cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
MOESM1 of The effect of local variation in malaria transmission on the prevalence of sulfadoxine–pyrimethamine resistant haplotypes and selective sweep characteristics in Malawi
Creators: name: Artimovich, Elena
name: Atupele Kapito-Tembo
name: Pensulo, Paul
name: Osward Nyirenda
name: Brown, Sarah
name: Sudhaunshu Joshi
name: Taylor, Terrie
name: Mathanga, Don
name: Ananias Escalante
name: Laufer, Miriam
name: Takala-Harrison, Shannon
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Neuroscience
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 60506 Virology

description: Additional file 1: DHFR and DHPS microsatellite haplotypes. Description: Table of DHFR and DHPS microsatellite haplotypes. Reference strains V1S, 3D7 and HB3. “C”=Chikwawa, rural-high, “T”=Thyolo, rural-moderate, and “N”=Ndirande, urban-low. Mita 2011 (22) and Alam 2011 (21) refer to other publications which provide microsatellite haplotypes identified and shared between Southeast Asian and Malawian parasites at the pfdhps locus.
Additional file 1: of Polymorphisms on PAI-1 and ACE genes in association with fibrinolytic bleeding after on-pump cardiac surgery
Creators: name: Ozolina, Agnese
name: Strike, Eva
name: Nikitina-Zake, Liene
name: Jaunalksne, Inta
name: Krumina, Angelika
name: Lacis, Romans
name: Bjertnaes, Lars
name: Vanags, Indulis
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Marine Biology

description: Supplemental methods. (PDF 94 kb)
Additional file 5: Table S4. of Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes
Creators: name: Melisha Kenedy
name: Scott, Edgar
name: Binu Shrestha
name: Anand, Arvind
name: Iqbal, Henna
name: Radolf, Justin
name: Dyer, David
name: Akins, Darrin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 60506 Virology

description: Servers utilized in this study. List of all servers utilized in the study as well as URLs and references for each server. (DOCX 14 kb)
Additional file 7: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: GO enrichment analysis in lung exposed to low-dosage radiation of 20Â Gy. (PDF 195 kb)
Additional file 12: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Comparison of module composition between two network structures obtained from focally irradiated regions and non-irradiated neighboring lung regions. Both network structures were composed of 11 modules. Each spot represents a common gene present between modules. (PDF 272 kb)
Additional file 10: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Network structure of GO terms associated with modules from (A) focally-irradiated (90Â Gy) regions and (B) non-irradiated neighboring lung regions. The network structure among non-redundant GO terms was constructed from all enriched GO terms (FDR <0.01) using the REIVGO program. The node size and color intensity are proportional to the hierarchical status and statistical significance of each node, respectively. The edge thickness between nodes represents the closeness of two nodes. (PDF 211 kb)
Additional file 5: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Tree distribution of GO terms altered by focal exposure to high-dose radiation. Tree structures composed of non-redundant GO terms were constructed using the REIVGO program from all enriched GO terms (FDR <0.01) in focally irradiated regions and non-irradiated neighboring lung regions. In each tree structure, closely related terms are presented in the same color. The size of each GO term is proportional to the level of statistical significance. (PDF 238 kb)
Additional file 3: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Temporal gene expression patterns after exposure to 20Â Gy radiation. Temporally altered genes were identified by the Short Time-series Expression Miner (STEM) analysis in mouse lung. Genes were classified into two patterns (FDR <0.001). (A) Down-pattern and (B) Up-pattern comprised 147 and 145 genes, respectively. These genes were compared with genes obtained from focally exposed (90Gy) regions and non-irradiated neighboring lung regions in a Venn diagram. (PDF 138 kb)
Additional file 9: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Pathway enrichment analysis in lung exposed to low-dosage radiation of 20Â Gy. (PDF 192 kb)
Colicus pichindensis , Brennan & Reed 1975
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Colicus
Colicus pichindensis

