dataesr/scientific-paragraphs-categorization huggingface dataset:
The few metazoans in the networks were assigned to the Nematoda and Annelida (Table  S4 ). Although we found protists, fungi, and metazoans cooccurring with the short-branch microsporidians, the network analyses do not directly demonstrate that they actual hosts. Co-occurrences can be inferred because of similar environment preferences, and actual biotic interactions may not have been inferred because the signal was too weak in the data  [15]. Additionally, some of the co-occurrences here could have been inferred just because the cercozoans, fungi, and apicomplexans were extremely OTU-rich in the dataset. Potentially more of the short-branch microsporidians could have metazoan hosts, but the use of the SSU-rRNA environmental sequences likely underestimated their diversity, highlighted by the low proportion (1.
All primer sequences used in standard PCR and sequencing are listed in Table  2. All PCR reactions were performed in an Applied Biosystems 2720 Thermal Cycler model (Thermo Fisher Scientific Courtaboef, France) using AmpliTaq 360 Master Mix (Thermo Fisher Scientific Courtaboef, France) according to the manufacturer's recommendations. Negative and positive controls were included in each reaction. PCR products were visualized by electrophoresis on a 1. 5% agarose gel stained with Syper Safe stain (Invitrogen, USA) and analyzed using Lab Image software (BioRad, Marnes-La-Coquette, France). PCR products were purified using NucleoFast 96 PCR plates (Macherey Nagel, EURL, Hoerdt, France), according to the manufacturer's recommendation. The purified PCR products were sequenced using the Big Dye Terminator Cycle Sequencing Kit (Perkin Elmer Applied Biosystems, Foster City, CA, USA) with an ABI automated sequencer (Applied Biosystems).
Phylogenetic analyses Multiple sequence alignments were performed between the obtained sequences and other reference sequences in GenBank using CLASTAL W in MEGA software version X  [83]. Phylogenetic trees were inferred using the Maximum-Likelihood method and Tamura-Nei model with 500 bootstrap replicates in MEGA X software  [83, 84]. Anaplasmataceae 23S rRNA (TtAna) 23S rRNA Ana-rpoB TtAna-F-TGACAGCGTACCTTTTGCAT TtAna-R-GTAACAGGTTCGGTCCTCCA TtAna-S-CTTGGTTTCGGGTCTAATCC Ana23S-212F-GTTGAAAARACTGATGGTATGCA Ana23S-753R-TGCAAAAGGTACGCTGTCAC rpoB-F-GCTGTTCCTAGGCTYTCTTCGCGA rpoB-R-AATCRAGCCAVGAGCCCCTRTAWGG - 55˚C 52˚C [24] Rickettsia sp. gltA (RKNDO3) gltA OmpB RKNDO3-F-GTGAATGAAAGATTACACTATTTAT RKNDO3-R-GTATCTTAGCAATCATTCTAATAGC RKNDO3-S-CTATTATGCTTGCGGCTGTCGGTTC CS2D-ATGACCAATGAAAATAATAAT CSEnd-CTTATACTCTCTATGTACA 120-M59-CCGCAGGGTTGGTAACTGC 120-607-AATATCGGTGACGGTCAAGG 120-1497-CCTATATCGCCGGTAATT - 50˚C 50˚C [136] [137] [138] Borrelia sp.
The overall prevalence of anaplasmoses in different animals was 8. 6%, with 28. 4% in cattle (25/88), 6. 9% in buffaloes (4/58), 7. 7% in sheep (2/26), 6. 7% in camels (10/149) and 3. 4% in dogs (7/203), while goats were free of Anaplasma DNA. BLAST analysis revealed that cattle, sheep and camel were positive An. marginale, including two different genotypes of An. marginale, the first originated from sixteen cattle, two sheep and one camel with 100% (455/455) similarity to those of An. marginale detected in Rh. bursa collected from cattle in France (GenBank KY498335), and another new genotype was detected in two cattle with 99% (454/455) identity to the same reference dataset (GenBank KY498335). Moreover, one case of cattle was positive for An. centrale with 100% identical to An. centrale strain Israel (GenBank NR076686).
