dataesr/scientific-paragraphs-categorization huggingface dataset:
Although many hypocenters were also manually computed using the CVGHM network during the crisis, these were used primarily to verify and supplement BMKG solutions and were not consistently catalogued. The description of activity below is a brief summary of the observed seismicity from all data sources. A swarm of earthquakes (M2. 3-3. 9) was recorded in mid-May 2017, located NW of the Batur caldera, with a maximum reported intensity of MMI III. After several months of gradual increases, earthquake rates and seismic energy increased rapidly between 16 and 22 September 2017 from tens of earthquakes per day to hundreds of earthquakes per day (Fig. 2 ). Felt reports and seismic-wave-arrival times on local stations suggested that the observed volcano-tectonic (VT) earthquakes were located between Mount Agung and Batur Caldera (i.
In retrospect, by this time, magma was clearly invading the upper levels (<5 km) of the Mount Agung edifice. VT and LF earthquakes continued at low rates and RSAM values gradually increased through the first phreatomagmatic eruption on 21 November, but the eruption itself was not recorded seismically. More tremor was recorded a day after the 21 November phreatomagmatic eruption, and VT and LF event rates continued at low levels. The onset of magmatic eruption was preceded by a swarm of 22 larger LF earthquakes on the morning of November 25 local time, although the onset of lava effusion, which was first detected in satellite data the same day, was not recorded seismically. After the onset of effusion, earthquake rates and RSAM values continued at pre-eruptive levels until a significant increase on 8 December.
After the first explosive activity on 21 November, satellite data detected a new 100-m-diameter crater centered in the larger summit crater that served as the conduit for subsequent eruptions. Ash samples from the 21 November event include minor juvenile components, but are dominated by remobilized edifice lithic material (Fig. 4D, E ). Collected bulk ash samples were analyzed for their major-element chemistry and had bulk chemistry of andesite. Sequential sampling revealed an apparent increase from 55 to 59 wt. % SiO 2 in bulk composition of the erupted ash from 22 November 2018 to 29 November 2018. Semi-quantitative analyses of juvenile glass confirmed an andesitic composition. A small lava flow was first observed within this crater on 25 November and by 27 November had covered the crater floor (Fig.
2D ). Three different drone flights on 23 and 24 November found large CO 2 anomalies (ΔCO 2 = 49-98 ppmv), very low SO 2 mixing ratios (SO 2, MAX = 0. 55 ppmv on 23 November; 0. 05 ppmv on 24 November), and trace H 2 S (<0. 17 ppmv on 24 November. These data showed that gas emissions were very CO 2 -rich and S-poor, and average molar CO 2 /SO 2 ratios increased dramatically from 77 to 824 on 23-24 November prior to the start of the main magmatic explosive phase at 9:20 UTC on 25 November (Fig. 2F ). The highest SO 2 emission rate was measured on 26 November (5,500 t/d) but quickly fell to 180 t/d by 1 December. Gas emissions during lava effusion in December were highly variable (SO 2 = 140-1500 t/d; monthly median = 390 t/d, n = 14) and magmatic in character; a drone flight on 19 December intercepted a dense plume with clear H 2 O, CO 2 , and SO 2 peaks (H 2 O/CO 2 = 21, CO 2 /SO 2 = 3.
Toward the end of the period 12-22 November, magma reached shallow depths (<1-2 km) and CO 2 was detected with multi-GAS drone flights, but SO 2 was not detected during DOAS traverses due to scrubbing by the groundwater system. We currently lack both seismic and geodetic data to constrain the shallow plumbing system for final ascent of magma to the surface. 4. The eruption began on 21 November with phreatomagmatic explosions, and high SO 2 emissions were measured. On 25 November a small lava flow was detected in the crater, coincident with continued explosions. By the end of November, a 24 million m 3 lava flow filled about one-third of the crater volume. Ash-rich explosions through the lava continued over subsequent months. Initially, cracks and explosion craters that formed in the flow were filled with lava, but as the flow stiffened with time, subsequent cracks remained unhealed.
