dataesr/scientific-paragraphs-categorization huggingface dataset:
Paleomagnetic Measurements and Data Analysis The sample set of  Segal (2003)  was measured in the paleomagnetic lab in the Geophysical Institute of Israel using a 2G cryogenic magnetometer, and in the paleomagnetic laboratory at the University of Rennes, France, using a spinner magnetometer and a Leti cryogenic magnetometer. Part of the sample set of  Hassul (2015)  was measured in the paleomagnetic laboratory at the Helmholtz Centre Potsdam, GFZ Germany using a 2G cryogenic magnetometer. The majority of the data were measured in the paleomagnetic laboratory at the Institute of Earth Sciences, the Hebrew University of Jerusalem using a 2G cryogenic magnetometer. Specimens from all sites underwent progressive demagnetizations with Alternating Field (AF). All the raw measurement data, except the dataset of  Segal (2003)  were translated into the community standard MagIC format  (Tauxe et al.
, 2016)  and merged into a single measurement file. All the data with the exception of  Segal (2003)  were re-analyzed, including previously published data, using the Demag GUI program, which is part of the PmagPy software package  (Tauxe et al. , 2016). Paleomagnetic directions of specimens and site means were calculated using the principal component analysis technique  (Kirschvink, 1980)  and Fisher statistics  (Fisher, 1953). The interpretations follow a fairly strict set of selection criteria listed in Table  2 , accepting only specimens with MAD  (Kirschvink, 1980)  ≤ 5, DANG  (Tauxe and Staudigel, 2004 ) ≤ 5, and sites with n (number of specimen per site) ≥ 8, k  (Fisher, 1953 ) ≥60, and α 95 ≤ 6. The measurement data and the interpretations (except Segal's dataset) are available in the MagIC database (https://www2.
RESULTS AND DISCUSSION The catalog consists of 76 paleomagnetic sites collected from 33 different locations (archaeological sites) in Israel. Forty seven sites passing the acceptance criteria in Table  2  are listed in Table  3 , and their locations are shown in Figure  1B. The declinations and the inclinations of the accepted sites are shown in Figures  3A, B , where the inclination error bar is the α 95 value and the declination error bar is calculated using the equation: △ D = sin -1 sin α 95 cosI , where D is the declination error and I is the inclination. Sites that do not pass the criteria in    Fisher (1953). in Table  4. In the catalog we distinguish between sites that have all their measurement data available in the MagIC database and can be downloaded and re-interpreted by others using different criteria (labeled "this study" in Tables  3, 4  and marked with filled symbols in Figures  1, 3 ) and sites of which we have only the site's mean parameters (labeled  "Segal, 2003"  in Tables  3, 4  and marked with open symbols in Figures  1, 3 ).
Comparison With Sedimentary Data There are several advantages of archaeomagnetism over sedimentary magnetic data. The archaeomagnetic TRM does not suffer from inclination shallowing, lock-in depth, and post-depositional effects associated with depositional remanent magnetization (DRM). Hence, paleomagnetic directions from archaeomagnetism can sometimes provide better precision and age control than sedimentary data. However, sedimentary magnetism provides continuous datasets spanning much larger time intervals than archaeomagnetism. Both types of records are available in Israel and we compare them in Figure  4  that shows data from four Holocene cores available in the GEOMAGIA50 database  (Brown et al. , 2015). Figures  4A-C  show data from three piston cores raised from the Holocene Dead Sea  (Frank et al.
, 2016)  and 71 • (QTMB; Hassul, 2015; this study), considerably higher than the expected geocentric axial dipole (GAD) inclination in Jerusalem (51 • ). We note that one site in  Segal (2003)  dataset (Ceramic kiln from Kfar Menachem, see Supplementary Material) showed an even higher inclination of 81 • around this time. Yet, this site did not pass the selection criterion for the age as the age of the kiln was not supported by any direct dating method, only by a correlation with nearby archaeological sites. The declinations during the Levantine Iron Age Anomaly interval show large scatter in the ninth century with declinations ranging from -3 • to 23 • , and closely grouped values around 5 • in the eighth century. The angle between the archaeomagnetic directions and the axial dipole field (Figure  3C ) show exceptionally high values between 19 • and 22 • around the ninth century in Tel Megiddo.
