cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7743104
title: Molecular detection of Mycoplasma suis in extensive pig production systems in the State of Maranhão, northeast Brazil

description: Abstract Mycoplasma suis is a bacterium that causes hemoplasmosis in pigs. This agent is capable of adhering to the surface of porcine erythrocytes, inducing structural changes on these cells. In Brazil, there are few reports about the disease, its causal agent, and the economic impact of this pathogen on pig production systems and farm sanitation. The present study aimed to investigate the occurrence of M. suis in extensive swine farms located in the counties of Itapecuru Mirim, Santa Rita and Rosario, State of Maranhão, northeast Brazil. For such purpose, 64 blood samples of pigs from these facilities were tested for M. suis using a 16S rRNA gene-based quantitative real-time PCR (qPCR); 82.3%, 65.2% and 25% of blood samples of swine from farms in the cities of Itapecuru Mirim, Santa Rita and Rosario were positive for M. suis by qPCR, respectively. This study shows, for the first time, that M. suis circulates in pig populations from the state of Maranhão, Northeast Brazil.
DOI: 10.6084/m9.figshare.7743101.v1
title: Microscopic alterations in Fasciola hepatica from sheep treated with albendazole

description: Abstract Currently, albendazole is one of the most commonly used drugs because of its affordability. The objective was to evaluate the histopathology of Fasciola hepatica specimens. For this, the efficacy test was performed on sheep treated with albendazole at the dose recommended for F. hepatica, in which the helminths recovered at necropsy were counted and separated for histology. Spermatogenic cells from parasites recovered from treated and control sheep were examined by microscopy. The fecal egg-count reduction test revealed 97.06% efficacy of albendazole in the treatment of F. hepatica. Changes in testicular tubule cells started 48 hours after treatment and became evident within 72 hours, at which point it became difficult to identify cell types. Primary and secondary spermatogonia became increasingly rare and intercellular vacuolization was more evident. Signs of apoptosis, with pycnotic nuclei and evidence of keriorrexia were observed at all times. Cell debris was identified 96 hours after treatment. The results indicated that parasitic spermatogenesis was severely affected by albendazole and demonstrated the importance of the use of histopathology for the diagnosis of therapeutic efficacy in field strains.
DOI: 10.6084/m9.figshare.7743104.v1
title: Molecular detection of Mycoplasma suis in extensive pig production systems in the State of Maranhão, northeast Brazil

description: Abstract Mycoplasma suis is a bacterium that causes hemoplasmosis in pigs. This agent is capable of adhering to the surface of porcine erythrocytes, inducing structural changes on these cells. In Brazil, there are few reports about the disease, its causal agent, and the economic impact of this pathogen on pig production systems and farm sanitation. The present study aimed to investigate the occurrence of M. suis in extensive swine farms located in the counties of Itapecuru Mirim, Santa Rita and Rosario, State of Maranhão, northeast Brazil. For such purpose, 64 blood samples of pigs from these facilities were tested for M. suis using a 16S rRNA gene-based quantitative real-time PCR (qPCR); 82.3%, 65.2% and 25% of blood samples of swine from farms in the cities of Itapecuru Mirim, Santa Rita and Rosario were positive for M. suis by qPCR, respectively. This study shows, for the first time, that M. suis circulates in pig populations from the state of Maranhão, Northeast Brazil.
DOI: 10.6084/m9.figshare.7743107.v1
title: Dermatitis in humans caused by Ornithonyssus bursa (Berlese 1888) (Mesostigmata: Macronyssidae) and new records from Brazil

description: Abstract Ornithonyssus bursa, known as the “tropical fowl mite”, is a hematophagous mite of domestic and wild birds, occasionally biting humans. Infestation on humans occurs mainly when the abandoned nests are close to homes, or by manipulation of infested birds by humans. In Brazil, this species occurs in the south and southeast of the country. In the present study we are reporting bites on humans, new localities records, host associations, and molecular information of O. bursa.
DOI: 10.7284/106668
title: Multibeam Echosounder data collected during research cruise AMAT06RR using a Kongsberg EM120 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7743095
title: Frequency and factors associated with Theileria equi, Babesia caballi and Trypanosoma evansi in equids from Bahia (Northeast Brazil)

