dataesr/scientific-paragraphs-categorization huggingface dataset:
The HTS library for bacteria species was also prepared using a one-step PCR amplification, while both the forward and reverse amplification primers contained the Illumina adapters and Illumina sequencing primers. For this purpose, 5-base in-line barcodes were used to read the forward sequence and a 6-base indexing barcode was used for a dedicated indexing read. The final three libraries were sent to The Australian Cancer Research Foundation (ACRF) Biomolecular Resource Facility (BRF) at the Australian National University for paired-end sequencing on the MiSeq platform using the V3 2x300bp sequencing kit. All data can be accessed in Supplementary S2.
Bioinformatics Pipeline Raw FASTQ files for the bacteria library were downloaded from the Illumina Basespace online platform and processed using QIIME2  (Bolyen et al. , 2019). Paired-end reads with barcodes in-sequence were demultiplexed and primer sequences were trimmed from the reads using the q2-cutadapt plugin. Raw demultiplexed sequences were quality filtered and denoised with DADA2 in QIIME2  (Callahan et al. , 2016) , wherein forward and reverse reads were truncated to 260 bp and 200 bp, respectively. Following,  MAFFT (Katoh et al. , 2002)  was employed to align all Amplicon Sequence Variants (ASVs) and the taxonomy was assigned to all ASVs using the q2-featureclassifier against the Naive Bayes classifier  (Price et al. , 2010) , trained on the SILVA (132 release) reference database  (Quast et al.
, 2012)  with the trimmed sequences only include the 16S rRNA V3-V4 region sequenced in this study. Raw FASTQ files obtained for the remaining three libraries (Actinopterygii, Crustacea and Cephalopoda) were downloaded from the Illumina Basespace online platform and processed following the MiFish pipeline  (Sato et al. , 2018) with modifications. Overall sequence quality was determined using FASTQC and low quality 3'-tails (Phred score < 10) were trimmed as per the MiFish pipeline. Then, sequences were paired following the MiFish pipeline. Reads that merged incorrectly or displayed PCR and sequencing errors were filtered from the analysis (i. e. , Phred < 33, mismatched forward and reverse barcodes = PCR & sequencing error filtering). Then, the Cutadapt script was employed to demultiplex the reads with barcodes in-sequence, remove adapter and primer sequences from the paired reads  (Martin, 2011) , and filter paired sequences with the incorrect length (i.
e. minimum length ≥ 190 bp for Actinopterygii, Crustacea and Cephalopoda). Lastly, Specieslevel taxonomic assignment was performed using UCLUST  (Edgar, 2010)  to cluster ASVs into Operational Taxonomic Units (OTUs) followed by identification using NCBI BLAST+  (Camacho et al. , 2009). Blastn searches of these 3 libraries were conducted against the related reference database of MitoFish (Actinopterygii  (Iwasaki et al. , 2013) , the National Centre for Biotechnology information (Crustacea) and The European Molecular Biology Laboratory (Cephalopoda) using a 98% identity cut-off and an e-value of 10 -5 to remove unassigned OTUs from the analysis (i. e. unassigned read filtering). Taxonomic identity for each prey species was curated by checking each species valid name and distribution in the World Register of Marine Species: WoRMS (http://www.
Data Analysis Differences in stomach content (based on molecular results and morphological examination) and microbiome were compared between predator species, capture location and El Niño Southern Oscillation temperature anomalies (i. e. , ENSO) in the Pacific. Molecular and stomach morphological assessment data were analysed within a model-based framework using the 'manyglm' function of the 'mvabund' package (v. 4. 1. 12) in R (v. 4. 1. 0) (R Core Team, 2021;  Wang et al. , 2012). This function fits a Generalised Linear Model to each response variable whilst correctly accounting for the correlations observed between the response variables (Supplementary S4). The response variables for each dataset (bacteria, prey identified by metabarcoding, prey identified by morphology) were analysed based on presence/absence of each taxa within each sampled stomach (i.
Nodal support for each tree was obtained using Bayesian analysis (MrBayes v. 3. 2. 7  (Ronquist et al. , 2012)  and Maximum Likelihood (MEGA v. 10. 1. 7). Trees were curated using the Interactive Tree of Life online phylogenetic software and rooted using closely related outgroup species (iTOL v. 5  (Letunic and Bork, 2019). Phylogenetic trees are provided as a supplementary file for this research (Supplementary S5).