From cattle and sheep, a genotype of An. ovis was identified with 100% (454/454) similarity to An. ovis in sheep blood from Niger (GenBank KY644694). We found that dogs and camels were positive for An. platys, including two different genotypes of An. platys, one genotype from six dogs and one camel with 100% (458/458) identity to An. platys in dog blood from France (GenBank KM021425) and another genotype from one dog with 100% (458/458) homology to An. platys in dog blood from France (GenBank KM021414). Finally, from cattle, buffaloes, sheep and camels, a new potential Anaplasma sp. was identified including, four different genotypes of this Anaplasma sp. , the first genotype from six camels, the second from two camels, the third from one cattle and one sheep and the last from two cattle and two buffaloes with 98% (450/458), 98% (448/458), 98% (447/458) and 97% (446/458) similarity, respectively, to An.
platys in dog blood from France (GenBank KM021414). Sequence analysis of this Anaplasma species revealed that this species has a homology score below 99% (more than 10 nucleotides different) and are closely related to An. platys, that means these sequences could be considered as potential new species of Anaplasma and can be called as An. platys-like. The phylogenetic tree showed that the new potential Anaplasma sp. in two separates and well-supported branches (bootstraps 99 and 96) belong to the cluster of An. platys (Fig  3 ). To better characterize different Anaplasma genotypes, rpoB genus-specific PCR primers were applied and 23 good quality sequences were identified. The result revealed that, 12 cattle and one sheep were positive for a genotype of An. marginale with 100% (487/487) homology with An.
marginale in Rhipicephalus bursa from France (KY498345), and another genotype of An. marginale from one cattle with 99% (486/487) similarity with the same reference dataset. We also identified that cattle and sheep were positive for An. ovis, one genotype was found in two cattle and another in a sheep with 100% (489/489) and 99% (487/489) identical to those of An. ovis in sheep blood from Niger (GenBank KY644695), respectively. From dogs, we identified a new genotype of An. platys obtained from two dogs with 99% (488/489) homology to An. platys in dog blood from France (GenBank KX155493). Finally, from cattle, buffaloes and sheep, a new potential species of Anaplasma. was identified, its sequences had a homology score of less than 90%, confirming that these sequences are likely to be a new potential species of Anaplasma (like 23S rRNA gene).
The only two different genotypes (one from two buffaloes and another from a cattle and a sheep) showed a low identity of 89% (432/486) and 88% (431/ 486), respectively, with An. platys in dog blood from France (GenBank KX155493), while identification of the genotype derived from camels failed. Phylogenetic analysis revealed a new potential Anaplasma sp. (An. platys-like) in a separate and well-supported branch (bootstraps 99) with the same clade belonging to An. platys (Fig  4 ). Rickettsial infection was detected by qPCR targeting gltA gene in dogs (3/557; 0. 54%); the other animal hosts were free of rickettsiosis. To identify Rickettsia sp. , standard PCR and sequencing were performed using gltA gene, and it was possible to amplify a 728 bp fragment of this gene from these three positive samples.
A BLAST search of the obtained sequences with those in GenBank revealed that two different genotypes, one genotype was 100% (728/728) identical with R. africae previously detected in H. dromedarii from Egypt (GenBank: HQ335126), and the other sequence had 99% (726/728) identity with the same reference. Moreover, ompB gene was used to confirm the detection of R. africae-like infection in dogs. Based on the BLAST search, the sequences obtained from dogs were identified as R. africae (GenBank: MN629894) and showed (757/758) 99% similarity with the reference stain of R. africae detected in a traveler returning from Tanzania (GenBank: KU721071). The phylogenetic tree of these R. africae-like in dogs based on gltA was shown in Fig  5. Screening of Borrelia sp. in all animal hosts we found that 3 cattle and 2 sheep were positive for Borrelia sp.