description: Abstract The aim of this study was to determine the frequency and factors associated to Babesia caballi, Theileria equi and Trypanosoma evansi in naturally infected equids from the northeast Brazil. Blood samples from 569 equids (528 horses, 8 mules, and 33 donkeys) were collected and tested for the presence of DNA of each of these protozoan parasites by PCR. Generalized linear models were used to evaluate risk factors associated with the infection. The frequency of T. equi infection was 83.5% (475/569) - 84.3% in horses, and 73.2% in donkeys and mules. The results of the final model indicated that age (senior group) and animal species (mule and donkey group) were protective factors against this pathogen. The frequency of B. caballi infection was 24.3% (138/569) - 23.5% in horses and 34.1% in donkeys and mules. Age (adult and senior group) was considered a protective factor against B. caballi infection whereas animal species (donkey and mule group) were considered a risk factor for the infection. Trypanosoma evansi infection was not detected in any of animals. Our results suggest that equids from the area studied may be infected earlier in life with the etiological agents of equine piroplasmosis and become asymptomatic carriers.
DOI: 10.6084/m9.figshare.7743098.v1
title: Using a Multivariate Approach to Compare Lipid Extraction Protocols from Microalgae Scenedesmus sp.

description: Microalgae lipid-derived biofuels is considered promising candidates for substitution of petroleum-based energy sources. However, the lipid extraction from the algal biomass stands as a challenge due to its low yields and cost-intensive cell disruption procedures. In this study a multivariate optimization of the extraction conditions was suggested, aiming a maximization of the lipid extraction from Scenedesmus sp. microalgae grown using wastewater as a nutrient medium. The extraction method, extraction time, solvent mixture and pretreatment were considered between upper and lower levels in order to access their significance, including their interactions, on the experimental response, while using a reduced number of experiments. The studies were performed using low-cost extraction methods (magnetic stirring and ultrasonication). The optimal extraction condition was obtained using CHCl3:MeOH (2:1) solvent mixture, in a 2-hour extraction period using ultrasonication. Fatty acid profiles of extracted lipids were also evaluated.
DOI: 10.6084/m9.figshare.7743026
title: ALL_GENE_EXPR_DEG_ANALYSIS.xlsx

description: Information for each sample, including the expression abundance of each gene, testing statistics and DEGs<br> ---------------------------------<br>target_id gene ID test_stat sleuth DEG testing statistics pval p-value qval adjusted p-value ext_gene gene symbol description gene categories including protein_coding, lincRNA, antisense_RNA, NOVEL_lncRNA, sense_intronic and sense overlapping HCM269-sc6.LV expression abundance (TPM) for each gene in each sample HCM the mean of expression abundance of all HCM samples Normal the mean of expression abundance of all Normal samples Log2FC log2 fold change between HCM and Normal StatSig Statistically significant BioSig Biologically significant Sig Both statistically and biologically significant
DOI: 10.6084/m9.figshare.7743092
title: Use of Mini-FLOTAC and Fill-FLOTAC for rapidly diagnosing parasitic infections in zoo mammals

description: Abstract Animals reared in restricted environments are highly susceptible to gastrointestinal infection by helminths and protozoa and therefore zoos are characterized as being parasite-rich environments. Successful implementation of control programs of these parasites in zoo environment depends upon precise and rapid diagnosing of gastrointestinal infections. The aim of this study was to demonstrate the role of the Mini-FLOTAC technique in combination with Fill-FLOTAC for rapidly diagnosing parasitic infections in zoo mammals. Fecal samples were collected from 70 animals in four different zoos located in central and southern Italy. All the samples were analyzed using Mini-FLOTAC in combination with Fill-FLOTAC. Out of the 70 pooled samples examined, 80% (24/30) were positive for at least one parasite. Among the gastrointestinal nematodes, Strongyles were the most frequent (40%), followed by Trichuris spp. (23.3%), Parascaris spp. (13.3%) and Capillaria spp. (3.3%). Among the protozoa, Blastocystis spp., Giardia spp. and Eimeria spp. were detected in 6.6%, 3.3% and 3.3%, respectively. These results show that Mini-FLOTAC in combination with Fill-FLOTAC can be used, not only for rapidly diagnosing parasitic infections in zoo mammals, but also for monitoring control programs in which large numbers of fecal samples need to be examined rapidly and reliably.
DOI: 10.6084/m9.figshare.7743095.v1
title: Frequency and factors associated with Theileria equi, Babesia caballi and Trypanosoma evansi in equids from Bahia (Northeast Brazil)