RESULTS Out of 96 collected stomach samples, a total of 88, 90, 25 and 17 fish stomach samples passed quality control and ASV read filtering for bacteria, actinopterygians, crustaceans and cephalopods, respectively. Out of these samples, a total of 14,053,270 (bacteria), 37,668,878 (actinopterygians), 12,903,281 (crustaceans) and 7,942,872 (cephalopods) curated and fully assigned reads were obtained using Illumina MiSeq, with a sequencing depth range of 1,926-404,877 for bacteria, 89,169-705,076 for actinopterygians, 1,802-894,870 for cephalopods and 5,052-1,198,067 for crustaceans. Out of the 14,364,515 total sequence reads for bacteria, 4,273,304 sequence reads represented uncultured or ambiguous bacteria without taxonomic information. Similarly, out of the 37,642,984 total sequence reads for actinopterygians, 18,706,984 had a 100% similarity with Katsuwonus pelamis (GenBank Accession Number: KM605252) and 12,519,207 had a 100% similarity with Thunnus albacares (GenBank Accession Number: KY400011), indicating the amplification of host DNA.
Next, we tested the enrichment of the set of genes resulting from the KEGG database. As expected, we found a significant decrease in the enrichment of cell cycle genes in the responding CD3 tumors (p = 0. 04), such as TOP2A (p = 2. 2 e -26 ), MKI67 (p = 4. 3 e -20 ), and AURKB (2. 5 e -8 ). Moreover, we compared in a supervised analysis the gene expression of control untreated CD3 PDX tumors and control untreated CD7 PDX tumors in order to find predictive biomarkers of intrinsic palbociclib resistance (Supplementary Table  S3 ). We observed an upregulation of genes implied in hypoxia such as S100A4 (p = 6. 5 e -79 ) and CA3 (p = 3. 8 e -56 ) in the resistant CD7 PDX model (Figure  5A ). Among the top 1000 genes in which we observed a significant gene expression variation in both the models (adjusted p-value), we noted an enrichment of the oxidative phosphorylation genes in the resistant CD7 PDX model (p = 0.
However, it should be noted that other signaling pathways, in addition to CDKN2A loss, are inputted in cyclin D overexpression and promote CDK4/6 activity, leading to uncontrolled cell proliferation  (42). Palbociclib, a specific inhibitor of CDK4/6, has recently been tested in in vitro cell line chordoma models harboring the loss of CDKN2A and showed an efficient inhibition of the tumor cell growth  (41). Finally, the efficacy of palbociclib has been tested in numerous clinical trials for cancers, and is also currently being tested in a phase II trial, in patients with locally advanced/metastatic chordomas (NCT03110744). Volcanoplots illustrating the top 1000 genes (A) and all genes related to the oxidative phosphorylation (OxPhos) pathway (B), in which we observed a significant gene expression variation in both untreated CD3 and CD7 PDX models (adjusted p-value).
Transcripts were coded using both deductive and inductive approaches and compiled in MS Excel. We followed the recommended steps of thematic approach namely: data familiarization; generating initial codes; searching for themes; reviewing potential themes; defining and naming themes and producing the report  (19). To check the coding reliability, two individual researchers independently coded the same data and reviewed the codes applied. We described findings under key components of social capital theory; information flow and decision making. Additionally, a conceptual framework for the patron-client relationship between farmers and poultry dealers was developed. We reached data saturation within the sample size.
The transcribed data was coded using the constant comparative method  (36)  to identify emerging categories of data. Analysis was supported by the use of NVivo (NVivo qualitative data analysis Software; QSR International Pty Ltd. Version 12, 2018). Validity and reliability was established through rigorous record keeping, reporting of data collection, analysis and then verification of findings by two researchers with transcripts being read and re-read by two researchers CD and AR. The researchers' analyzed the data in matrices for each respondent until data saturation was achieved. There were three steps to the coding process: initial coding, focused coding and theoretical coding. Initial coding was the first step where many codes are produced. Focused coding then narrowed down the number of codes by selecting the most suitable ones.
