dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis Tools and Methods In order to allow analysis of the intrinsic properties of background lensed galaxies, the BUFFALO survey follows the HFF philosophy of releasing high-level data products through the MAST archive for the scientific community. The BUFFALO team will produce several strong, weak, and joint strong+weak lensing models from independent teams using different techniques described further in § 3. BUFFALO will then deliver mass, magnification, deflection, and associated error maps for different redshifts provided by each independent modeling team of the collaboration, as well as weak-lensing catalogues. An online magnification calculator will also be available for fast magnification estimates and errors within the modeled field-of-views for each modeling pipeline.
2016a ) impact the mass measurements in the cluster core, which in turn affects magnification estimates of high redshift sources. Lagattuta et al. (2019)  studied Abell 370 by extending the Multi-Unit Spectroscopic Explorer (MUSE) mosaic around Abell 370 together with deeper imaging data from the HFF program. Their best-fit strong lensing model needed a significantly large external shear term that is thought to come from structures along the line-of-sight and at larger projected radii in the lens plane. Moreover,  Acebron et al. (2017)  analyzed the impact of distant and massive substructures on the overall mass and density profiles reconstruction with HFF -like simulated clusters  (Meneghetti et al. 2017). They found that the density profile in the outskirts of the cluster (≥ 600kpc) was underestimated by up to ∼ 30%.
These recent studies have thus further proven the need for extended data coverage around galaxy clusters. With its extended spatial coverage of the HFF clusters, BUFFALO will provide unprecedented weaklensing measurements thanks to HST high-resolution imagery, allowing for precise measurement of the shapes of weakly-lensed galaxies. The combination of BUF-FALO weak-lensing and HFF strong-lensing analyses will provide the most precise mass measurements ever obtained for those clusters. BUFFALO will detect structures that can only be significantly detected with HST weak-lensing. While residing in the cluster outskirts, they still introduce a significant bias in the mass measurements as explained earlier, and thus on the magnification estimates that are crucial for high redshift studies. Following the success of a similar program with the original HFF observations, the lensing profile in BUF-FALO will be modeled by several independent teams, with each result released for public use ( § 4).
However, recent results using HST photometry  (Bouwens et al. 2015 (Bouwens et al. , 2016;; Davidzon et al. 2017)  indicate that the galaxy luminosity function flattens between z ∼ 7 (where there is likely an exponential cutoff) and z ∼ 10 (where no cutoff is observed), consistent with the epoch around z ∼ 8 -10 is the critical transition window. Uncertainties at this epoch are currently dominated by a combination of cosmic variance, insufficient area in current sightlines, and lack of ultra-deep Spitzer data needed to confirm luminous z > 8 systems. To illustrate the point, all published z ∼ 9 -10 CANDELS galaxies are in just two of the five possible fields where they could be discovered  (Oesch et al. 2014; Roberts-Borsani et al. 2016). The BUFFALO survey is optimized to efficiently search for these early, high-mass galaxies over the remaining areas where mass estimation will be possible (Fig.
Spitzer data are essential for z > 8 galaxy studies (cf. Bradač et al. (2014) , Fig. 3 ) because they constrain the age and mass of high-redshift galaxies and can be used to effectively remove z < 3 contaminants. Spitzer has already invested ∼1500h (2 months) imaging the HFF areas to 50-75h depth, but HST WFC3-IR data exists over only 10% of this deep Spitzer coverage. The BUFFALO pointings were chosen to overlap with the existing Spitzer HFF coverage as efficiently as possible in regions central enough that there is still likely to be non-negligible magnification from weak lensing. The BUFFALO coverage areas also expands WFC3 coverage to an area which is well matched with the JWST NIRSPEC field of view. BUFFALO will complete the WFC3-IR and ACS coverage of areas with Spitzer-IRAC deep enough to study the high-z universe over a large area, resulting in the best study of this key period currently possible.