(5/557; 0. 9%). Standard PCR and sequencing using 16S rRNA gene identified it as Bo. theileri. Alignment of five obtained sequences of Borrelia sp. from our samples revealed that all sequences were identical to each other. Furthermore, comparison of the obtained sequences with sequences from the GenBank database showed that 1139/1143 (99%) identity with Bo. theileri detected in Rh. geigyi in Mali (GenBank: KF569941). The phylogenetic position of this new Bo. theileri genotype was shown in Fig  6. Two out of 557 (0. 36%) blood samples from one sheep and one goat tested positive for C. burnetii DNA by qPCR targeting IS1111. MST genotyping was performed using Cox2, Cox5 and Cox18, with only Cox2 successfully identified and the other spacers failing amplification. A BLAST search for the two sequences obtained showed that (351/351) 100% identity with the reference sequences of C.
burnetii recorded in GenBank. Concerning Filariidae, four out of 557 (0. 7%) animal hosts collected from three dogs and one camel tested positive for Filaria sp. DNA. By BLAST analyses, two dogs were found to have D. repens with 100% identity to those of D. repens previously detected in a Japanese woman returned from Europe (GenBank AB973229), and another sequence obtained from one dog showed 99% (1114/1119) similarity to Ac. viteae (GenBank: DQ094171). Moreover, S. digitata with (1107/1111) 99% identity to S. digitata from UK (GenBank: DQ094175) was found in a camel. The phylogenetic analysis of these Filaria sp. was constructed and presented in Fig  7. Finally, seven of different animal hosts were positive for more than one vector-borne pathogen (co-infections; 7/557; 1. 3%). In cattle, five co-infections were observed (5/88; 5.
ovis in sheep from Giza and Beni-Suef and buffaloes from Beni-Suef. In Egypt, there are few studies reporting T. ovis in sheep  [90]  and buffaloes  [91]. In parallel, a recent study reported that T. ovis was detected in sheep from Menoufia and El-Wady El-Geded province  [92] , implying that this pathogen is widespread in sheep throughout Egypt. Finally, we detected one case of Ba. canis in a dog from Cairo province with 100% identity with Ba. canis vogeli detected in a dog from Egypt (GenBank: AY371197). Canine babesiosis is distributed worldwide and was later detected in Egypt by Passos et al. [93]  and Salem and Farag  [94]. In Africa, Ba. canis vogeli has been detected in different regions such as South Africa  [95] , Tunisia  [96]  and Cote d'Ivoire  [80]. Family Anaplasmataceae was known to cause human and animal diseases, is transmitted by ticks and has a worldwide distribution  [26, 97].
In this study, the overall prevalence of Q fever in sheep and goats from Sinai province is 0. 3% (3% in goats and 1. 7% in sheep). This result was in accordance with Abdel-Moein and Hamza  [71]  who reported an overall prevalence of Q fever of 0. 9% and 3. 4% in goats. PCR and sequencing amplified only Cox2 with a 100% match with the C. burnetii reference recorded in GenBank, while genotyping and sequencing of the positive samples with other spacers (Cox5 & Cox18) failed. This result can be explained by the fact that the high sensitivity of qPCR can detect low DNA concentrations and the lower prevalence of C. burnetii in blood is lower than feces and urine  [121, 122]. For filarial infections, we detected four cases of filarial infection with an overall prevalence of 0. 7%, 1. 5% (3/203) in dogs and 0.
7% (1/148) in camels. In dogs from the capital Cairo, we identified two different species of Filariidae as D. repens and Acanthocheilonema sp. Acanthocheilonema viteae is the filarial nematode of rodents, while Ac. reconditum is the etiological agent of filariasis in dogs. Also, there is no sequence of Ac. reconditum for the 18S rRNA gene in GenBank. Therefore, we suspect that the identified species is, however, Ac. reconditum. Therefore, this is the first report of D. repens and Ac. reconditum in dogs in Egypt. Subcutaneous dirofilariasis of domestic dogs is caused by D. repens and is common in Africa, Asia and Europe  [123]. It is a mosquito-borne nematode that is a public health problem  [124]. Acanthocheilonema reconditum colonizes the peritoneal cavity and adipose tissue and can cause skin lesions with allergy and is transmitted by fleas and biting lice  [78, 125, 126].