Finally, connections are made between codes to produce categories. Categories can then be related to each other to establish a script. Enticott and Vanclay (37)  describe scripts as a unique sequence of actions that define a well-known situation-scripts are learned through people's perceptions of the regular and repeated features of the world. Sociological scripts stress the flexibility and capacity of the script writer to learn and update them thus in making sense of a particular situation people develop appropriate roles for themselves that match the given situation to their actions  (37). The scripts were then used to assess the RUMA targets set for the sheep and beef sectors. This was based on recommendations from a policy analysis of target setting in the NHS  (38). The policy analysis introduced five tests that must be met for targets to be appropriate and effective.
], that information is stored within our database and number crunched, that gives us a score of each farm. We can than benchmark each farm one against another, and use that information to develop strategies for those farmers who we believe and we can identify using far more antibiotics than the average or good dairy farms" (Interview retailer 2). Herd health performativity standards moreover enable new commercial platforms to emerge for those retailers who are chasing differentiation in milk quality with their contracted farmers. "Retailers are given a competitive marketplace and they are all seeking to find whether there is an opportunity for commercial advantage, so retailers and processors have their own policies and strategies on this" (Interview respondent livestock organisation 4). "They want their own schemes, they want their own control, they want their points of differentiation.
Data Collection In-depth interviews were conducted face-to-face by the first author between March and April 2015. A semi-structured guide, tailored to each category of participant (farmer, technician, veterinarian, manager) was used to conduct the interviews and allow themes to emerge from the participants' narratives. The guide included open-ended questions covering the interviewee's personal and professional development, daily work (husbandry practices, relation to animals, technical, and economic performance), animal health and animal disease management, relations with other stakeholders regarding animal health (technicians, veterinarians, hatchery, feed mill, auditor/inspector, slaughter house, distributor, consumer, etc. ), and use and perception of antimicrobials. To capture change over time in AMU practices, interviewees were asked to describe their personal trajectories regarding the use of antimicrobials over the past 10 years.
Acknowledging that "diagnostics have had less impact on antimicrobial prescribing than might have been expected, " the Wellcome Trust argued in 2016 that: "Rapid diagnostics are thought to have a vital role to play in the battle against drug-resistant infections. They have the potential to guide more rational use of antibiotics, by distinguishing between viral and bacterial infections, and by identifying specific pathogens and their antibiotic resistance characteristics"  (73). Returning to the final report of the O'Neill review of 2016, we find a similar emphasis on the use of diagnostics: "Fundamental change is required in the way that antibiotics are consumed and prescribed, to preserve the usefulness of existing products for longer and to reduce the urgency of discovering new ones. Rapid point-of-care diagnostic tests are a central part of the solution to this demand problem, which results currently in enormous unnecessary antibiotic use" (3).
Most interviewees worked at independent veterinary practices (though many of these had multi-site offices) and a few were either employed by larger corporate veterinary companies or acted as independent veterinary consultants. The majority of the interviews were carried out face-to-face at the veterinary practice (23 of the 30, with seven being undertaken on "Skype") and were, in each case, undertaken by two interviewers drawing across the social and the veterinary sciences. Interviews lasted between one and two hours and were recorded, anonymized and transcribed. Ethical approval for the survey was granted by the University of Exeter Geography Ethics Committee, approval reference number eCLESGeo000069v. 3. 0. Analysis of the interview transcripts was initially undertaken through standard systematic thematic coding techniques, allowing a series of common themes to emerge from the responses  (83).
The second sub-objective was to identify knowledge gaps of relevance for changing AMU practices within the VHHC setting, as well as challenges and opportunities for future research. The initial inclusion criterion for the literature search was studies on dairy cattle and AMU (other types of medication were excluded). Secondly, studies had to be conducted in an intensive production context characterised by high milk production and relation to a global market, as we argue that there are different AMU-related factors at play in intensive and extensive farming. Finally, studies had to place an emphasis on the farmerveterinarian relationship. The review began with a systematic literature search across seven databases, and 39 out of 122 articles were used in this review after screening for relevance.