description: Abstract The aim of this study was to determine the frequency and factors associated to Babesia caballi, Theileria equi and Trypanosoma evansi in naturally infected equids from the northeast Brazil. Blood samples from 569 equids (528 horses, 8 mules, and 33 donkeys) were collected and tested for the presence of DNA of each of these protozoan parasites by PCR. Generalized linear models were used to evaluate risk factors associated with the infection. The frequency of T. equi infection was 83.5% (475/569) - 84.3% in horses, and 73.2% in donkeys and mules. The results of the final model indicated that age (senior group) and animal species (mule and donkey group) were protective factors against this pathogen. The frequency of B. caballi infection was 24.3% (138/569) - 23.5% in horses and 34.1% in donkeys and mules. Age (adult and senior group) was considered a protective factor against B. caballi infection whereas animal species (donkey and mule group) were considered a risk factor for the infection. Trypanosoma evansi infection was not detected in any of animals. Our results suggest that equids from the area studied may be infected earlier in life with the etiological agents of equine piroplasmosis and become asymptomatic carriers.
DOI: 10.7284/106669
title: Singlebeam Echosounder data collected during research cruise AMAT06RR using a Knudsen 320B/R instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742948
title: stringtie_merged.strand.lncRNA.proteincoding.fa

description: Transcirpt sequence for lncRNA and protein-coding genes assembled in 37 samples (fasta format)
DOI: 10.6084/m9.figshare.7742954
title: Supplementary Table 1-2

description: Supplementary Table 1. Primers used for quantitative real time PCR.Supplementary Table 2. Overlapped DEGs among five microarray datasets.<br><br>
DOI: 10.6084/m9.figshare.7743092.v1
title: Use of Mini-FLOTAC and Fill-FLOTAC for rapidly diagnosing parasitic infections in zoo mammals

description: Abstract Animals reared in restricted environments are highly susceptible to gastrointestinal infection by helminths and protozoa and therefore zoos are characterized as being parasite-rich environments. Successful implementation of control programs of these parasites in zoo environment depends upon precise and rapid diagnosing of gastrointestinal infections. The aim of this study was to demonstrate the role of the Mini-FLOTAC technique in combination with Fill-FLOTAC for rapidly diagnosing parasitic infections in zoo mammals. Fecal samples were collected from 70 animals in four different zoos located in central and southern Italy. All the samples were analyzed using Mini-FLOTAC in combination with Fill-FLOTAC. Out of the 70 pooled samples examined, 80% (24/30) were positive for at least one parasite. Among the gastrointestinal nematodes, Strongyles were the most frequent (40%), followed by Trichuris spp. (23.3%), Parascaris spp. (13.3%) and Capillaria spp. (3.3%). Among the protozoa, Blastocystis spp., Giardia spp. and Eimeria spp. were detected in 6.6%, 3.3% and 3.3%, respectively. These results show that Mini-FLOTAC in combination with Fill-FLOTAC can be used, not only for rapidly diagnosing parasitic infections in zoo mammals, but also for monitoring control programs in which large numbers of fecal samples need to be examined rapidly and reliably.
DOI: 10.6084/m9.figshare.7742927
title: stringtie_merged.strand.lncRNA.proteincoding.gtf

description: Annotation for lncRNA and protein-coding genes in 37 samples (gtf format)
DOI: 10.6084/m9.figshare.7742927.v1
title: stringtie_merged.strand.lncRNA.proteincoding.gtf

description: Annotation for lncRNA and protein-coding genes in 37 samples (gtf format)
DOI: 10.6084/m9.figshare.7742954.v1
title: Supplementary Table 1-2

description: Supplementary Table 1. Primers used for quantitative real time PCR.Supplementary Table 2. Overlapped DEGs among five microarray datasets.<br><br>
DOI: 10.7284/106666
title: Winch data collected during research cruise AMAT06RR using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742933
title: Supplementary Figure 1-3 and Table 1-2