However, camels and goats were free of Piroplasmida DNA. The overall prevalence of piroplasmoses in different animal hosts was 23/557 (4. 1%) as it was 17% in cattle, 8. 6% in sheep, 7. 7% in buffaloes and 0. 5% in dogs. In our study, BLAST analysis revealed that cattle were positive for T. annulata and Ba. bigemina, including two genotypes of T. annulata, one genotype in 13 cattle with 100% (910/910) similarity to those of T. annulata detected in donkey blood in Turkey (GenBank: MG569892), a new genotype in one cattle with 99% (908/910) identity to the same reference dataset, and a new genotype of Ba. bigemina in one cattle with 99% (865/866) identity to those of Ba. bigemina detected in cattle blood from Switzerland (GenBank: KM046917). Similarly, we found that 5 sheep and 2 buffaloes were positive for a genotype of T.
This study was supported by the  Institut Hospitalo-Universitaire (IHU)  Mediterranee in cattle, a new An. platys-like in buffaloes, An. National Research Agency  under the program " Investissements d'avenir", reference ANRfunding FEDER PRIMI. The authors acknowledge funding from the  Science and Technology Development Fund (STDF)  and  Institut Francais d'Egypte (IFE)  (ID:  30652 ) for the support of this research. The funders just supported the study through chemicals availability. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
00" N, 32˚42' 59. 99" E Cattle households 10 Beheira 30. 61˚N, 30. 43˚E Cattle households 2 https://doi. org/10. 1371/journal. pntd. 0009767. t001 (ChromasPro 1. 7, Technelysium Pty Ltd. , Tewantin, Australia), and the corrected sequences were compared with the sequences available in GenBank by BLAST (https://blast. ncbi. nlm. nih. gov/Blast. cgi).
58 (3. 4%) 1/58 (1. 7%) 1/58 (1. 7%) However, camels and goats were free of Piroplasmida DNA. The overall prevalence of piroplasmoses in different animal hosts was 23/557 (4. 1%) as it was 17% in cattle, 8. 6% in sheep, 7. 7% in buffaloes and 0. 5% in dogs. In our study, BLAST analysis revealed that cattle were positive for T. annulata and Ba. bigemina, including two genotypes of T. annulata, one genotype in 13 cattle with 100% (910/910) similarity to those of T. annulata detected in donkey blood in Turkey (GenBank: MG569892), a new genotype in one cattle with 99% (908/910) identity to the same reference dataset, and a new genotype of Ba. bigemina in one cattle with 99% (865/866) identity to those of Ba. bigemina detected in cattle blood from Switzerland (GenBank: KM046917). Similarly, we found that 5 sheep and 2 buffaloes were positive for a genotype of T.
ovis with 100% (897/897) identity to T. ovis detected in wild sheep from Turkey (GenBank: KT851427). Finally, we identified Ba. canis in a dog with 100% (884/884) similarity to those of Ba. canis vogeli detected in a dog from Egypt (GenBank: AY371197). The phylogenetic tree of these genotypes was illustrated in Fig 2. Goat 33 Coxiella burnetii 1/33 (3%) Camel 149 Anaplasmataceae 10/149 (6. 7%) An. marginale 1/149 (0. 7%) An. platys 1/149 (0. 7%) An. platys-like 8/149 (5. 4%) Filariidae 1/149 (0. 7%) S. digitate Dog 203 Piroplasmida 1/203 (0. 5%) Ba. canis Anaplasmataceae 7/203 (3. 4%) An. platys Rickettsia sp. 3/203 (1. 5%) Rickettsia africae-like Filariidae 3/203 (1. 5%) D. repens 2/203 (1%) Ac. reconditum 1/203 (0. 5%) Co-infection : 1/203 (0. 5%) R. africae-like + Anaplasma https://doi.