description: Colicus pichindensis (Brennan, 1968a):
NEO
Euschoengastia pichindensis Brennan, 1968 a
Colicus pichindensis, Brennan & Reed 1975
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 48, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Additional file 6: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: GO terms altered by focal exposure to 90Â Gy and diffused exposure to 20Â Gy. Significantly enriched non-redundant GO terms at each time point were temporally distributed. The columns represent individual samples, while the rows represent statistically significant GO terms (FDR <0.01). The positions of the organ development-related terms and immune-related terms are indicated as bars. (PDF 121 kb)
Additional file 8: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Top five pathways enriched in Pattern 1, Pattern 2, and Pattern 3 in focally irradiated regions and non-irradiated neighboring lung regions. The position of each gene in the pathways is colored red for the focally irradiated regions, blue for the non-irradiated neighboring lung regions, and yellow for both regions. The image of each pathway was adopted from KEGG homepage ( http://www.kegg.jp ). (PDF 656 kb)
Additional file 1: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Experimental confirmation of expression of genes included in each pattern after focal exposure to high-dose radiation of 90 Gy in the lung tissue. (A) Expression of genes included in each pattern were confirmed in triplicate by quantitative real-time PCR. Each mRNA expression was normalized to GAPDH and presented in mean ± standard deviation, in which statistical significance was measured using t-test. (B) Primers used in RT-PCR (C) Immunohistochemical staining of CDKN1A was performed in focally irradiated lungs. Positively stained cells were counted in representative images of immunohistochemistry (×200). Statistical significance was measured using t-test by comparing counts from irradiated samples with those from non-irradiated control. (PDF 607 kb)
Additional file 11: of Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Creators: name: Bu-Yeo Kim
name: Jin, Hee
name: Yoon-Jin Lee
name: Ga-Young Kang
name: Jaeho Cho
name: Yun-Sil Lee
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Genes included in each module of network structure. (PDF 363 kb)
Additional file 2: of Comparison of the effects of Crataegus oxyacantha extract, aerobic exercise and their combination on the serum levels of ICAM-1 and E-Selectin in patients with stable angina pectoris
Creators: name: Jalaly, Leila
name: Gholamreza Sharifi
name: Faramarzi, Mohammad
name: Alireza Nematollahi
name: Rafieian-Kopaei, Mahmoud
name: Amiri, Masoud
name: Fariborz Moattar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Ecology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 60506 Virology
subject: Computational Biology

description: Appendix B. Table S1. Random numbers between 1 and 44 (males). Table S2. Random numbers between 45 and 80 (female). (DOCX 23 kb)
Additional file 1: of Comparison of the effects of Crataegus oxyacantha extract, aerobic exercise and their combination on the serum levels of ICAM-1 and E-Selectin in patients with stable angina pectoris
Creators: name: Jalaly, Leila
name: Gholamreza Sharifi
name: Faramarzi, Mohammad
name: Alireza Nematollahi
name: Rafieian-Kopaei, Mahmoud
name: Amiri, Masoud
name: Fariborz Moattar
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Ecology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Hematology
subject: Computational Biology

description: Appendix A. (DOCX 6257 kb)
Additional file 5: Figure S2. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?
Creators: name: Barazani, Oz
name: Keren-Keiserman, Alexandra
name: Westberg, Erik
name: Hanin, Nir
name: Dag, Arnon
name: Ben-Ari, Giora
name: Fragman-Sapir, Ori
name: Yizhar Tugendhaft
name: Kerem, Zohar
name: Kadereit, Joachim
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: â  K values for the different Ks were calculated according to Evanno et al. [56], showing that K = 3 is the optimal K for the Structure analysis. (PDF 69 kb)
Additional file 6: Figure S3. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?
Creators: name: Barazani, Oz
name: Keren-Keiserman, Alexandra
name: Westberg, Erik
name: Hanin, Nir
name: Dag, Arnon
name: Ben-Ari, Giora
name: Fragman-Sapir, Ori
name: Yizhar Tugendhaft
name: Kerem, Zohar
name: Kadereit, Joachim
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Location of populations of naturally growing olives analyzed in this study and of groves of cultivated old olive trees sampled in our previous study (Barazani et al. [33]). (PDF 79 kb)
Additional file 4: Figure S1. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?
Creators: name: Barazani, Oz
name: Keren-Keiserman, Alexandra
name: Westberg, Erik
name: Hanin, Nir
name: Dag, Arnon
name: Ben-Ari, Giora
name: Fragman-Sapir, Ori
name: Yizhar Tugendhaft
name: Kerem, Zohar
name: Kadereit, Joachim
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Plant Biology
subject: Computational Biology

description: Number of private alleles per locus in combinations of populations. A to D present values for the combination of two to five populations (treating scions and suckers of old olive trees as populations). (PDF 217 kb)
Additional file 1: Table S1. of Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild?
Creators: name: Barazani, Oz
name: Keren-Keiserman, Alexandra
name: Westberg, Erik
name: Hanin, Nir
name: Dag, Arnon
name: Ben-Ari, Giora
name: Fragman-Sapir, Ori
name: Yizhar Tugendhaft
name: Kerem, Zohar
name: Kadereit, Joachim
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology
subject: Computational Biology