description: Figure S1: Schematic overview of the proposed approach.Figure S2: THBS2 mRNA expression in HSCs and hepatocytes.Figure S3: THBS2 and αSMA protein expression in BDL rats.Table S1. Primers used for quantitative real time PCR.Table S2. Overlapped DEGs among five microarray datasets.<br><br>
DOI: 10.7284/106676
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AMAT08RR using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742900
title: Endemic infection can shape exposure to novel pathogens: Pathogen co-occurrence networks in the Serengeti lions

description: These data sets include pathogen, environmental and behavioural data from 105 lions sampled as part of the Serengeti Lion Project. Tabs 1-4 are the pathogen data based on qPCR results and serological evidence at two levels of taxonomic resolution (see Table S2 in the associated text for details); High resolution (HighRes) down to species or genotype level and medium resolution (mediumRes) down to genus level or sub-type level. Tabs 5-6 include pathogen trait data for both levels of taxonomic resolution. Tab 7 are associated lion, pride and environmental data (see Table 2 in the associated text for details).
DOI: 10.7284/106673
title: Expendable Probe data collected during research cruise AMAT08RR using a Sippican MK21 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742900.v1
title: Endemic infection can shape exposure to novel pathogens: Pathogen co-occurrence networks in the Serengeti lions

description: These data sets include pathogen, environmental and behavioural data from 105 lions sampled as part of the Serengeti Lion Project. Tabs 1-4 are the pathogen data based on qPCR results and serological evidence at two levels of taxonomic resolution (see Table S2 in the associated text for details); High resolution (HighRes) down to species or genotype level and medium resolution (mediumRes) down to genus level or sub-type level. Tabs 5-6 include pathogen trait data for both levels of taxonomic resolution. Tab 7 are associated lion, pride and environmental data (see Table 2 in the associated text for details).
DOI: 10.6084/m9.figshare.7742933.v2
title: Supplementary Figure 1-3 and Table 1-2

description: Figure S1: Schematic overview of the proposed approach.Figure S2: THBS2 mRNA expression in HSCs and hepatocytes.Figure S3: THBS2 and αSMA protein expression in BDL rats.Table S1. Primers used for quantitative real time PCR.Table S2. Overlapped DEGs among five microarray datasets.<br><br>
DOI: 10.7284/106670
title: GNSS (Global Navigation Satellite System) data collected during research cruise AMAT08RR using a Furuno GP-90D instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742933.v4
title: Supplementary Figure 1-3 and Table 1-2

description: Figure S1: Schematic overview of the proposed approach.Figure S2: THBS2 mRNA expression in HSCs and hepatocytes.Figure S3: THBS2 and αSMA protein expression in BDL rats.Table S1. Primers used for quantitative real time PCR.Table S2. Overlapped DEGs among five microarray datasets.<br><br>
DOI: 10.6084/m9.figshare.7742888
title: Monitoring the Stability of the Cosmetic "Sabonete Artesanal Cacau e Hortela".

description: Monitoring of the stability of the hand made cosmetic product with the name "Sabonete Artesanal Cacau e Hortela" from Da Minha Casinha, Cosmetica Natural. The study included the monitoring of the pH, density and the organoleptic properties color and shape. Image analysis and statistical analysis of data was conducted using software developed in python by BioenhancerSystems. Data was obtained during 3 months form April to Jully 2018.
DOI: 10.6084/m9.figshare.7742933.v3
title: Supplementary Figure 1-3 and Table 1-2

description: Figure S1: Schematic overview of the proposed approach.Figure S2: THBS2 mRNA expression in HSCs and hepatocytes.Figure S3: THBS2 and αSMA protein expression in BDL rats.Table S1. Primers used for quantitative real time PCR.Table S2. Overlapped DEGs among five microarray datasets.<br><br>
DOI: 10.7284/106671
title: GNSS (Global Navigation Satellite System) data collected during research cruise AMAT08RR using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742888.v2
title: Monitoring the Stability of the Cosmetic "Sabonete Artesanal Cacau e Hortela".