From very early, the virus was able to replicate in the upper respiratory tract and to transmit readily from human to human. Since the beginning of the epidemic, an enormous amount of sequence data has been generated and these data are shared on the GISAID database, which is an asset for the surveillance of the virus. From these data, three general groups were identified, G, V and S, based on spatial distribution. The G group has a substitution in the spike protein (D614G) and this substitution has a competitive advantage, which enabled the G group to overwhelm the other viruses in less than two months' time, although it did not completely displace the other ones, which are still circulating in different places around the world. One theory is that the G viruses have a better fitness with a higher transmissibility rate, which is still under investigation.
Epidemiology Arnaud Fontanet, Director of the Department of Global Health, Head of the Emerging Diseases Epidemiology Unit, Institut Pasteur, France, shared the recent findings of studies with a focus on Europe, which are also relevant for other countries and regions. Mathematical modeling was done to construct the epidemic dynamics using data on hospitalization for COVID-19 in France. At the end of the lockdown in France, 5% of the population had been infected, with 10% for the two regions most impacted by the epidemic: the eastern part and the area around Paris. The basic reproductive number was estimated at 2. 9, which means that to stop virus circulation, at least two-thirds of the population need to develop immunity, either through natural infection or vaccination  [1]. To investigate if the lockdown had been effective in France to stop the virus from circulating and whether it was necessary to perform the lockdown at the national level as opposed to the regional level, hospital admission data were investigated by region for the 13 regions of France.
Background: Topical psoriasis treatment relies on a reactive rather than a long-term proactive approach to disease relapse. Objective: Assess long-term efficacy and safety of proactive psoriasis management with twice-weekly calcipotriene 0. 005%/betamethasone dipropionate 0. 064% (Cal/BD) foam. Methods: Phase III trial (NCT02899962) included a 4-week open-label lead-in phase (Cal/BD foam once daily) and a 52-week, randomized, double-blind, maintenance phase. A total of 545 patients achieved treatment success (physician's global assessment ''clear''/''almost clear,'' $2-grade improvement from baseline) and were randomized to proactive management (Cal/BD foam; n = 272) or reactive management (vehicle foam; n = 273) twice-weekly, with rescue treatment of Cal/BD foam once daily for 4 weeks upon relapse.
Trial design and interventions This phase III, multicenter trial (NCT02899962) included a screening and washout phase of up to 4 weeks, a 4-week open-label lead-in phase, a 52week randomized double-blind, vehicle-controlled maintenance phase, and an 8-week follow-up period (Supplementary Fig Eligible patients were $18 years, with truncal or limb psoriasis, or both, involving 2% to 30% of body surface area (BSA), physician's global assessment of disease severity (PGA) score of mild or higher (PGA $2) and modified psoriasis area and severity index (m-PASI) score $2 at baseline of the open-label leadin phase (hereafter referred to as baseline). Patients were not eligible if they had received systemic treatment with biologic therapies with a possible effect on psoriasis within 4 to 16 weeks (depending on therapy) and systemic treatment with other therapies with a possible effect on psoriasis within 4 weeks before baseline.
This trial was funded by  LEO Pharma, Ballerup, Denmark. LEO Pharma  supported the trial concept and design. Dr Warren  is supported by the  Manchester National Institute for Health Research Biomedical Research Centre. Conflicts of interest:  Dr Lebwohl  is an employee of  Mount Sinai  and receives research funds from  AbbVie Inc ,  Amgen, Arcutis Biotherapeutics, Boehringer Ingelheim, Dermavant Sciences Ltd, Eli Lilly and Company, Incyte ,  Janssen  Research  Dr Lacour  has received grants/research support as an investigator from  AbbVie Inc, Bristol-Myers Squibb ,  Boehringer Ingelheim ,  Celgene ,  Dermira ,  Galderma ,  Janssen Pharmaceuticals ,  Eli Lilly and Company, LEO Pharma ,  Merck ,  Novartis ,  Dr Perrot  has been an advisor and/or received speakers honoraria and/or received grants and /Author Takhar  has received grants/research support and/or been a medical advisor for  Amgen, AstraZeneca ,  Bayer ,  Boehringer Ingelheim, Cambridge and Peterborough Clinical Commissioning Group, Daiichi Sankyo, Dermal Laboratories, GlaxoSmithKline, LEO Pharma ,  Merck ,  Novartis ,  Pfizer ,  Roche , and  Sanofi ;  Author Takhar  has received grants/ research support from  National Institute of Health Research UK.