description: SSR markers used, their expected size range, repeated motives and number of alleles found in naturally growing olive populations. Raw microsatellite data is available and enclosed as Additional file 2: Table S2. (PDF 188 kb)
Additional file 5: Fig. S5. of Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Creators: name: Singer, Mirko
name: Marshall, Jennifer
name: Heiss, Kirsten
name: Mair, Gunnar
name: Grimm, Dirk
name: Ann-Kristin Mueller
name: Frischknecht, Friedrich
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology

description: Overview of all microhomology sequences used by SI parasites to repair DSBs. Microhomology sequences are shown in bold. Ten base pairs flanking each homology region are shown prior to the DSB break and the remaining bases in the SI parasites. The number of base pairs lost after repair is indicated. The mismatch in the microhomology sequence used for repair of Uis4ZFN SI 1â  3 is highlighted in orange. (PDF 280 kb)
Additional file 6: Fig. S6. of Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Creators: name: Singer, Mirko
name: Marshall, Jennifer
name: Heiss, Kirsten
name: Mair, Gunnar
name: Grimm, Dirk
name: Ann-Kristin Mueller
name: Frischknecht, Friedrich
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Results of qPCR on gDNA. a Localisation of qPCR probes on chromosomes 12 and 13. The centromere of chromosome 12 is shown in red. Binding sites for primer pairs used in qPCR are shown. Primer pair C1 amplifies the product over the cutting site of the ZFNs, while primer pairs L1 and R1 bind approximately 100 kb away from the telomeres on the left and right arm of chromosome 12, respectively. L2 and R2 bind around 8 kb away from the cutting site. N1 and N2 bind on the ‘control’ chromosome 13 and are used for normalization. b Chromosome 12 integrity is shown for samples from salivary gland (SG) and midgut (MG). Values were normalised to N1 and N2 on chromosome 13 and to results from blood-stage gDNA amplification. Positive and negative error is calculated from standard error of the mean from technical duplicates. (PDF 350 kb)
Additional file 3: Fig. S3. of Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Creators: name: Singer, Mirko
name: Marshall, Jennifer
name: Heiss, Kirsten
name: Mair, Gunnar
name: Grimm, Dirk
name: Ann-Kristin Mueller
name: Frischknecht, Friedrich
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences

description: Alignment of zfnL and zfnLcm. (PDF 1188 kb)
Additional file 2: Fig. S2. of Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Creators: name: Singer, Mirko
name: Marshall, Jennifer
name: Heiss, Kirsten
name: Mair, Gunnar
name: Grimm, Dirk
name: Ann-Kristin Mueller
name: Frischknecht, Friedrich
Publisher: name: Figshare
Year: 2015
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Characterisation of SpZFN SI 2. a Liver stages of parasites in HepG2 cells 48Â h after sporozoite invasion. CSP staining shows the plasma membrane of the parasite within the hepatocyte. b C57BL/6 mice were challenged with 10,000 sporozoites i.v. or by the bites of ten infected A. stephensi mosquitoes (bb). Peripheral blood parasitaemia was monitored by Giemsa-stained blood smears from three days post-infection. Percentage of mice that are blood stage (BS) parasite free and percentage of mice alive is shown over time. Parasitaemia over the course of the experiments is shown as growth curves. Control infections with SpZFN resulted in no blood stage parasitaemia. (PDF 1601 kb)
Additional file 1: Fig. S1. of Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Creators: name: Singer, Mirko
name: Marshall, Jennifer
name: Heiss, Kirsten
name: Mair, Gunnar
name: Grimm, Dirk
name: Ann-Kristin Mueller
name: Frischknecht, Friedrich
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Integration PCRs of parasites used in this study. a Integration of SpZFN and LsZFN. PCR with P53/P54 amplifies the whole Chr12 locus, resulting in 1448 bp in WT, 7850 bp for SpZFN and 7141 bp for LsZFN. The 5’ integration was amplified with P53/P12 or P53/P24, resulting in 1226 bp and 1610 bp for SpZFN and LsZFN, respectively. The 3’ integration was performed with P54/P55, resulting in 1181 bp. b Integration of Sp2ZFN and Ls2ZFN. PCR of the whole locus resulted in 6758 bp or 7145 bp for Sp2ZFN and Ls2ZFN, respectively. The 5’ integration was performed with P53/P56 or P53/P24, resulting in 1226 bp or 1610 bp for Sp2ZFN and Ls2ZFN. The 3’ integration was verified with P54/P10 (1982 bp). c Integration of TrapZFN and Uis4ZFN. PCR of the whole locus resulted in 6988 bp and 6970 bp for TrapZFN and Uis4ZFN, respectively. The 5’ integration was performed with P53/P22 or P53/P38, resulting in 1462 bp and 1504 bp for TrapZFN and Uis4ZFN, respectively. The 3’ integration was verified with P54/P8 (2588 bp). (PDF 1088 kb)
Raw data of manuscript (1501400)
Creators: name: Zou, Qianmei
name: Zhao, Longyuan
name: Xie, Yong
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 300411
subject: Fertilisers (incl. application)
classificationCode: 300204
subject: Agricultural management of nutrients
classificationCode: 300210
subject: Sustainable agricultural development

