dataesr/scientific-paragraphs-categorization huggingface dataset:
This is particularly relevant given the prominence of peanut cultivation in central Argentina  (9). Knowledge of the strain's genome is crucial for maintaining and developing further the current agricultural model. To date, although 581 genome assemblies are registered in NCBI for Bradyrhizobium strains, most are draft sequences. No genome data were available until now for strains used in commercial peanut inoculants. Here, we introduce the complete genome sequence of Bradyrhizobium sp. C-145. A pure culture of the strain, provided by INTA, was grown in liquid yeast extract-mannitol medium  (5). This was the source for the total DNA, obtained using a DNeasy blood and tissue kit (Qiagen) for Illumina sequencing and using a Promega Wizard high-molecular-weight (HMW) DNA extraction kit (Promega) for Oxford Nanopore Technologies sequencing.
Illumina sequencing was performed on the P2M (Plateforme de Microbiologie Mutualisée) platform at Institut Pasteur. The library was prepared using a Nextera XT DNA library preparation kit and then sequenced on an Illumina NextSeq 500 instrument in paired-end (PE) 150-bp read configuration. Nanopore sequencing was carried out at the Oxford Genomics Centre. The sample was processed using both an Oxford Nanopore Technologies rapid barcoding sequencing kit (SQK-RBK004) and a native barcoding genomic DNA sequencing kit (SQK-LSK109 with EXP-NBD104). The products of each were sequenced in two Flongle flow cells. Data were base called using Guppy v4. 2. 2 using high-accuracy mode and the -trim_barcodes option. We obtained 6,542,626 Illumina PE reads and 41,545 Nanopore long reads (average, 5,030 bp), predicting 102-fold and 22-fold coverage, respectively.
ACKNOWLEDGMENTS This work was supported by grants from the  Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) ,  Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) , the  Spanish Ministerio de Ciencia e Innovación  (research grant  PID2020-113207GB-I00 ),  ERDF  ( European Regional Development Funds) , and the  Biotechnology and Biosciences Research Council (BBSRC). It was also supported by  Wellcome Trust   Core Award  grant number  203141/Z/16/Z  and the  NIHR Oxford BRC. We thank the  Oxford Genomics Centre at the Wellcome Centre for Human Genetics  (funded by  Wellcome Trust  grant reference  203141/ Z/16/Z ) for the sequencing data. We are also grateful to  Vincent Enouf  from  Unité de Génétique Moléculaire des Virus  à  ARN-UMR3569   CNRS ,  Université de Paris ,  Centre National de Référence Virus des Infections Respiratoires  (dont la grippe); to  Plateforme de Microbiologie Mutualisée  ( P2M ) and the  Pasteur International Bioresources network (PIBnet) ; to  Institut Pasteur Paris  for providing the resources for Illumina sequencing; and finally, to  F.
Introduction: Pathogen-focused, randomized, controlled trials (PF-RCT) are important in the fight against carbapenem-resistant (CR) Gram-negative infections. Some recently approved antibiotics and older generic antibiotics with activity against CR Gram-negative bacteria were investigated in PF-RCTs in a variety of infections. Areas covered: We searched Pubmed, Cochrane database and international clinical trial databases for PF-RCTs for the period between 2005 and 2020 and compared the study designs, patient populations, infection types, pathogens, and Day-28 all-cause mortality (ACM). Expert opinion: PF-RCTs are particularly challenging to quantitatively assess and compare due to the heterogeneity in infection types, pathogens, CR mechanism, inclusion/exclusion criteria, and endpoints. Data interpretation is further complicated by lack of formal statistical analysis plans and/or noninferiority design, and limited power across most PF-RCTs.
While the broad enrollment criteria in the CR pathogen-focused studies result in more heterogeneous study populations, limiting the data interpretation  [26, 37, 38] , they are important in gaining a better understanding of the efficacy of new antibiotics, as well as the effectiveness of older approved agents, where they are intended to be used  [26, 37]. To gain an overview and understanding of the totality of the data generated by pathogenfocused, multicenter trials, we conducted a literature and database search in order to review data from randomized, prospective, interventional, pathogen-focused trials in patients with CR Gram-negative infections. Our evaluation included studies of approved older generics and new antibiotics, and considered baseline patient demographics, infection types, and outcome of Day 28 or Day 30 all-cause mortality (ACM).
