1. 37 (3H, s), 1. 45-1. 58 (2H, m), 1. 92 (1H, sept, J = 7; 6. 95; 6. 9 Hz), 1. 97-2. 11 (2H, m), 6. 41 (1H, d, J = 8. 5 Hz), 6. 49 (1H, d, J = 8. 5 Hz);  13    (26), 79 (24), 97 (22), 91 (21), 107 (17), 92 (15), 77 (15), [M] + = 168. 05. Optical rotation and spectral data were in accordance with previous reports. 17, 39, 53, 80  Flash Chromatography Fractionation. Fractionation of R. subarcticum essential oil was done by flash chromatography on a silica gel column (Silicycle, SiliaFlash P60, 40-63 μm) using a hexanes/methylene chloride (both purified using the VAC 103991 solvent purification system) gradient (50 mL each: 90/10, 70/30, 50/50, 20/80, and 0/100). The essential oil (500 mg) was fractionated on a 30 g silica gel column, and fractions were collected in 5 mL volumes.
■ ACKNOWLEDGMENTS The authors wish to thank the  Whapmagoostui Cree Nation Council and Kuujjuarapik Inuit Community Council  for their suggestion of the dwarf Labrador tea as an interesting plant to investigate and for sharing their knowledge about this shrub and its traditional uses. Without the discussions with representatives from the local communities, we would not have investigated this plant. The authors also wish to thank the  Natural Science and Engineering Research Council of Canada (NSERC) ,  Fonds de Recherche du Québec�Nature et Technologies (FRQNT), Sentinel North , and  IDEX UCA jedi  for financial support and the  Center for Northern Studies  for privileged access to the Research Station at Boniface River. J. -C. S. acknowledges the  FRQNT, Sentinel North , and  MITACS  for scholarships.
Objective To evaluate survival, hospitalisations and surgical procedures for children born with Pierre Robin sequence (PRS) across Europe. Design Multicentre population-based cohort study. Setting Data on 463 live births with PRS from a population of 4 984 793 from 12 EUROCAT congenital anomaly registries. Methods Data on children with PRS born 1995-2014 were linked electronically to data on mortality, hospitalisations and surgical procedures up to 10 years of age. Each registry applied a common data model to standardise the linked data and ran common syntax scripts to produce aggregate tables. Results from each registry were pooled using random-effect meta-analyses. Main outcome measures Probability of survival, proportion of children hospitalised and undergoing surgery, and median length of hospital stay.
METHODS This is a EUROlinkCAT population-based data-linkage cohort study. The EUROlinkCAT project aimed to evaluate health outcomes in children with CAs up to 10 years of age by linking data on liveborn children registered in EUROCAT registries  10 11  to data in healthcare databases (eg, mortality, hospital admission and discharge data). Linked data were included up to the child's 10th birthday or to 31 December 2015 (whichever was earlier). 12 EUROCAT registries collect standardised data on all major CA cases in their population using multiple sources of ascertainment according to EUROCAT guidelines (EUROCAT Guide V. 1. 5, https://eu-rd-platform. jrc. ec. europa. eu/eurocat/ data-collection/guidelines-for-data-registration_en#inline-nav-2). All registries with the ability and capacity to link to their mortality and hospital discharge databases were included in the EUROlinkCAT project.
12 he study included data from 12 registries in nine European countries (table  1 ) covering different time periods between 1995 and 2014. The different time periods were due to registries having different years of EUROCAT membership and that only years with good quality healthcare data and high levels of linkage were included. 13 Three registries (Norway, Wales and Malta) were national registries covering the whole country. Four registries covered all 20 birth years of the study period. All liveborn children with PRS during the specified birth years were included. For the investigation of survival rates, data on mortality were obtained through linkage with vital statistics and mortality databases. ] [16]  Data on hospitalisations and surgical procedures were obtained by electronic linkage to the hospital databases used in the regions and countries covered by the registries.
For three participating registries (ie, Paris, Norway and Malta), data on hospitalisations were not available for this study. Indicators of hospitalisation in children with PRS were compared with those in (1) all children born with any CA and (2) reference children without a CA, previously calculated by the EUROlinkCAT project. 17 Reference populations were all liveborn children without CAs from the same population covered by the registry in the same birth years. The Tuscany and Northern Netherlands registries used a random sample of their population (10% and 20%, respectively). No reference children were available for the three English registries. A detailed description of the EUROlinkCAT methods on hospitalisations has been published elsewhere. 17.
Statistical analysis The EUROlinkCAT common data model standardised the linked variables obtained by each participating registry. Common Stata syntax scripts were run by all registries to check the quality of data linkage and to analyse the data. Aggregated data and analytical results were uploaded to the Central Results Repository based at Ulster University (UK) and then transferred to the research team using a secure web platform. 12 ithin each registry, Kaplan-Meier survival analyses were performed to account for censoring, that is, children who were lost to follow-up due to death or emigration from the study area or who had not reached their 10th birthday by 31 December 2015. The Kaplan-Meier survival estimates with 95% CIs from each registry were combined in a random-effect meta-analysis using a modified method by Combescure et al  18  to estimate the overall survival for children with PRS at the following ages: 1 and 4 weeks and 1, 5 and 10 years.
In addition, the 10-year survival conditional on having survived at 4 weeks was estimated. The length of stay (LOS) in the hospital was calculated as the number of days spent in hospital between the date of admission and the date of discharge. For hospital stays in which the date of admission and discharge occurred on the same day, the LOS was considered to be 0. 5 days. The median LOS per year, for those with at least one admission, was calculated within each registry and random-effect meta-analyses were performed using the 'metamedian' package in R V. 4. 0. 3 for the following age groups: <1, 1-4 and 5-9 years. The aforementioned methods were also used to estimate the median age at first surgery and the median number of surgical procedures for the following age groups: <1, 1-4 and 0-4 years.
Hospitalisation Almost all children with PRS were admitted to the hospital within the first year of life. The 0. 8% without a hospital admission may have died shortly after birth and/or were not linked to the hospital databases. Hospital admissions reduced with age, but 60% of the children had at least one hospital admission at age 5-9 years with a much shorter median LOS compared with children admitted in the first year of life. The number of hospitalisations of children with PRS exceeded those for all children with any CA at all ages. Stubenitsky et al reported that LOS was higher in children with respiratory disorders and feeding problems. 26 A study by Lee et al on infants admitted to a tertiary referral centre with failure to thrive due to airway obstruction or feeding difficulties reported an average primary LOS of 64 days.
Original research About of the children were admitted to ICU and 14% needed a ventilator within the first 5 years. These children may represent the proportion of patients with major respiratory complications. These proportions are likely to be underestimated as there were some difficulties in defining the treatment codes used for the registration in the hospital databases. Furthermore, we did not have information about home mechanical ventilation. We are not aware of other studies that investigated ICU admissions or mechanical ventilation use. Effective and timely clinical management, including an appropriate surgical treatment, is fundamental to ensure an adequate level of quality of life especially during childhood and adolescence. 6 32.