All three of these trees placed equal conditional probabilities of VEI 0-1 and VEI 2-3 (each at 45%) scenarios over the 2-week interval and only a 10% probability of a VEI 4 or greater (i. e. , another 1963-size event), if an eruption were to occur. These probabilities were based on the global eruption magnitude-frequency distributions modified by the current rate and style of seismicity, and analogy with characteristics of the 1963 eruption. As the crisis continued (mid-October to November), additional monitoring streams aided short-term forecasting efforts, including the GNSS data retrieved in early to mid-October and initial InSAR data that were processed, corrected, and interpreted by mid-November. Eruption likelihoods were estimated at 50% and 40% on 17 October and 15 November, respectively, as time since peak seismicity increased and the possibility of waning activity was increasingly considered.
However, uncertainty (±20%) also increased over previous trees due to slow rates of change in seismicity and increasing duration of unrest without eruption. Conditional probabilities for eruption magnitude remained the same as in earlier trees because their basis remained the same, but were subdivided, placing VEI 0-1 at 45%, VEI 2 at 25%, VEI 3 at 20%, and VEI 4-5 at 10%. The 15 November tree further highlighted a phreatic eruption scenario, which was deemed to be the most likely (80%) conditional eruptive scenario. Both trees preceded the addition of drone-assisted multi-GAS geochemical measurements, the results of which would have increased expert estimation of eruption probability, and the first of which was rapidly followed by eruptions on 21 November. For all of these event trees, forecasts of PDC runout relied on comparisons with global data from the FlowDat database  27, 28  , energy cone models, and past runout of PDC's during the 1963 eruptive sequence.
Acknowledgements Ignasius Jonan  ( Minister of Energy and Mineral Resources of Indonesia ) and  Rudy Suhendar  ( Head of Indonesian Geological Agency)  supported the CVGHM team including facilitating the drone missions. CVGHM receives funding from the  Ministry of Energy and Mineral Resources of the Republic of Indonesia. For their efforts in the field and at the observatory, we thank Agung volcano observers ( I Dewa Made Merthe Yasa ,  I Gede Sudarsana ,  Anwar Sidiq ,  I Nengah Wardana ,  Wahyu Ardi  and  Nurul Husaeni ), Batur volcano observers ( Anak Agung Anom Karsana ,  I Gede Bagiarta ,  I Nyoman Gina Wijaya ,  Achmad Nurin Kausar  and  Maryani ), technician team ( Ferry Rusmawan ,  Charles Yulius ,  Sulus Setiono ,  Syarif Abdul Manaf ,  Anna Mathovanie  and  Hartati ) and socialization team ( Agus Budianto ,  Agus Solihin ,  Nia Haerani ,  Nugraha Kartadinata ,  Imam Santosa  and  Mamay Surmayadi ).
All VARS variants were deemed pathogenic based on their absence or presence in very low frequency in ExAC and the Genome Aggregation Database (gnomAD)  26  , impact on protein level, different prediction tools, and segregation (Supplementary Table  1 ). All identified variants were located in the catalytic or the anticodonbinding domain of the protein with the exception of the frameshift variant, which was not located in a specific domain (Fig. 1b ). In silico modeling in T. thermophilus ValRS. To gain insights into the potential structural and functional consequences of the human missense variants, the sequence of the human enzyme was aligned to ValRS sequences from various taxa (Supplementary Figure  1 ), including the T. Thermophilus ValRS sequence, whose structure has been determined in complex with its cognate tRNA  27, 28.