description: Excessive use of chemical fertilizers and extensive farming can degrade soil properties so that leading to decline in crop yields. Combining plant growth-promoting rhizobacteria (PGPR) with biochar (BC) may be an alternative way to mitigate this situation. However, the proportion of PGPR and BC at which crop yield can be improved, as well as the improvement effect extent on different eco-geographic region and crops, remain unclear. This research used cabbage [Brassica pekinensis (Lour.) Rupr.] as the target crop and established as treatment conventional fertilization as a control and a 50% reduction in nitrogen fertilizer at the Yunnan-Guizhou Plateau of China, adding BC or PGPR to evaluate the effects of different treatments on cabbage yield and the soil physicochemical properties. Specifically, high-throughput sequencing probed beneficial soil microbial communities and investigated the impact of BC and PGPR on cabbage yield and soil properties. The results revealed that the soil alkaline hydrolyzable nitrogen (AH-N), available phosphorus (AP), and available potassium (AK) contents were higher in the BC application than in control. The BC application or mixed with PGPR significantly increased the soil organic matter (OM) content (P<0.05), with a maximum of 42.59 g/kg. Further, applying BC or PGPR significantly increased the abundance of beneficial soil microorganisms in the whole growth period of cabbage (P<0.05), such as Streptomyces, Lysobacter, and Bacillus. Meanwhile, the co-application of BC and PGPR increased the abundance of Pseudomonas, and also significantly enhanced the Shannon index and Simpson index of bacterial community (P<0.05). Combined or not with PGPR, the BC application significantly enhanced cabbage yield (P<0.05), with the highest yield reached 1.41 fold of the control. Our research indicated that BC is an suitable and promising carrier of PGPR for soil improvement, combining BC and PGPR can effectively ameliorate the diversity of bacterial community even in acid red soil rhizosphere, and the most direct reflection is to improve soil fertility and cabbage yield.
Additional file 7: Fig. S7. of Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Creators: name: Singer, Mirko
name: Marshall, Jennifer
name: Heiss, Kirsten
name: Mair, Gunnar
name: Grimm, Dirk
name: Ann-Kristin Mueller
name: Frischknecht, Friedrich
Publisher: name: Figshare
Year: 2015
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified

description: Map of chromosomal location of multiplex target sites using CAS9. a All perfect matches for the possible gRNA sequence TTATATTAGTATTCGTTATTTGG targeting 104 loci of the P. berghei genome in different bir genes and bir pseudogenes. Archived contigs represent sequences that have not successfully been mapped to a chromosome. b The same sequence targets 532 targets in the P. yoelii genome within 522 different yir and yir pseudogenes. c Possible gRNA sequence GGTAACAACACAACAGCTAGTGG matches 39 targets within 31 var genes in P. falciparum. Figures were created with Plasmodb.org [65]. (PDF 996 kb)
MOESM1 of Shotgun proteomic analysis of Yersinia ruckeri strains under normal and iron-limited conditions
Creators: name: Gokhlesh Kumar
name: Hummel, Karin
name: Ahrens, Maike
name: Menanteau-Ledouble, Simon
name: Welch, Timothy
name: Eisenacher, Martin
name: Razzazi-Fazeli, Ebrahim
name: El-Matbouli, Mansour
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. List of quantitative real-time PCR primers. PCR primers specific for the selected genes were designed using NCBI Primer-BLAST software and used in this study.
Additional file 1: Table S1. of How does an integrated primary care approach for patients in deprived neighbourhoods impact utilization patterns? An explorative study
Creators: name: Kringos, Dionne
name: Broeke, Jennifer Van Den
name: Lee, Arnold Van Der
name: Plochg, Thomas
name: Stronks, Karien
Publisher: name: Figshare
Year: 2016
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Science Policy

description: Activities implemented in Utrecht Overvecht to promote renewal of expertise from 2006-2011. (DOCX 19Â kb)
Repository of Exploring the Schumpeterian Entrepreneur's Personality: A Natural Language Approach with Neural Networks estimates
Creators: name: Peralta, Guillermo
name: Gallardo, Mauricio
name: Bekios-Calfa, Juan
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 460208
subject: Natural language processing
classificationCode: 350704
subject: Entrepreneurship