These are from two sites from  Shaar et al. (2016) (mgq05t1, mgq05t2)  and from two sites from this study (QTMA, QTMB). Today, angular deviations from the axial dipole exceeding 20 • occur only in the southern     hemisphere in the area affected by the South Atlantic Anomaly  (Thebault et al. , 2015; Figure 7 in Shaar et al. , 2016). To inspect how irregular is the angular deviation from axial dipole field during the Iron Age Anomaly, we gathered all the global archaeoamgnetic and volcanic data from the past four millennia from the GEOMAGIA50 database (shown in Figure  1A ). We applied the same acceptance criteria to the global data, and plot on Figure  6  the angular deviation from axial dipole. Only 1% show angular deviations larger than 19 • , demonstrating that the high inclination high declination episode in the tenth-ninth century BCE is a unique phenomenon.
SUMMARY AND CONCLUSIONS We initiate here the first catalog of archaeomagnetic directions from Israel, with 76 sites that have been collected and analyzed since 2003. From this catalog, 47 sites pass a set of strict selection criteria and serve as a basis for future development of a master archaeomagnetic secular variation curve for the Levant. The measurement data of this catalog can be approached from MagIC database (https://www2. earthref. org/MagIC) and the archaeological information is provided in the Supplementary Material of this article. Some misfits with the global models prior to the second half of the first millennium BCE imply that more archaeomagnetic data are needed to refine our knowledge of fast secular variations during early periods in the Holocene. The most prominent feature in the new catalog is the high inclinations and high declination interval in the ninth century BCE.
ACKNOWLEDGMENTS We kindly thank all the archaeologists who helped in the sampling process and provided their most appreciated assistance:  Israel Finkelstein  ( Tel Megiddo ),  Ruth Shahack Gross  ( Tel Megiddo ),  Amihai Mazar  ( Tel Rehov ),  Uri Davidovich  ( Tel Rehov ),  Aren Maeier  ( Tel es-Safi ),  Oded Lipschitss  ( Tel Azekah ),  Sharon Zuckerman  ( Tel Hazor ),  Shlomit Bechar  ( Tel Hazor ),  Amnon Ben-Tor  ( Tel Hazor ),  Rami Arav (Bethsaida) ,.
Strikingly, this transition was abrogated in MZpitx2c mutants (Figure  4g-i ). Endodermal cells in MZpitx2c mutants displayed meandering trajectories rather than oriented migration, as evidenced by decreased overall displacement (Figure  4i ) and a lower straightness index (Figure  4j ), and endodermal cell speed remained the same as during early gastrulation (Figure  4h ). We then examined the anterior endoderm at 24 hpf in the Tg(sox17: GFP) background. Using the level of the fifth pharyngeal pouch as a landmark to measure endodermal width, we observed that it was significantly increased in MZpitx2c mutants compared to wild types (Figure  4m ). Taken together, these data indicate that Pitx2c is required for the transition from random walk to oriented, persistent endodermal cell migration at late gastrulation stages.
Transcriptomic and candidate gene expression approaches identify potential pathways downstream of Pitx2c To screen for genes potentially acting downstream of Pitx2c, we used both transcriptional profiling and a candidate gene approach. We performed microarray analysis on MZpitx2c mutant embryos at shield stage, as well as on dome stage embryos following injection of 25 pg pitx2c mRNA as a gainof-function (GOF) approach (Figure  1 -figure supplement 3), and both sets of embryos were compared to stage-matched controls. We performed gene enrichment and functional annotation analyses on the transcriptomic datasets using the Database for Annotation, Visualization and Integrated Discovery (DAVID)  (Huang et al. , 2009a; 2009b)  to gain an overview of the biological processes, molecular functions, and KEGG pathways overrepresented in the datasets (Figure  7 -figure supplement 1).
To further test whether early embryonic patterning was affected in MZpitx2c mutants, we examined the expression levels of several key mesendodermal specification and dorsal organizer genes (Figure  7 -figure supplement 2a). We observed that some genes in these categories were differentially expressed in the pitx2c GOF transcriptome, including chd, foxa2, sox32, pcdh8, and vox, whereas the expression level of many of the genes in these categories were not highly changed following the loss of Pitx2c function (Figure  7 -figure supplement 2a). From the list of differentially expressed genes, we selected several candidates for further analysis. One of the most highly upregulated genes in the GOF dataset was cxcl12b, which encodes the chemokine Cxcl12b that has previously been implicated in endodermal migration  (Mizoguchi et al.