Database and literature search strategy We sought to identify prospective, randomized, controlled, interventional studies in hospitalized adult patients (≥18 years old) focusing on a single species or group of species based on their antibiotic resistance profiles. Phase 2, 3, and 4 studies, and those from which phase information was not available, in patients with a laboratory-confirmed CR Gram-negative pathogen (Enterobacterales, especially Klebsiella spp. , Acinetobacter spp. , or Pseudomonas spp. ), registered from 2005 in clinical trial registries and with outcome data (including Day 28 or Day 30 ACM) reported from 2010, were included. The following sources were searched: ClinicalTrials. gov registry database, European Union Drug Regulating Authorities Clinical Trials Database, WHO International Clinical Trials Registry Platform, Cochrane database, and PubMed.
Primary analysis outcomes Each study identified was described according to a number of categories. Study design features recorded were: study dates; number of patients screened/enrolled and randomization ratio; number of study sites and geographical locations; antibiotics and dose regimens used; study design and development phase; treatment duration; target pathogens; key inclusion and exclusion criteria; study endpoints and the primary analysis population. Intervention treatments were described as either older generic or new antibiotics. Patient Data summarized from the analyses were descriptive and no formal statistical analysis plan was utilized. Day 28 (or Day 30) ACM rates were analyzed by treatment arm; point estimate and within-arm 95% confidence intervals (CIs) calculated by the Clopper-Pearson test are presented.
Of note, the degree of heterogeneity and risk of bias were not assessed in this review as it was not a full systematic review, and it was not registered in the PROSPERO database. Instead, a comprehensive review of the registered studies and the available literature to identify studies with Day 28 ACM result in CR Gram-negative infections was conducted. However, two recently published review papers included quality appraisal of six of the analyzed studies included in our review. Five of the analyzed studies in this review were assessed in a systematic literature review conducted by Savoldi et al. [38]. According to their assessment, the AIDA study had low risk of bias in all six domains, the Durante-Mangoni study had moderate or critical risk of bias, the Sirijatuphat, TANGO II, and CARE studies had low, moderate and critical risk of bias.
Acknowledgments Editorial assistance was provided by  Highfield Communication , funded by  Shionogi. The data included in the current analysis were partly presented in an abstract for the 30 th European Congress of Clinical Microbiology & Infectious Diseases in 2020: Lodise T,  Bassetti M, Ferrer R ,  Naas T ,  Niki Y, Paterson D ,  Zeitlinger M, Tillotson G, Echols R. Comparison  of 28-day mortality rates of recently completed prospective, randomised treatment studies of adult patients with carbapenem-resistant Gram-negative bacterial infections. Abstract 2497. Available at: https://www. escmid. org/escmid_publications/eccmid_abstract_book/. Accessed:  20 October 2021.
aeruginosa • Hospitalized adults • Hospitalized • Hospitalized adults in • Hospitalized adults ≥18 years ≥18 years adults ≥18 years the ICU • HAP/VAP, cUTI, or cIAI • BSI, HAP/VAP, or • CR A. • Pneumonia, cIAI, BSI, caused by IMI-non- cIAI baumannii cUTI, and other sites susceptible, IMI/RELE- • Life-threatening infection susceptible, colistin- nosocomial requiring COL susceptible organisms infection due to therapy • Failure on prior antibiotic XDR A. baumannii therapy • Prior treatment with • Infections caused • No criteria specified • APACHE II score >30 COL or RIF during by CS pathogens the index hospitalization (Continued ) AIDA NCT01732250 [32] 2013-2016 802 406 6 (Israel, Greece, Italy) COL + MEM COL 9 MIU loading 9 MIU dose + 4. 5 loading MIU q12h + dose + 2 g q8h 4. 5 MIU q12h Open label 4 1:1 7-14 CR Enterobacterales and CR non-fermenters • Hospitalized adults with severe infections caused by CR NS, COL-susceptible, GN bacteria BSI, HAP/VAP, or urosepsis • Prior COL for >96 h • Polymicrobial CS GN bacteria TANGO II CREDIBLE-CR NCT02168946 [30] NCT02714595 [31] 2014-2017 2016-2019 85 257 77 152 27 (Argentina, 95 (16 countries) b Brazil, Colombia, Greece, Israel, Italy, UK, USA) MEM/ VAB BAT CFDC BAT 2 g/2 g, q8h -2 g, q8h - Open label Open label 3 3 2:1 2:1 7-14 7-14 CR CR Enterobacterales Enterobacterales and CR non- fermenters • Hospitalized • Hospitalized adults ≥18 years adults ≥18 years • cUTI, HAP/ • HAP/VAP/HCAP, VAP, BSI, or cIAI BSI, or cUTI • Suspected/ caused by CR GN confirmed CRE bacteria infection • Antibiotic • Antibiotic therapy therapy for <72 h before >24 h before enrollment with enrollment a continuous • Confirmed duration of CRE-producing >24 h for cUTI or NDM, VIM, or >36 h for other OXA-encoded infections beta-lactamases • APACHE II score • APACHE II >30 score >30 CARE a NCT01970371 [29] 2014-2016 >2000 69 5 (Brazil, Greece, Italy, Turkey, USA) PLAZ COL 15 mg/ 5 mg/ kg kg Open label d 3 1:1 7-14 CR Enterobacterales • Hospitalized adults 18- 85 years • BSI, HAP/VAP, or cUTI/AP caused by suspected/ confirmed CRE infection • Antibiotic therapy for >72 h (HAP/ VAP) or <48 h (cUTI) before enrollment • CRE pathogen resistance to colistin Study period No.