Improvement in Magnification Estimates As discussed in § 3, a lack of knowledge of the presence of substructures in the outskirts of clusters can lead to underestimation of the mass and thus the density profile of the cluster by up to 20%  (Acebron et al. 2017 ). Magnification at a given location in the cluster is a di-rect product of the mass estimate (and the redshift of a background source). Therefore, the expanded BUF-FALO observing area provides a unique dataset which can overcome the lack of accuracy of core-only mass models by being able to detect precisely where substructures are located and estimate precisely their mass (down to a few percent precision thanks to HST resolution,  Jauzac et al. 2015a ). The exact improvement in magnification estimates with BUFFALO is difficult to predict as it strongly depends on the dynamical state of each clusters, i.
2012; Jauzac et al. 2012; Eckert et al. 2015a; Connor et al. 2018). BUFFALO now allows an unprecedented resolution for mapping of the dark matter and will deliver data to detect material (both baryons and dark matter) falling on the clusters by the direct detection of galaxies and enhanced star-forming regions as tracers of the filaments and indirect detection of dark matter densities using weak lensing. Clearly identifying and locating individual filaments and the local cosmic web could be useful in constraining their effect on star formation and quenching  (Aragon Calvo et al. 2019) , galaxy angular momentum  (Goh et al. 2019 ) and even, through a "spiderweb test"  (Neyrinck et al. 2018) , a redshift-todistance mapping. In addition, reaching further away from the cluster center at the HST resolution will sharpen our under-standing of merging events.
Catalogs BUFFALO will produce several value-added catalogs, with an initial release for Abell 370 and updated planned as additional clusters are completed. These catalogs will exploit BUFFALO photometric data along with all available multi-wavelength observations from the HST archive. A list of existing datasets can be found in Table 5. It will also include ancillary data from near-IR surveys (Brammer et al. 2016; Nonino et al. , in prep. 2 ) and the Spitzer images that are a cornerstone of the BUFFALO program (see § 2). Photometric redshifts will be derived from such a large photometric baseline by means of state-of-the-art software as EAZY  (Brammer et al. 2008)  and LePhare  (Arnouts et al. 1999; Ilbert et al. 2006) , fitting galaxy (and stellar) templates to the spectral energy distribution (SED) of each object.
Mass Models The BUFFALO team includes groups which have been responsible for producing a variety of independent mass models for the HFF clusters from earlier datasets  (Jauzac et al. 2014; Johnson et al. 2014; Lam et al. 2014; Richard et al. 2014; Diego et al. 2015a,b; Jauzac et al. 2015a,b; Oguri 2015; Sharon & Johnson 2015; Wang et al. 2015; Williams et al. 2015; Diego et al. 2016a,b; Harvey et al. 2016; Jauzac et al. 2016b; Johnson & Sharon 2016; Kawamata et al. 2016; Sebesta et al. 2016; Treu et al. 2016; Priewe et al. 2017; Diego et al. 2018; Figure 9. BUFFALO composite color image of Abell 370. The BUFFALO field of view is four times larger than the previous Frontier Fields coverage (shaded in the central region for both the cluster and parallel fields) in addition to increasing the depth in the central region.
acknowledges support from the ERC Consolidator Grant funding scheme (project ConTExT, grant No. 648179). The Cosmic Dawn Center is funded by the Danish National Research Foundation under grant No. 140. MJ is supported by the United Kingdom Research and Innovation (UKRI) Future Leaders Fellowship 'Using Cosmic Beasts to uncover the Nature of Dark Matter' [grant number MR/S017216/1]. This project was also supported by the Science and Technology Facilities Council [grant number ST/L00075X/1]. Joseph Allingham is supported by the Postgraduate Research Scholarship in Astroparticle Physics/Cosmology in the University of Sydney. AA acknowledges the support of Royal Society through Wolfson Fellowship program. YMB acknowledges funding from the EU Horizon 2020 research and innovation programme under Marie Sk lodowska-Curie grant agreement 747645 (Clus-terGal) and the Netherlands Organisation for Scientific Research (NWO) through VENI grant 016.