, 2008; Nair and Schilling, 2008). cxcl12b mRNAs are maternally contributed and subsequently found in the mesodermal lineage during gastrulation; the gene encoding its receptor Cxcr4a is expressed by endodermal cells  (Mizoguchi et al. , 2008; Nair and Schilling, 2008). We analyzed mRNA levels of cxcl12b and cxcr4a in wild-type, MZpitx2c mutant embryos, and pitx2c GOF embryos at 80% epiboly. These data indicate that cxcl12b is positively regulated by Pitx2c, as mRNA levels were reduced by half in MZpitx2c mutants and increased ~5 fold after pitx2c overexpression (Figure  7a ), confirming the observed increase in the microarray analysis. We did not observe any appreciable changes in cxcr4a mRNA levels (Figure  7b ) after manipulating pitx2c expression. It has been shown that Cxcl12b-Cxcr4a signaling controls ECM-integrin-dependent adhesion during gastrulation cell movements  (Nair and Schilling, 2008).
Therefore, we considered whether genes in this pathway were modulated in the transcriptomics datasets. We observed that several genes encoding integrin subunits and ECM remodelers were affected (Figure  7 -figure supplement 2b), while the expression level of a few genes encoding cadherins were also changed (Figure  7 -figure  supplement 2c ). Using a candidate gene approach, we investigated whether expression of itb1b was affected as it is one of the most highly expressed integrin genes during gastrulation  (Nair and Schilling, 2008). We found that itb1b mRNA levels were increased ~3 fold in MZpitx2c mutants at 80% epiboly and observed a slight reduction in mRNA levels following pitx2c GOF (Figure  7c ). We also sought to determine whether fibronectin deposition was affected given changes to the upstream chemokine signaling and integrin levels, and because fn1a is highly expressed by mesodermal cells during gastrulation  (Trinh and Stainier, 2004).
, 2017; Ding et al. , 2017). In mouse, Pitx2 expression is detected at embryonic day (E) 6. 25 by transcriptome profiling  (Mitiku and Baker, 2007). Single cell RNAseq datasets indicate that Pitx2 expression can be detected during gastrulation from E6. 5 to E7. 5 in the epiblast, pharyngeal mesoderm, nascent mesoderm, posterior mesoderm, allantois, and visceral endoderm (data obtained from online resource found at http://gastrulation. stemcells. cam. ac. uk). Together, these observations indicate that the early wave of pitx2 expression is highly evolutionarily conserved. Pitx2 was recently described as one of the earliest markers of embryonic anterior-posterior polarity and as essential for axis formation  (Torlopp et al. , 2014). This function appears to have been retained during mammalian evolution as a similar relationship was recently reported in rabbit embryos (Plo ¨ger and Viebahn, 2018); however, little is known about the role of Pitx2 at these early stages in mice.
Cell division imaging To assess angles of cell divisions, embryos were injected with 100 pg of membrane tdTomato and nuclear H2B-GFP mRNA at the 1 cell stage. Primer sequences for cloning are listed in Supplementary file 3. Embryos were incubated at 28. 5 ˚C until they reached shield stage. Images were acquired every 3 min for 60 min using a Zeiss Spinning Disk confocal microscope, and the embryos were oriented with the lateral side facing the objective and the shield at 90 ˚. Angles were measured using FIJI software and binned into groups using GraphPad. Chi-square tests were performed using GraphPad. Individual angles were converted to radians and input into MatLab to generate rose diagrams.
Microarray expression profiling For gain-of-function analysis, total RNA was isolated from a pool of 20 dome stage embryos following global pitx2c overexpression (25 pg) as well as a pool of 20 dome stage uninjected control embryos. For loss-of-function analysis, total RNA was isolated from a pool of 20 shield stage MZpitx2c mutant embryos as well as a pool of 20 stage-matched pitx2c +/-control embryos. Sample quality was tested using a Bioanalyzer. Microarray analysis was performed by Oak Labs (Germany). Dataset analysis was performed using DAVID Functional Annotation Tool  (Huang et al. , 2009a; 2009b)  using gene lists generated by filtering genes for a fold-change >2 (LOF dataset) or >2. 5 (GOF dataset) and removing genes detected below a cutoff of 10. Gene IDs that were unmapped by DAVID (e.