VI. ACKNOWLEDGMENTS This work has been done within the framework of the project MOLINT which has received funding from the  Excellence Initiative of Aix-Marseille University -A*Midex , a  French "Investissements d'Avenir" programme. This work was also partially supported by the  Seventh Framework Programme for Research of the European Commission  under  FET-Proactive grant TOPDRIM  ( FP7-ICT-318121 ),  Matteo Gori  thanks the financial support of  DARPA (USA)  for his long term visit at  Howard University at Washington  D. C. during which part of this work was done.
| Study design We performed a systematic review of the literature on the association between dog ownership and mental health in older adults living at home. The eligibility criteria and search strategy are described below. We reported our results in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines  34  (supplementary file). The systematic review's protocol was registered prospectively in the PROSPERO (reference: CRD42020216464). We searched the PROSPERO and clinicaltrials. gov databases for similar studies; none were found.
| Search strategy We searched the PubMed, EMBASE, Cochrane Library, Google Scholar, PsycInfo, Web of Science, OpenGrey and Grey Literature databases, together with a list of French MD theses. The search period ran from January 2005 and December 2020. A four-step strategy was applied. Firstly, we searched PubMed using the keywords "dog", "dog owner", "pet", "pet owner", "depress*", "anxiety", "anxious", "insomnia", "sleep", "elderly", and "aged". Secondly, we used the results of this preliminary search to expand our list of relevant keywords. Thirdly, we searched all the databases using the expanded list of keywords. Lastly, we screened the reference lists of the selected articles, reviews and meta-analysis. The search was limited to full-text articles published in English or French. Data were extracted from the selected publications and summarised in a table.
| Data extraction and analysis The risk of bias was assessed by scoring the Newcastle Ottawa Scale (NOS, for observational epidemiological studies)  35  or the Effective Practice and Organisation of Care scale (EPOC, for clinical trials). 36 The EPOC scales includes 8 risks, each classified as high risk and low risk. For the review, we rated the low risk 1, the high risk 0 and this on a scale ranging from 0 to 8. The NOS scale was scored from 0 to 9 with quality considered good for a score greater than or equal to 6. The studies' outcomes were examined in order to determine whether a meta-analysis of a common outcome was feasible. We included original publications grade I to IV of Sackett's level of evidence. 37.
54  are now conducting a prospective, comparative study (NCT04032340) of adults aged 75 and over, in France, in which the dog-owner relationship is characterised in detail. We shall then assess the association between having a dog as a companion on one hand and the feeling of loneliness and other mental health variables on the other. Lastly, it is possible that some breeds of dog are less suitable as pets for older adults. Dog breeders and sellers might require specific training on the best breeds in this context. Furthermore, the documented, positive impact of dog-mediated interventions  39  may suggests that specific training for dogs and for people who buy or adopt a dog might help to improve the owner's mental health. Greater access to canine services (e. g. pet sitters) might facilitate the acquisition of a pet dog by older adults.