3b ). Absence of vars in vars-/-larvae led to premature death between 8 and 12 dpf (vars+/+ and vars+/-siblings remained alive), suggesting an essential role for VARS in survival (Fig. 3c ). At 7 dpf about 35. 3% of vars-/-larvae showed no touch response, which was in marked contrast to the increasing touch response demonstrated by vars+/+ and vars+/-over the course of development (Fig. 3d ). Loss of posture could be observed in about 88. 2% of vars-/-larvae already at 6 dpf (Fig. 3d ) and from 6 to 8 dpf ~50% of vars-/-larvae displayed abnormal motor behavior such as jerky spasmodic movements during touch response, in contrast to vars+/+ and vars+/-(data not shown). Severe morphological abnormalities were observed in vars-/-larvae from 3 dpf onwards, which were progressing over the course of time.
3f  and Supplementary Data 2). Measurements taken from different head areas identified significant reductions (p < 0. 0001, one-way ANOVA) in head and eye size at 3 dpf (Fig. 3g, i ), that became even more prominent at 5 dpf, where also the brain size was smaller compared to vars+/+ and vars+/-siblings (Fig. 3g-i ). To determine whether the microcephaly was due to excessive cell death in the brain, we assessed apoptosis by using antibody to active caspase-3. There were significantly more apoptotic cells detected in 3-5 dpf vars-/-brains (p < 0. 001, one-way ANOVA) than in those of their +/+ and +/siblings (Supplementary Figure  5b ), whereas no statistically relevant difference was observed at 2 dpf. Collectively, these results suggest that loss of vars expression compromises zebrafish head and eye development and that Vars is essential for neuronal survival.
This interpretation is further supported by the fact that parents of patients with recessive VARS-associated phenotypes, who carry the mutation in a heterozygous state, are consistently reported to be phenotypically normal. Indeed, a 50% reduction in VARS activity can be tolerated without significant pathology, which is also supported by the presence of heterozygous truncating variants in public databases like ExAC and gnomAD  26. Noteworthy, pathogenic variants in other genes that encode proteins with a prominent role in translation, can cause similar neurological disease traits to the ones associated with pathogenic variants in ARSs. For instance, CLP1, which encodes an RNA kinase responsible for tRNA splicing required for tRNA maturation, causes microcephaly in humans, mice and zebrafish and peripheral neuropathy in humans  38, 39.
Families 3 and 6 were ascertained through the program Gen-eMatcher  24. The seven novel VARS variants were all identified with WES or WGS in patients for whom standard diagnostic work-up failed to identify the cause of their neurodevelopmental phenotype. Variant filtering was done through locally developed pipelines taking into account the quality of the variant calling, presence in population databases, predicted impact on the encoded protein and segregation of the variants. VARS transcript NM_006295. 2 was used for variant nomenclature. Clinical information was collected using standardized clinical templates that were completed by collaborating clinicians and geneticists. International League Against Epilepsy (ILAE) criteria were used for epilepsy syndrome classification when applicable  41.
In silico modeling of VARS variants. The protein coding sequences of valyl-tRNA synthetases (VARS) were extracted from the UniProt server. The organisms and the UniProt accession numbers for their VARS sequences are as follows: Escherichia coli (E. coli), P07118; Thermis thermophilus (Thermis), P96142; Saccharomyces cerevisiae (yeast), P2637; Drosophila melanogaster (fruit fly), Q0E993; Caenorhabditis elegans (worm), Q23360; Danio rerio (zebrafish), F1Q740; Mus musculus (house mouse), Q9Z1Q9; Homo sapiens (human), P26640. Multispecies alignments were generated by use of Clustal Omega  42. The alignment was further annotated in the protein ENDscript  43  with secondary structures derived from the structure of the ValRS-tRNA Val from Thermis thermophilus (PDB ID: 1IVS) as reported earlier  27, 28.