Acknowledgements We would like to thank  Sebastien Gauvrit ,  Rashmi Priya ,  Chi-Chung Wu ,  Felix Gunawan , and  Anna Sokol  for discussion and comments on the manuscript, the reviewers for constructive feedback,  Marianne Ploch  and  Rebecca I-Ching Lee  for technical assistance,  Radhan Ramadass  for microscopy and MatLab advice,  Rita Retzloff  and  Martin Laszczyk  for zebrafish care, and  Scott Holley  for sharing his fibronectin staining protocol. This work was supported by grants from the  Fondation pour la Recherche Medicale  ( DEQ20131029166 , PB),  Deutsches Zentrum Fu ¨r Herz Kreislauf Forschung (DZHK) (MMC) , and the  Max Planck Society (DYRS).
Parasitoids of the genera Anagrus spp. , Oligosita spp. , Gonatocerus spp. and Paracentrobia spp. were collected in eight study landscapes located in Luzon. We found discrepancies between the morphological and the molecular analysis. Morphological and molecular results were only valid for Paracentrobia spp. Anagrus spp. and Gonatocerus spp. showed more genetic diversity, than expected after the morphological analysis, indicating cryptic species. The sequences for Oligosita spp. revealed less variation than expected. This is the first study on molecular diversity of rice parasitoids in the Philippines. More research combining morphological, behavioural and genetic methods as well as the establishment of a comprehensive DNA database is urgently needed to assess the performance and suitability of these organisms as biocontrol agents.
Data analysis Forward and reverse DNA sequences were processed with Gap5 v 1. 2. 14-r  [34]. DNA sequence alignment and analysis was performed using MEGA 6  [35]. The best model to construct parasitoid identities was determined assuming partial deletion, site coverage cut-off of 95% and the branch swap filter set to 'very strong'. Additional Chalcidoidea (the super family containing all four genera) amino acid sequences as reference material were selected by using the National Center for Biotechnology Information (NCBI) BLAST tool  [36]  and the BOLD Identification System (http://www. boldsystems. org) (Table  S3 ). were constructed using the software NETWORK v. 4. 6. 1. 2 [37]. The genetic diversity between and within species was estimated using additional sequences from the superfamily Chalcidoidea (Table  S3 ).
Genetic Analysis Molecular analyses were successfully performed on a total of 105 parasitoid samples (Table  S2 ). We failed to sequence 162 specimen, which could not be processed further. A total of 86 (COI) and 105 (28S) sequences were used to create the neighbouring joining trees. The final dataset for comparison of the two gene fragments included the sequences from 74 parasitoid individuals. Rarefaction analysis for the local hopper egg parasitoids diversity revealed that sampling saturation was reached for the gene 28S (Figure  S2 ). In contrast, the curve for COI was not saturated (Figure  S3 ). Peer-reviewed version available at Insects 2018, 9, 19; doi:10. 3390/insects9010019.
This is supported by our results as we found that sampling saturation was only reached for the gene 28S, but not for the COI gene. Our study showed further that an accurate identification relies on both, molecular and morphological techniques. A similar conclusion was drawn previously[21,23]. In the tropical rice agroecosystem, more research combining morphological, behavioural and genetic methods are necessary to improve the identification of cryptic species[53]. Once a reliable and comprehensive DNA database is established, the identification of hopper parasitoids using DNA sequencing will be a vital step towards assessing the performance and suitability of these organisms as biocontrol.
Acknowledgments: We thank  Bianca Tappe ,  Daniel Kretzschmar  and  Heike Rollwage  for their technical assistance. We also want to thank  Jo Catinding  from the  International Rice Research Institute (IRRI)  for the help to identify the insects. The work has been funded by the  LEGATO  project [26], which is part of the  BMBF (German Federal Ministry of Education and Research) Framework Program Research for Sustainable Development (FONA, FKZ :  01LL0917A & 01LL0917N ).
This is supported by our results as we found that sampling saturation was only reached for the gene 28S, but not for the COI gene. Our study showed further that an accurate identification relies on both, molecular and morphological techniques. A similar conclusion was drawn previously[21,23]. In the tropical rice agroecosystem, more research combining morphological, behavioural and genetic methods are necessary to improve the identification of cryptic species[53]. Once a reliable and comprehensive DNA database is established, the identification of hopper parasitoids using DNA sequencing will be a vital step towards assessing the performance and suitability of these organisms as biocontrol Preprints (www. preprints. org) | NOT PEER-REVIEWED | Posted: 13 November 2017 doi:10. 20944/preprints201711.