Manually devitellinized embryos were stored in 0. 01% Tween 20 in PBS (PBS-T and embryos devitellinized with 50% methanol were stored in 100% methanol at -20°C and rehydrated in PBS-T). Embryos were washed in PBS-T, blocked with 10% BSA in PBS-T, and incubated with antibodies diluted in PBS-T. Embryos were incubated with primary antibodies at room temperature for 2 hr. Antibodies used in this study are listed in Supplementary file 1. Secondary antibodies used were conjugated with Alexa Fluor 488, 568, or 647 (Invitrogen) diluted at 1:500 in 5% BSA in PBS-T incubated overnight at 4°C. After antibody incubation, embryos were mounted onto glass slides using AquaPolymount (Polysciences). All images were taken on a Zeiss LSM 710 confocal microscope with a 40×/1. 2 Apochromat water objective lens, an argon-ion, 561 nm diode, 594 nm HeNe, 633 HeNe laser, and Zen software.
Laser ablation Laser ablations were performed using a two-photon Mai-Tai laser set to 800 nm on an LSM710 confocal microscope (Zeiss) through a 40×/1. 1 objective, using the Zen software (Zeiss) (WM Keck Microscopy Facility, Cambridge, MA). For ablations, laser power was set at 20%, with a scan speed of 1. 58 ms/px. Ablations were performed with four overlapping linear ROIs around one side of MD1. Sham ablations were performed with the same setup as the laser ablations except the laser power was set at 10%. This caused the ROIs to become bleached, but not ablated.
Acknowledgements We thank members of the  ACM lab  for helpful discussions on this work and comments on the manuscript. We thank  Apolonia Gardner  for examining PCP protein localization and coding assistance. We also thank the anonymous reviewers for their feedback. This work was funded by  NIGMS   R01GM105984  and  R35GM144115  to ACM. In addition, JC was supported by  NIH   Pre-doctoral training grant   T32GM007287. This material is also based upon work supported by the  National Science Foundation Graduate Research Fellowship  under Grant No. 2019275094.
Similarly, sys- We further analyzed human biopsies from patients with different subtypes of renal cell carcinoma (RCC). In all cases of RCCs, Notch3 was expressed by tubular epithelial cells (Figure  1B ). Reanalysis of publicly available data from The Cancer Genome Atlas (TCGA) revealed that NOTCH3 mRNA was expressed most strongly in clear cell renal cell carcinomas (Figure  1C ).
Experimental For the data acquisition the samples were dispersed in powder form on a copper grid covered with a holey amorphous carbon film. The electron diffraction data were obtained on a Philips CM300ST transmission electron microscope (TEM). The TEM is equipped with a Bruker AXS EDX, a Nanomegas spinning star precession module, a TVIPS F416 CMOS camera, and an in-house modified single tilt sample holder that allows tilt angles up to ±55 •. The chosen LD-EDT method  [13]  is based on a tomography of the reciprocal space. An isolated particle of the powder is selected for data acquisition. The size of the crystal should typically be between several tens of nanometers and around a micron. The crystal is then carefully adjusted at the eucentric height of the goniometer in order to move as little as possible during the tomography.
Without any prior orientation of the crystal, it is then placed inside a large selected area aperture (typically 2 µm in apparent diameter). The tomography data are then recorded over a large angular domain (usually between 60 • and 110 • ) in discrete steps of typically 1 •. In order to fully integrate the intensities over the reciprocal rods we applied precession to the diffraction  [15]  with a precession half-angle of 1. 05 •. In order to minimize the electron dose, the sample undergoes during the data acquisition, the electron beam was blanked at all times except for the recording of the diffraction frames. For more details about the LD-EDT method see  [13]. After each tomography an image of the vacuum close to the sample was recorded in the same illumination conditions as used for a single frame of the tomography.
Knowing the number of counts on the camera created by a single incident electron the electron dose for an individual diffraction frame was determined. The total dose used for the experiment is then obtained by multiplying the dose per frame with the number of frames. The values of the experimental parameters are given in Table  1. Starting from the recorded frames the indexing and reconstruction of the 3-dimensional reciprocal lattice was done using the PETS2 software  [16]. The structure solution was then attempted by SIR2014  [17]  and Superflip  [18]  embedded into Jana2006  [19]. For the refinement based on the dynamical theory of diffraction Jana2006 was used.