The alignments were used to identify residues in the Thermis thermophilus complex corresponding to the residues altered by the VARS mutations, and then the resulting structures were rendered in space filling or stick representation using the program PyMOL (The PyMOL Molecular Graphics System, Version 1. 2r3pre, Schrödinger, LLC). Isolation of patient-derived cell lines and cell culture. Skin biopsies of patients 4 and 5 of family 3 (p. Leu78Argfs*35/p. Arg942Gln) and of a control individual were obtained following the local standard protocol and fibroblasts lines were generated. Fibroblasts, continuously kept at 37 °C in a humidified atmosphere with 5% CO 2, were cultivated in Dulbecco's Modified Eagle Medium (DMEM), high glucose (Gibco) enriched with 10% heat-inactivated fetal bovine serum (Gibco), 1% L- glutamine (Life Technologies), 1% penicillin-streptomycin (Life Technologies).
The density of the resulting bands, corrected for loading, was quantified using ImageJ and statistical significance assessed by one-way ANOVA with Bonferroni's multiple comparisons test. The following primary antibodies were used: anti-VARS antibody (1:2500, Atlas Antibodies, HPA046710) and anti-alpha-tubulin (1:5000, Abcam, ab4074). The following secondary antibodies were used: anti-rabbit HRP-conjugated (1:10,000, Promega, W401B), antimouse HRP-conjugated (1:10,000, Southern Biotech, 1070-05). Uncropped scans of blots are available in Supplementary Figure  7. qPCR of cycloheximide-treated cells. Confluent T75 flasks of fibroblasts of patients 4, 5 and a control individual were treated for 6 h with (i) cycloheximide (CHX) (150 µg/mL), with (ii) dimethyl sulphoxide (DMSO) as a negative solvent control, or (iii) without treatment.
The ΔΔCq method was used to determine the relative levels of mRNA expression between experimental samples and The results consist of data from at least two separate experiments where samples were run in triplicate. One-way ANOVA with Tukey's multiple comparisons test was used to determine statistical significance. Immunocytochemistry. For immunofluorescence (IF) staining of intracellular VARS protein, 50,000 fibroblasts of patients 4, 5 and a control individual were seeded on 12 mm diameter coverslips and 24 h later fixed with 4% paraformaldehyde (PFA) for 20 min at RT. Fibroblasts were permeabilized with 0. 5% Triton X-100 in phosphate-buffered saline (PBS) for 2 min, blocked with 0. 5% bovine serum albumin and 0. 2% goat serum for 1 h and incubated overnight at 4 °C with following primary antibodies: anti-VARS protein (1:500; Atlas Antibodies, HPA046710), anti-KDEL (1:100; Enzo Life Sciences, 10C3), anti-Golgin-97 (1:200, Life Technologies, A21270), and anti-TOMM20 (1:200, Abcam, ab56783).
Lysis was performed at 55 °C for 3 h, followed by 10 min at 95 °C. Lysed samples were genotyped by performing a PCR to amplify a 466 bp-region of interest (containing vars 4 bp deletion) using Titanium® Taq DNA Polymerase (Takara) and vars-specific primers (Supplementary Table  3 ). Successfully amplified PCR products were purified using ExoProStar (Illustra™) and Sanger sequenced with the same primers used for amplification. The genotypes of the individual larvae were analysed using SeqMan software (LaserGene). mRNA extraction and RT-qPCR for zebrafish studies. Total RNA from 1, 3, and 5 dpf vars+/+, vars+/-, and vars-/-larvae, respectively, was extracted using TRIzol (Ambion, Life Technologies). Residual genomic DNA was removed by treatment with DNase I (Roche) with Protector RNase inhibitor (Roche).
Reverse transcription of total RNA to single-stranded cDNA was performed on 1 μg of total RNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) and further diluted 1:20. Real-time PCR was performed in HardShell ® Low-Profile Thin-Wall 96-Well Skirted PCR Plates (Bio-Rad) using CFX96 Touch Real-Time PCR Detection System (Bio-Rad). Primer and probe sequences for realtime detection of endogenous vars, as well as injected human WT VARS were custom-made (Supplementary Table  3 ). Reaction mixture containing diluted cDNA template, primers and 2x SsoAdvanced Universal SYBR Green Supermix (Bio-Rad) was amplified under cycling conditions according to the manufacturer's protocol. Data generated were analysed using CFX Manager Software (Bio-Rad). vars transcripts were normalized against ribosomal protein S18 (rps18) housekeeping genes that were experimentally determined to have the most stable expression in our reaction conditions.