183. 011. RJB gratefully acknowledges the support of TOP grant TOP1. 16. 057. RC is supported by the MERAC foundation postdoctoral grant awarded to CL, and by the Consejo Nacional de Ciencia y Tecnología CONA-CYT CVU 520137 Scholar 290609 Overseas Scholarship 438594. The work of TC was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with NASA. B. D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. JMD. acknowledges the support of project PGC2018-101814-B-100 (MCIU/AEI/MINECO/FEDER, UE) Ministerio de Ciencia, investigación y Universidades. A. C. E. acknowledges support from STFC grant ST/P00541/1. S. E. acknowledges financial contribution from the contracts ASI 2015-046-R.
Purpose Data on primary (PH) and incisional hernias (IH) are often pooled, even though several studies have illustrated that these are different entities with worse outcomes for IHs. The aim of this study is to validate previous research comparing PHs and IHs and to examine whether hernia width is an important contributor to the differences between these hernia types. Methods A registry-based, prospective cohort study was performed, utilizing the French Hernia Club database. All patients undergoing PH or IH repair between September 8th 2011 and May 22nd 2019 were included. Baseline, hernia and surgical characteristics, and postoperative outcomes were collected. Outcomes were analyzed per width category (≤ 2 cm, 3-4 cm, 5-10 cm and > 10 cm). Results A total of 9159 patients were included, of whom 4965 (54%) had PH and 4194 (46%) had IH.
Stirler et al. [8]  also found a higher total conversion rate and longer hospital stay for patients with IH compared to patients with PH. In 2018 Kroese et al. [7]  performed a prospective cohort study of 4565 patients, based on the French Hernia Club database. Besides having similar conclusions as previous research, they found that PH and IH differed significantly in terms of baseline characteristics. Whether the different outcomes are caused by underlying differences in etiology is not yet completely understood. Other possible causes are the higher incidence of comorbidities in IH patients or differences in hernia width  [7]. Larger IHs are more prone to unfavorable outcomes than smaller IHs  [10]. On average, IHs are significantly larger than PHs, and the difference in postoperative outcomes between PH and IH may be due to the difference in hernia width.
Methods This prospective cohort study was performed within the French Hernia Club registry. The Hernia Club registry is approved by the French 'Commission Nationale de l'Informatique et des Libertés' (CNIL; registration number 1993959v0) and complies to the General Data Protection Regulation. Additional consent by participants and institutional review board approval were not required since this is a registry-based study and patient data is anonymized, which is in accordance with the Dutch and French national ethical standards. This study was conducted according to the European Registry of Abdominal Wall Hernias (EuraHS) recommendations and follows the STROCSS criteria and STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for observational studies  [11] [12] [13].
Study design This is a registry-based, prospective cohort study within the Hernia Club database. All adults undergoing ventral hernia repair of both PH and IH between the 8th of September 2011 until the 22nd of May 2019 in the French Hernia Club registry were compared. Parastomal hernias were excluded. To compare PH and IH and to validate previous research on the subject, baseline, hernia and surgical characteristics, and postoperative outcomes were collected. To determine whether hernia width explains these differences, baseline characteristics and postoperative outcomes were compared for different width categories. The constructed width categories are as follows: 0 up to and including 2 cm, 3 up to and including 4 cm, 5 up to and including 10 cm, and wider than 10 cm. Hernia width was only available in whole centimeters.
Hernia Club registry The Hernia Club registry is a collaborative, prospective, anonymized online database of all surgical procedures for primary and incisional hernias. All surgical procedures were performed by French surgeons specialized in abdominal wall surgery. The Charter of Quality must be signed and accepted by each participating surgeon, which states that: ''all input must be registered in a consecutive, un-selected, and exhaustive manner and in real time''. 191 parameters, including the pre-, peri-and post-operative periods, are prospectively collected by the operating surgeon and blinded, independent clinical research associates using online forms. In case of any discrepancies the medical records are checked. Patients consent to random peer review of medical charts to ensure high-quality data.