Reverse Transcription (RT)-quantitative PCR analysis A RT-quantitative PCR (RT-qPCR) protocol was developed to meet the minimum information for publication of quantitative real-time PCR experiments (MIQE) criteria. Total RN, from frozen cell line samples and frozen tissues, was extracted using the RNeasy Purification kit (QIAGEN, Hilden, Germany). RT of 1 mg each RNA was performed using the QuantiTect Reverse Transcription kit (QIAGEN, Hilden, Germany), which includes elimination of genomic DNA contamination in RNA samples. The qPCR analyses were performed using the Maxima SYBR Green/ROX qPCR Master Mix (Stratagene; Agilent Technologies, Santa Clara, CA, USA) on a CFX96 qPCR instrument (Bio-Rad). Data were analyzed using CFX Manager software and the ΔΔC(t) method (Livak & Schmittgen 2001).
Whole genome sequencing of the INS-1E cell line Whole genome sequencing of INS-1E cells was performed by Integragen (Evry, France). Briefly, 200 ng of each genomic DNA are fragmented by sonication and purified to yield fragments of 300-400 bp. Pairedend adaptor oligonucleotides from NEBNext ultra 2 kit are ligated on repaired, A tailed fragments then purified and enriched by 8 PCR cycles. These generated libraries are purified and quantified by QPCR to obtain sufficient DNA template for downstream applications. Each elutedenriched DNA sample is then sequenced on an Illumina HiSeq4000 as paired-end 100 bases reads. Image analysis and base calling is performed using Illumina Real Time Analysis (2. 7. 6) with default parameters. Base calling is performed by using the Real-Time Analysis software sequence pipeline (2.
7. 7) with default parameters. Sequence reads are mapped to the rat genome (Rnor 6. 0) by using the Burrows-Wheeler Aligner (BWA) tool. The duplicated reads (e. g. paired-end reads in which the insert DNA molecule showed identical start and end locations in the rat genome) are removed (sambamba tools). Variant calling, allowing the identification of genetic alterations as well as SNV (Single Nucleotide Variation) small insertions/deletions (up to 20bp) is performed via the Broad Institute's GATK Haplotype Caller GVCF tool (3. 7) for constitutional DNA and via the Broad Institute's MuTect tool (2. 0) for somatic DNA. Variant annotation is performed via Ensembl's Variant Effect Predictor tool (VEP). It takes into account data available in dbSNP (dbSNP142) and PhastCons database. Functional consequences of variants on genes, transcripts, and protein sequence, as well as regulatory regions, are predicted by Variant Effect Predictor (VEP release 87) (stop, splicing, missense, synonymous…), as well as by location of the variants (e.
g. upstream of a transcript, in coding sequence, in noncoding RNA, in regulatory regions). Regarding missense changes, two bioinformatics predictions for pathogenicity are available: SIFT, PolyPhen. Other information like quality score, homozygote/heterozygote status, count of variant allele reads are reported. The Manta software (0. 29. 1) is used to discover, assemble and score large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
RNAPII pausing and transcription termination occur at ARS borders Although considerable efforts have been made to annotate transcription units independently from the production of stable RNAs, many transcribed regions still remain imprecisely or poorly annotated in the S. cerevisiae genome. Addressing the potential impact of transcription on the function of replication origins therefore requires taking into account the actual physiological levels of transcription, regardless of annotation. For these reasons, we relied on high-resolution transcription maps derived from the direct detection of RNAPII by the sequencing of the nascent transcript (RNAPII PAR-CLIP, photo-activable ribonucleoside-enhanced UV-crosslink and immunoprecipitation)  (Schaughency et al. , 2014). We also generated additional datasets using the analogous RNAPII CRAC, (crosslinking analysis of cDNAs,  Granneman et al.
(2006) (compare Figure 4A and Figure 1B). As in the previous analysis, many unstable transcripts are produced by termination around origins as witnessed by the overall higher level of 3'-ends mapped in an exosome-deficient strain (Figure  4A ). The distribution of RNA 3'-ends around the set of nr-ACSs is however radically different, with transcription events presumably crossing the nr-ACS in both directions and terminating downstream (Figure  4B ). Interestingly, at nr-ACSs, the amounts of 3'-ends detected are very similar in wild-type conditions or upon depletion of both Rrp6 and Dis3 subunits of the nuclear exosome, indicating that termination downstream of nr-ACSs does not produce unstable transcripts and is presumably dependent on the CPF pathway (Figure  4B ). Because the ACS sequence is nearly identical in the two datasets, it is unlikely that it alone could be responsible for the termination pattern observed at ORC-ACSs.