Primer and probe sequences for real-time detection of vars in Hi558Tg line were purchased from IDT (Supplementary Table  3 ). 2x TaqMan Universal Master Mix (ABI, USA) was used for the reaction. vars transcripts normalization was done against elongation factor 1-alpha (ef-1 alpha) and rps18. The ΔΔCq method was used to determine the relative levels of mRNA expression between experimental samples and controls. The results consist of data from at least two separate experiments run in triplicate. One-way ANOVA with Tukey's multiple comparisons test was used to determine statistical significance. Morphological studies in vars-/zebrafish larvae. Surviving vars+/+, vars+/-, and vars-/-larvae were counted daily and examined for major dysmorphologies, such as edema, head, and eye malformations, and for the presence of touch response, from 1 until 12 dpf.
Dead larvae and all larvae from 12 dpf onwards were collected, stored at -80 °C and genotyped. For head size measurements, vars+/+, vars+/-, and vars-/-larvae were positioned in 3% methylcellulose. Lateral images of the head and the whole body of 3 and 5 dpf larvae were acquired using Leica MZ 10F fluorescence microscope with a Leica DFC310 FX digital camera and Leica Application Suite V3. 6 software. Measurements were done blinded, manually in ImageJ software. Body length was measured from the anterior tip of the snout to the base of the posterior caudal fin. Head, brain, and eye areas were measured by tracing the boundary of the surface of interest using some predetermined spots on the head such as the otic vesicle or dorsal indentation just above the eye, at the level of the pineal gland.
The specimens were stained with hematoxylin and eosin (H&E stain) using Varistain™ Gemini ES Automated Slide Stainer (Thermo Fisher Scientific) according to laboratory protocols. The resulting sections were imaged at ×20 magnification in a SPOT 5. 1 software (SPOT Imaging) by a SPOT-RT3 camera mounted on a Leica microscope. Brightness of the images was adjusted for the white background. Immunohistochemistry for active caspase-3. IHC detection of cell death was carried out on 5-μm-thick deparaffinised and rehydratated sections. Prior to IHC, the specimens were subjected to heat-induced antigen retrieval by incubation in 10 mM sodium citrate (pH 6. 0) for 10 min at 98 °C, followed by a 30 min cool down and treatment with 3% hydrogen peroxide (2 × 8 min). The sections were blocked for 30 min in 5% normal goat serum in 1X TBST, and further incubated with primary antibody against active caspase-3 (BD Biosciences, Clone C92-605, 1:500 dilution) for 1 h at RT.
After rinsing with 1X TBST, HRP-conjugated secondary antibody (Jackson ImmunoResearch, 111-035-003, 1:200 dilution) was applied for 1 h at RT. Next, the slides were treated with DAB+/chromogen (DAKO) for 1 min at RT and rinsed with deionized water. Nuclear counterstain was performed in hematoxylin for 3 min. After clearing in ethanol and histoclear, the slides were coverslipped under mounting medium. For each staining a negative control was included by processing sections in the absence of the primary antibody. The images were taken at ×40 magnification in a SPOT 5. 1 software (SPOT Imaging) by a SPOT-RT3 camera mounted on a Leica microscope. Three to four equivalent sections were selected for each group and DAB positively stained nuclei were counted using Fiji. The results were expressed as percentage of apoptotic cells of the total cell number within a selected brain area.