Examination of the diffraction pattern revealed the presence of the mixed Na, Mn germanate Na 2 (Mn 0. 26 Na 0. 74 ) Mn 5 Ge 6 O 20  [23] , the remaining peaks being indexable in a body-centered cubic unit cell with a ≈12 Å, similar to that of garnets such as e. g. , CdGeO 3  [24]. A successful Rietveld refinement was performed using the Fullprof Suite software  [25]  based on the garnet structure in the cubic Ia-3d (n • 230) space group symmetry. Ge atoms were placed at the 16a and 24d Wyckoff positions, a fixed composition Mn 1/3 Na 2/3 mixture at the 24c position, according to the stoichiometry deduced from the EDX measurements, and the oxygen atom at the 96c position. The scale factor, cell parameter, oxygen atom position, and an overall atomic displacement parameter (a. d. p. ) were refined.
8  shows the sections hk0, h0l, and 0kl of the reconstructed 3D reciprocal lattice and the cylindrical projection of the intensity clusters used for the refinement of the tilt axis orientation. The systematic extinctions were compatible with space groups Pn2 1 a and Pnma. The data set contains 2438 independent reflections which corresponds to a completeness of 80% up to 0. 8 Å resolution. The best structure solution was obtained by SIR2014 in space group Pnma with a final R value of 30%. All cation positions were obtained, attributed by SIR2014 to elements according to their number of electrons: the first position was attributed to As, followed by the Al. The next 14 positions correspond to the oxygen forming the coordination polyhedra around the cations. The following two positions that SIR2014 interpreted as being hydrogen correspond in fact to the oxygen positions of free water molecules in between the polyhedral layers (see Table  4  and Figure  9 ).
Biodiversity data Genetic diversity and differentiation. We used raw genotypes (i. e. called allele sizes) of North American amphibians compiled by  (Schmidt and Garroway 2021a). This data set was assembled from raw microsatellite datasets publicly archived in Dryad (DataDryad. org). To identify data sets we conducted a systematic search of the Dryad data repository with the following keywords: species name (e. g. Plethodon cinereus), "microsat*", "short tandem*", and "single tandem*". We used the IUCN Red List database to obtain a list of amphibian species native to North America for the search. We excluded datasets that lacked spatial reference, were not located in North America, did not sample neutral microsatellite loci, or had study designs that may have affected genetic diversity (including sampling island populations, or captive or managed populations).
In total the data sets include genotypes for 13680 individuals spanning 19 species sampled at 554 locations in the contiguous United States and Canada. We used gene diversity as a measure of genetic diversity because it is minimally affected by sample size  (Nei 1973; Charlesworth and Charlesworth 2010). Our measure of differentiation was population-specific FST  (Weir and Goudet 2017). Population-specific FST differs from pairwise FST in that it measures how far single populations in a sample have diverged from a common ancestor-this means it is comparable across studies and species. Population-specific FST was not estimable at 2 sites because it requires a minimum of 2 sample sites in the original dataset (n = 552). Species richness. We estimated species richness at each of our genetic diversity sample sites using amphibian range extent data from the IUCN RedList (IUCN 2019), applying filters for native, extant species ranges.
Structural equation modeling Environmental data. We measured resource and niche heterogeneity by computing Simpson's Diversity Index for landcover categories within buffers at each site. We obtained a 30 m resolution map of North American landcover data from the Commission for Environmental Cooperation  (CEC et al. 2015). This map is based on 2015 satellite imagery and has 19 standard land cover classifications which includes forests, shrubland, grassland, wetlands, cropland, barren land, and built-up land. Because this variable is scale-dependent, we recorded heterogeneity within 4 buffer sizes (10, 25, 40, and 80 km) around each site. We used two measures of resource availability because amphibians are habitat-limited by both temperature and water availability. Water availability can be measured by evapotranspiration, or the amount of water removed from the Earth's surface through soil or open water evaporation and plant transpiration processes.
We measured mean PET and AET (mm/yr) at sites within 10, 25, 40, and 80 km buffers using data from the CGIAR Consortium for Spatial Information  (Trabucco and Zomer 2019). Population size. Body size is a readily measured trait that is typically negatively correlated with long-term effective population size across a diversity of species  (Frankham 1996; Romiguier et al. 2014; Mackintosh et al. 2019). To explore whether body size was a useful substitute for longterm effective population size in amphibians, we obtained body length data from the AmphiBIO v1 database  (Oliveira et al. 2017). We then regressed it on gene diversity in a hierarchical model with species as a random effect allowing intercepts to vary and predicted a negative relationship. We found no relationship between body size and genetic diversity in our data (Fig.