Dr Warren receives research grants from AbbVie Inc, Almirall, Amgen, Celgene, Janssen Pharmaceuticals, Eli Lilly and Company, LEO Pharma, Novartis, Pfizer, and UCB and is a consultant for AbbVie Inc, Almirall, Amgen, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Janssen Pharmaceuti-cals, LEO Pharma, Eli Lilly and Company, Novartis, Pfizer, Sanofi, and UCB. Dr Wollenberg has received grants, personal fees, or nonfinancial support from AbbVie Inc, Almirall, Beiersdorf, Bioderma, Chugai Pharmaceutical Co, Galapagos NV, Galderma, Hans Karrer, Accepted for publication September 8, 2020. Correspondence and reprint requests to: Mark Lebwohl, MD, Department of Dermatology, 1 Gustave L. Levy Place, Box 1048, New York, NY 10029. E-mail: lebwohl@aol. com. Published online September 18, 2020. 0190-9622 Ó 2020 by the American Academy of Dermatology, Inc.
Study Selection and Data Extraction All articles were selected by CC, who was then audited by MV. All the studies collected were considered. The PRISMA flowchart is represented on Figure  1. Only data reporting the application of antibiotic treatments for adult UTIs linked with KPCs were collected, as assessed in the eligibility criteria. Studies with unavailable abstracts were excluded immediately, as were basic research studies. All studies using animal models or non-representative study population were excluded. Studies with languages other than English and French were excluded. The first part of this systematic review consisted in defining infections caused by KPCp and finding its risk factors, clinical situations, and associated population. The second part of the review presents the different antibiotics available and their potential usage.
Flow cytometry analysis Frozen PBMCs were thawed, washed and stained with monoclonal antibodies (Supplementary Table  1 ) at room temperature for 15 min. LIVE/DEAD Fixable Aqua (Invitrogen) was used for dead cell exclusion. Samples were acquired on a LSR Fortessa (BD Biosciences), and all flow cytometry analyses were performed with FlowJo Version 10 software (Tree star, Inc). The NK cell subset gating strategy is depicted in the Supplementary Fig. 1.
CD107a-based degranulation assay The HLA class 1 negative lymphoblastoid cell line LCL721. 221 (LCL221) was maintained in complete medium (RPMI-1640 medium; Sigma, Life Science) supplemented with 10% heat-inactivated FBS (Sigma), 2 mM Glutamax (Gibco by Life Technologies), 1% Penicillin Streptomycin (Gibco) and tested negative for mycoplasma. LCL221 (Cellosaurus, RRID:CVCL_6263) has been authenticated by Microsynth using STR profiling in February 2020. For the degranulation assay with rIL-2 pre-stimulation, frozen PBMCs from 7 EBV+ and 7 EBV-cHL were thawed and incubated overnight with 100 IU recombinant interleukin-2 (rIL2) per ml. For the antibody-based degranulation assay without rIL-2 pre-stimulation, frozen PBMCs from 5 EBV+ cHL, 5 EBV-cHL and 5 HC were thawed and incubated overnight without any supplementary cytokines.
Statistical analysis Data were analyzed using Prism software (version 8. 41. ; GraphPad Software, Inc. ). P values < 0. 05 were considered significant. For the categorical data, Chi 2 statistical test was used. For the numerical data comparing 2 groups, unpaired t test was used. For statistical analysis of 3 groups, we used the one-way ANOVA test with Tukey's multiple comparisons test. Comparison between paired samples was assessed with the paired t test. Correlation studies were assessed with the Pearson test. Figures were created in Adobe Illustrator. Tables were created in Excel.