Results were analysed using one-way ANOVA followed by Tukey's multiple comparisons test. Behavioral studies in vars-/zebrafish larvae. For the locomotor tracking, 3-7 dpf vars+/+, vars+/-, and vars-/-larvae were individually arrayed in a 96-well plate. After 30 min habituation, the larvae were placed in an automated tracking device (ZebraBox TM , Viewpoint, Lyon, France) and their locomotor behavior was followed for 1 h under dark conditions. The total movement was quantified using ZebraLab software (Viewpoint, Lyon, France) and expressed in actinteg units. The results were analysed by one-way ANOVA with Tukey's multiple comparisons test. For the habituation assay, 6 dpf vars+/+, vars+/-, and vars-/-larvae were individually arrayed in a 96-well plate and equilibrated for 3 h in a uniformly illuminated testing chamber in an automated video-tracking device (ZebraBox TM , Viewpoint, Lyon, France).
25 mM KH 2 PO 4 , 26 mM NaHCO 3 , and 10 mM glucose) and placed on larva's head above the optic tectum. The recordings were performed using WinEDR (John Dempster, University of Strathclyde, UK). Differential signal was amplified 10,000 times by DAGAN 2400 amplifier (Minnesota, USA), band pass filtered at 0. 3-300 Hz and digitized at 2 kHz via a PCI-6251 interface (National Instruments, UK). All the larvae used for LFPs displayed touch response. The duration of each recording was 10 min. An electrical discharge was classified as a positive event when its amplitude was at least three times the amplitude of the baseline, and had a duration of at least 100 ms. The analysis of the epileptiform events was done using automated detection software that was previously developed and validated by our group  46.
VARS rescue experiments. Full-length wild-type human VARS cDNA (GenBank BC012808. 2 from IRAUp969E0949D clone purchased from Source BioScience, UK) was cloned into a pCSDest vector (Addgene) using Gateway recombination technology according to the manufacturer's instructions (Life Technologies) (WT VARS-pCSDest). Single nucleotide variants, leading to substitutions p. Gln400Pro, p. Arg942Gln, and p. Arg1058Gln at protein level, were introduced into WT VARS-pCSDest vector via site-directed mutagenesis using PWO SuperYield DNA polymerase (Roche) and primers containing given variants (Supplementary Table  3 ). Subsequent DpnI digestion was done to remove parental plasmid. All templates were verified by direct Sanger sequencing. Wild-type, p. Gln400Pro, p. Arg942Gln, and p. Arg1058Gln VARS mRNA was transcribed from linearized template plasmids using the SP6 mMessage mMachine® kit (Ambion) and purified by lithium chloride precipitation (Ambion).
The rescue experiment was performed by cytoplasmic microinjection of 200 pg of WT or mutant VARS and GFP mRNA as control (1 nL volume) into 1-cell-stage vars-/-embryos. Following the injections, at 24 hpf only the healthy-looking embryos with normal morphology were selected for subsequent experiments (survival, behavioral tracking, and head measurements). Statistical analysis. Data are presented as mean ± SD or mean ± SEM. Pairwise statistical significance was calculated with Student's unpaired t-test or Mann-Whitney test for data that failed the normality test and multiple comparisons were determined with one-way ANOVA with Tukey's test, using GraphPad Prism7 software.
Acknowledgements We would like to thank and acknowledge all patients and their families. We further want to thank  Jolien Roovers  and  Pascal Simoens  for their aid with sequencing of the zebrafish larvae and the cloning experiments;  Michiel Krols ,  Sven Bervoets  and  Bob Asselbergh  for their help with western blots and microscopy. We acknowledge the contribution of  Peter De Rijk  (as developer of  GenomeComb-Antwerp pipeline ) and the  HPC  facilities of the  University of Luxembourg  (http://hpc. uni. lu) for computational support and the  VIB Genetic Support Facility  for the zebrafish sequencing (https://www. molgen. ua. ac. be/Public/Organization/NSF/GSF. cfm). We also thank the  Skeletal Biology and Engineering Research Center (KU Leuven, Belgium ) (L. - A. Guns ,  A. Hens ,  L.