Data collection Patient baseline characteristics extracted from the registry include age, sex, body mass index (BMI), smoking habits, diabetes mellitus, corticosteroid use, history of radiotherapy, chemotherapy, abdominal aortic aneurysm, connective tissue disorder, history of abdominal wall hernia, hiatal hernia, family history of hernia and American Society of Anesthesiologists (ASA) classification. Hernia characteristics extracted from the database comprised the type of hernia, hernia width, hernia length and preoperative symptoms. Surgical characteristics extracted from the database were planned or emergency surgery, duration of operation, open or laparoscopic approach, primary suture or mesh closure, mesh location, Altemeier wound classification and antibiotic treatment  [15]. Extracted postoperative data included the duration of admission, intra-operative complications (including penetrating digestive tract wound, bladder wound, severe bleeding, and general complications like an embolism or infarction), wound complications (including SSIs, SSOs and SSOPIs), surgical complications (including occlusion of the small intestine, peritonitis, intraperitoneal abscesses, retroor subperitoneal hematoma, abdominal wall hematoma, mesh migration, abdominal wall compartment syndrome and early recurrence), medical complications (including veinitis/lymfangitis, thrombophlebitis, deep venous thrombosis, urinary retention, pneumonia, cardiac rhythmic disorders, acute coronary syndrome and neurological complications) and re-intervention  [16].
Discussion To this day, data on PH and IH is often pooled, even though several studies suggest that these hernias are different entities  [6] [7] [8] [9]. The present analysis of 9159 patients of the prospective French Hernia Club database validates previous research stating that PH and IH are significantly different in terms of most baseline, surgical and hernia characteristics, and outcomes. After correcting for hernia width, however, most outcomes no longer showed significant differences, indicating that not the type of hernia, but the hernia width is an important factor that largely contributes to these differences. IH repair is often considered as a procedure with an increased risk of intra-operative and postoperative complications compared to PH repair. Based on the data in the present study this assumption seems only partly correct.
A meta-analysis by Stabilini et al. [9]  found that IH has a higher recurrence rate than PH. However, the question remains whether this is still the case after correcting for hernia width. Hernia recurrence is not reported in the present study due to insufficient data on PH recurrence in the Hernia Club database. A probable explanation for this is the fact that PH has a smaller average width, less frequently having concomitant defects at the surgery and a shorter operative time, resulting in a simpler procedure and, subsequently, a shorter post-operative follow-up period compared to patients with IH, resulting in less available data on PH recurrence  [9]. As both the formation of IH and hernia recurrence are the result of failed wound healing, it seems logical that hernia recurrence is more common in IH.
Limitations This study is limited by the fact that the data are not randomized, which may cause a potential risk of confounding by indication. However, since all patients who underwent ventral hernia repair were included in the registry, no selection has been made in patient inclusion and this study is, therefore, a good representation of the general patient population. Still, in the present study, 46% of the patients had IH which is much higher than the expected 30% found in previous research, and could potentially indicate a risk of selection bias  [23]. A possible explanation for this higher percentage is the fact that de Hernia Club registry is the collaborative work of surgeons with a special interest in hernia surgery, and might, therefore, attract more complicated patients. The expertise of the surgeons might also explain the relatively low rate of complications.
Findings: Here, we report the new long-reads assembly of Darmor-bzh genome ( Brassica napus ) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.
B. napus Darmor-bzh genetic map An integrated B. napus genetic map was obtained using BioMercator V4. 2 program  [17]  from three different genetic maps  [18]  : a cross between Darmor-bzh and Yudal (DH population with 248 lines), a cross between Darmor and Bristol (F2 population with 291 plants) and a cross between Darmor and Samouraï (DH population with 129 lines). These populations were genotyped using the Illumina 8K, 20K and 60K arrays  [18]  [8]  [19]  [20] and genetic maps were constructed using CarthaGene software  [21].