description: Monitoring of the stability of the hand made cosmetic product with the name "Sabonete Artesanal Cacau e Hortela" from Da Minha Casinha, Cosmetica Natural. The study included the monitoring of the pH, density and the organoleptic properties color and shape. Image analysis and statistical analysis of data was conducted using software developed in python by BioenhancerSystems. Data was obtained during 3 months form April to Jully 2018.
DOI: 10.6084/m9.figshare.7742888.v1
title: Monitoring the Stability of the Cosmetic "Sabonete Artesanal Cacau e Hortela.

description: Monitoring of the stability of the hand made cosmetic product with the name "Sabonete Artesanal Cacau e Hortela" from Da Minha Casinha, Cosmetica Natural. The study included the monitoring of the pH, density and the organoleptic properties color and shape. Image analysis and statistical analysis of data was conducted using software developed in python. Data was obtained during 3 months form April to Jully 2018.
DOI: 10.7284/106672
title: Meteorological Station data collected during research cruise AMAT08RR using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106677
title: Multibeam Echosounder data collected during research cruise AMAT08RR using a Kongsberg EM120 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106674
title: Winch data collected during research cruise AMAT08RR using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742819
title: Code and data for Nutrient stoichiometry shapes microbial coevolution

description: Data and code supporting 'Nutrient stoichiometry shapes microbial coevolution. Larsen, M.L., S.W. Wilhelm, and J.T. Lennon.'<br><br>ABSTRACT Coevolution is a force contributing to the generation and maintenance of biodiversity. It is influenced by environmental conditions including the scarcity of essential resources, which can drive the evolution of defense and virulence traits. We conducted a long-term chemostat experiment where the marine cyanobacterium <i>Synechococcus</i> was challenged with a lytic phage under nitrogen (N) or phosphorus (P) limitation. This manipulation of nutrient stoichiometry altered the stability of host-parasite interactions and the underlying mode of coevolution. By assessing infectivity with &gt;18,000 pairwise challenges, we documented directional selection for increased phage resistance, consistent with arms-race dynamics while phage infectivity fluctuated through time, as expected when coevolution is driven by negative frequency-dependent selection. The resulting infection networks were 50 % less modular under N- versus P-limitation reflecting host-range contraction and asymmetric coevolutionary trajectories. Nutrient stoichiometry affects eco-evolutionary feedbacks in ways that may alter the dynamics and functioning of environmental and host-associated microbial communities.
DOI: 10.6084/m9.figshare.7742813
title: Accessibility maps by twenty-four 2SFCA models

description: This dataset includes 24 maps generated by the two-step floating catchment area (2SFCA) method with 24 different distance decay functions. Please refer to Table 1 in the paper (Chen & Jia, 2019) for the formulation of these functions. <br>Reference: Chen, X., & Jia, P. (2019) A comparative analysis of accessibility measures by the two-step floating catchment area (2SFCA) method. <i>International Journal of Geographical Information Science</i>, In Press.<br>
DOI: 10.7284/106679
title: Expendable Probe data collected during research cruise AMAT09RR using a Sippican MK21 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7742819.v1
title: Code and data for Nutrient stoichiometry shapes microbial coevolution

description: Data and code supporting 'Nutrient stoichiometry shapes microbial coevolution. Larsen, M.L., S.W. Wilhelm, and J.T. Lennon.'<br><br>ABSTRACT Coevolution is a force contributing to the generation and maintenance of biodiversity. It is influenced by environmental conditions including the scarcity of essential resources, which can drive the evolution of defense and virulence traits. We conducted a long-term chemostat experiment where the marine cyanobacterium <i>Synechococcus</i> was challenged with a lytic phage under nitrogen (N) or phosphorus (P) limitation. This manipulation of nutrient stoichiometry altered the stability of host-parasite interactions and the underlying mode of coevolution. By assessing infectivity with &gt;18,000 pairwise challenges, we documented directional selection for increased phage resistance, consistent with arms-race dynamics while phage infectivity fluctuated through time, as expected when coevolution is driven by negative frequency-dependent selection. The resulting infection networks were 50 % less modular under N- versus P-limitation reflecting host-range contraction and asymmetric coevolutionary trajectories. Nutrient stoichiometry affects eco-evolutionary feedbacks in ways that may alter the dynamics and functioning of environmental and host-associated microbial communities.