MATERIALS AND METHODS This article is based on three distinct datasets from three different field studies conducted in different parts of France (Franche-Comté, Normandy and the Grand Ouest), within the framework of separate research projects. The methods of data gathering and analysis were qualitative: the goal of this article is not to provide a quantitative account of the phenomenon under investigation, but instead to assess its variations  (27). Compiling data gathered within the context of three distinct research projects in different regions enabled us to review a wide range of uses of alternative medicines by dairy farmers in France. The first two datasets come from ethnographic research conducted in Franche-Comté in 2016 (COPPECS project) and in Normandy in 2017 (Normandy region project) (In the remainder of this article, we will refer to these as Study FC and Study N, respectively).
The interviews conducted with the other actors (group leader, veterinarian) and the observations of group situations enabled us to better understand the social context within which familiarity with alternative medicines is acquired by dairy farmers. This analytical grid was then put to the test of analyzing the data from the third set of interviews, conducted in 2015 in the Grand Ouest  7  (Brittany and the Pays de la Loire) as part of a study of the use of homeopathy on organic dairy farms (European project IMPRO). We will call this Study GO. Study GO included 15 interviews with bovine dairy farmers who had converted to organic production and who were using or had used homeopathy to treat their herds. Interviews were conducted either with or without the farmers' veterinarian present. Interviewees were identified with the help of agricultural advisors and technicians specializing in organic farming, or through rural veterinarians.
The semi-directive portions of the interviews were recorded and transcribed in full. These sections were then analyzed using the analytical grid developed for the first two datasets. The analytical grid proved to be robust: the themes and sub-themes did not need to be modified. We were thus able to enrich and refine the results by adding these interviews with organic dairy farmers, whose experiences with veterinary homeopathy is notably different from that of non-organic dairy farmers. Data saturation was achieved by combining and comparing the results of these three studies. The analytical grid that emerged from this work featured the following themes: -Why the farmers became interested in alternative medicines; and what steps they took to learn more about these different approaches and treatments -The most important herd health issues on the farm; methods used to address these issues; any recent changes in this regard -The different alternative medicines used on the herd; for which kinds of health problems; and the advantages and limitations of these methods -Any other management changes made on the farm to address herd health -Use of local veterinarians and/or other advisors on livestock health In addition, we gathered factual data on the basic characteristics of the farms and their production systems, including herd size, number of employees, and participation in various quality schemes (organic, geographical indications, etc.
MATERIALS AND METHODS Data were collected through a scoping review (44) of academic work and grey literature containing empirical material. The main objective was to map existing knowledge and to identify gaps in knowledge on veterinary drug access in SSA. For the academic work, a scoping review was conducted using the scientific database Web of Science. The search terms used to identify publications were: [(drug * OR medicin * OR pharma * OR access) AND (veterinary * OR animal OR zoo * OR husbandry OR livestock OR poultry OR sheep OR goat OR pork OR cattle) AND (trade OR use OR delivery OR service * ) AND Africa AND (health OR disease OR epidemic OR epizoo * ) NOT ethno]. These terms were searched in the topic (= title, abstract key word) and for the publication period 1975 to 2021, in all types of documents.
Production and Imports The production of veterinary drugs is limited in SSA. Only a few countries have private drug manufacturers (mainly tertiary manufacturers), such as Bupo Animal Health (formerly Bedson) in South Africa and Cooper-K in Kenya, or the capacity to even partly supply neighboring countries. The production of veterinary drugs is often underpinned by public veterinary structures that focus on easy-to-produce generic medicines to support veterinary public health activities for small-scale farmers through vaccination campaigns or parasite control. Regarding the specific case of vaccines (see Figure  1 ), the information provided by the OIE Wahis database 1  for 19 countries in SSA suggests 500 million doses a year were produced in the region during the 2014-2018 period, covering around 20 different types of vaccines.
ACKNOWLEDGMENTS We would like to thank  Nathalia Brichet ,  Frida Hastrup , and  Esben Østergaard Eriksen  for commenting on the article and for the stimulating discussions on which this review was based. from funding from the  European Union  ( Seventh Frame work Programme  for research, technological development and demonstration under Grant Agreement n •  311824 ). The field study in Normandy received funding from the region of Normandy, through the  European Partnership in Innovation , under Grant Agreement n •  2017-AGRI-13.