Long reads genome assembly In order to get the best possible genome assembly, we used three assemblers : redbean  [22]  , SMARTdenovo  [23]  and Flye  [24]  with all nanopore reads or subsets of reads composed of either the longest reads or those selected by the Filtlong [25] software with default parameters (Table  S2 ) , as it has been proven that it could be beneficial for the assembly phase to downsample the reads coverage  [3]. We used the following options as input to SMARTdenovo : "-c 1" to generate a consensus sequence, "-J 5000" to remove sequences smaller than 5kb and "-k 17" to use 17-mers as it is advised by developers in the case of large genomes. Then, we selected the 'best' assembly based not only on contiguity metrics such as N50 but also cumulative size. The Flye assembler using the longest reads produced the most contiguous assembly and lead to a contig N50 of 10.
Correction of direct RNA reads Direct RNA reads were corrected using TALC  [34]  with default parameters (except -k=21) and Illumina reads from leaves and roots samples of B. napus downloaded from the EBI database (ERX397788 and ERX397800). Before the correction step, raw reads were masked using DustMasker  [35]  , and we kept reads with at least 150 unmasked positions and at least 75% of unmasked bases. From 10,416,515 input reads, we retained 9,099,437 nanopore reads and TALC successfully corrected 8,523,238 reads (93. 7%) with an average length of 645bp (Table  S9 ).
Comparison of available Brassica genome assemblies We downloaded the 14 available Brassica long-read assemblies (and annotations) and computed usual metrics. For each assembly, contigs were generated by splitting sequences at each gap and the gene completion was evaluated on predicted genes using BUSCO  [44]  and the conserved genes from the brassicales database (N=4,596 genes). Not surprisingly the gene content is high, between 97. 9% and 98. 8% for all the ten B. napus assemblies (Table  2 ), and is lower for the diploid species (due to the presence of a single-genome), except for B. rapa Chiifu that has a surprising number of genes (>60k). Likewise, the repetitive content of these ten genomes is similar, between 54% for Darmor-bzh and 60% for no2127. Concerning the diploid genomes and as already reported  [50]  , B.
In the case of Darmor-bzh, we were able to obtain more than 50,000 reads longer than 100Kb (representing 6X of coverage). This dataset allowed us to generate a contiguous assembly with only 268 gaps. As a comparison, we found 5,460 in the PACBIO assembly of the Zs11 genotype. This difference is observed in all the A and C genomes and subgenomes that have been sequenced using long reads, and may be directly related to the longer length of ONT reads (Figure  4 ). Although the number of gaps is higher in the PACBIO assemblies, the total number of N's is lower at least for the assemblies that have been organized with Hi-C data. Indeed, the Hi-C pipelines generally order contigs and add a fixed gap size between two contigs. We investigated the 500bp gaps in the Zs11 assembly and aligned their flanking regions on the Darmor-bzh assembly using blat  [39].
Sequencing of native RNA molecules The sequencing of RNA is traditionally performed using the Illumina technology where the RNA molecules are isolated and then reverse transcribed (RT) to cDNA that is more stable and allow the amplification prior to the sequencing. The Oxford Nanopore technology is the first to propose the sequencing of native RNA molecules without the RT step. One of the main advantage is a better quantification of gene expression when compared to methods that requires a RT  [41]. Moreover the sequencing of native RNA molecules preserves modified bases and theoretically allows to detect them  [52, 53]. Here, we sequenced a mix of leaf and root samples using the PromethION device and generated 10,416,515 reads with an average size of 559 bp (Table  S9 ). This dataset was corrected using TALC as described previously and corrected reads were used in the gene prediction workflow.
Conclusions In this study, we generated the most contiguous B. napus genome assembly thanks to the ONT long reads and Bionano optical maps. In addition, the ONT dataset allow to detect modified bases, such as C5-methylcytosine (5mC), without any specific library preparation. We have shown that the generation of ultra-long read is a game-changer for assembling complex regions, composed of transposable elements, common in plant genomes. The authors declare that they have no competing interests. JMA received travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences. JMA and CB received accommodation expenses to speak at Bionano Genomics user meeting. Tables  Table 1. Statistics of the Darmor-bzh assemblies.