FUNDING This work was supported by the  Antimicrobial Resistance Cross Council Initiative  in partnership with the  Department of Health and Department for Environment Food & Rural Affairs  (Award number:  NE/N019555/1 ). FUNDING FUNDING CD was funded by the  Agricultural and Horticultural Development Board Beef and Lamb  ( Ref 61110062 ). FUNDING This work was funded in part by the GREASE platform in partnership (https://www. grease-network. org/), France Veterinaire  FUNDING The research was funded by the  National Institute for Health Research Health Protection Research Unit (NIHR HPRU ) in Emerging and Zoonotic Infections at  University of Liverpool  in partnership with  Public Health England (PHE) , in collaboration with  Liverpool School of Tropical Medicine. SB was based at The Institute of Infection and Global Health.
The views expressed are those of the author(s) and not necessarily those of the  NHS , the  NIHR , the Department of Health or Public Health. FUNDING This study was supported by the  TRAJ  project (funded by  INRA GISA metaprogramme)  and the  OMAP  project (funded by  Institut Carnot-France Futur Elevage). FUNDING This research has been funded by the  Economic and Social Research Council  (Grant No. ES/P008194/1 ). FUNDING This work was fully funded by the  University of Copenhagen. FUNDING The  ROADMAP  project ( Rethinking of Antimicrobial Decisionsystems in the Management of Animal Production ) has received funding from the  European Union 's  Horizon 2020 research and innovation program  under Grant Agreement No. 817626. FUNDING This research is part of the  ROADMAP  project ( Rethinking of Antimicrobial Decision-Systems in the Management of Animal Production ).
Ecol Soc. (2017) 22:1-33. doi: 10. 5751/ES-09154-220133 5. Davey P, Brown E, Charani E, Fenelon L, Gould IM, Holmes A, et al. Interventions to improve antibiotic prescribing practices for hospital inpatients. Cochrane Database Syst Rev. (2013) 2:CD003543. doi: 10. 1002/14651858. CD003543. pub3 6. Landgren FT, Harvey KJ, Moulds RFW, Mashford ML, Guthrie B, Hemming M. Changing antibiotic prescribing by educational marketing. Med J Australia. (1988) 149:595-9. doi: 10. 5694/j. 1326-5377. 1988. tb120797. x 7. Weese JS, Giguere S, Guardabassi L, Morley PS, Papich M, Ricciuto DR, et al. ACVIM consensus statement on therapeutic antimicrobial use in animals and antimicrobial resistance. J Vet Intern Med. (2015) 29:487-98. doi: 10. 1111/jvim. Szymczak JE, Newland JG. The social determinants of antibiotic prescribing: implications for the development and implementation of stewardship interventions.
RGS14414-lentivirus The RGS14414-and vehicle-lentivirus solutions (1. 72 x 10 7 CFU/ml and 2. 75 x 10 6 CFU/ml respectively) were prepared and provided by Dr. Zafaruddin Khan at the University of Malaga (Malaga, Spain)  28 29. Briefly, the RGS14414 gene (GenBank, AY987041) was cloned into the commercial vector p-LVX DsRed Monomer-C1 (Clontech, France) using DNA recombinant technology. Then, both non-replicant RGS14414-and vehicle-lentivirus (empty vector) were prepared and titered using the Lenti-XTM (Clontech, France) according to the manufacturer's instructions. The animal's procedures related to the non-replicant lentiviral solution were approved and carried out in compliance with institutional regulation.
A total of 16 tetrodes were built, twisting four 10 cm polyimide-insulated 12 μm Nickel-Chrome wires (80 turns forward and 40 turns reverse) (Kanthal Precision, Florida) and fused by heat. Tetrodes were loaded in the inner tubes, and their free ends were connected to a customized 64 channels, 24 mm round electrode interface board (EIB) using gold pins (Neuralynx). Previously, 2 NPD dual row 32 contact connectors (Omnetics) had been attached to the EIB. The tetrode tips were cut using fine sharp scissors (maximum length 3. 5 mm and 3 mm for prelimbic cortex and HPC, respectively) and fixed to the inner tubes in the upper part. Tetrode tips were clean in distilled water and gold-plated (gold solution, Neuroalynx) using NanoZ software to lower their impedance to 100-200 kΩ and improve the signal-to-noise ratio.