description: This project focuses on predicting personality traits using statistical models and machine learning algorithms. The goal is to provide a tool capable of estimating personality traits based on social media text as input.
Additional file 2: of The beneficial effects of cognitive training with simple calculation and reading aloud in an elderly postsurgical population: study protocol for a randomized controlled trial
Creators: name: Kulason, Kay
name: Nouchi, Rui
name: Hoshikawa, Yasushi
name: Noda, Masafumi
name: Okada, Yoshinori
name: Ryuta Kawashima
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: Computational Biology

description: SPIRIT checklist. A table specifying where any SPIRIT item has been addressed in the protocol manuscript. (DOC 121 kb)
Additional file 1: of The beneficial effects of cognitive training with simple calculation and reading aloud in an elderly postsurgical population: study protocol for a randomized controlled trial
Creators: name: Kulason, Kay
name: Nouchi, Rui
name: Hoshikawa, Yasushi
name: Noda, Masafumi
name: Okada, Yoshinori
name: Ryuta Kawashima
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy

description: CONSORT checklist. A table specifying where any CONSORT item has been addressed in the protocol manuscript. (DOC 216 kb)
Additional file 5: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Plant Biology
subject: FOS: Biological sciences

description: Correlation matrix of all image metrics from pre-treatment samples. Correlation matrix of 15 image metrics derived from pre-treatment biopsies. Correlations are Pearsonâ  s coefficients. Text size is proportional to the strength of the correlation. Pink boxes denote positive correlations and blue boxes denote negative correlations. (PDF 82Â kb)
Additional file 6: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Cancer
subject: Science Policy
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Correlation matrix of all image metrics from post-treatment surgical samples. Correlation matrix of 15 image metrics derived from post-treatment surgical samples. Correlations are Pearsonâ  s coefficients. Text size is proportional to the strength of the correlation. Pink boxes denote positive correlations and those blue boxes denote negative correlations. (PDF 82Â kb)
Additional file 8: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Plant Biology

description: Univariate and multivariate logistic regression models for all 15 image metrics. (DOCX 16Â kb)
Additional file 4: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology

description: Histograms depicting the distribution of all image metrics from post-treatment surgical samples. (PDF 26Â kb)
Additional file 1: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Supplementary methods. (DOCX 38Â kb)
Metainferentially substructural validity theories
Creators: name: Pailos, Federico
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Mathematical Sciences not elsewhere classified

description: Porter (2023) [Three essays on substructural approaches to semantic paradoxes [PhD thesis]. City University of New York, New York, USA. https://academicworks.cuny.edu/gc_etds/5144/] has presented higher-level metainferential versions of the validity Curry argument introduced by Beall and Murzi (2013) [Two flavours of curry paradox. Journal of Philosophy, 110(3), 143–65]. What is peculiar of these paradoxes is that no operational rule nor any structural rule play any role in the derivation of the unpleasant result. Thus, to block them and have a uniform solution to, at least, every validity Curry paradox, something else needs to be done. We introduce, as an answer to Porter's challenge, validity theories that are substructural at every metainferential level. In this sense, they are free from Porter's criticism. These theories count as both theories of naïve validity (because they do not give up V P or V D, nor any higher-level version of them) and as offering a uniform solution to validity curries, in the more traditional and intuitive sense: either they give up every higher-level version of Cut – as well as every higher-level version of it – or they give up Contraction – as well as every higher-level version of it. Finally, we provide philosophical justifications for each of these options.
Additional file 12: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: 60506 Virology
subject: Computational Biology

description: Distribution of median lymphocyte density from pre-treatment biopsies by clinical variables. Horizontal gray lines represent median values. Results of Kruskal-Wallis tests are depicted within graphs; red text denotes p values <0.05. (PDF 62Â kb)
Colicus sinpretarsus Goff and Gettinger 1995
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Colicus
Colicus sinpretarsus

description: Colicus sinpretarsus Goff and Gettinger, 1995:
NEO
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 48, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Additional file 11: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences

description: Examples of images and associated metrics from cases with varying median lymphocyte density. Depicted density metrics have been arbitrarily offset to depict positive values but are normalized across samples, hence comparable between plots (right y-axis). Note that absolute counts are depicted against different scales (left y-axis). (PDF 63Â kb)
Velia rhadamantha subsp. cyrenaica TAMANINI 1947
Creators: name: Heiss, Ernst
name: Eckelt, Andreas
name: Lederwasch, Manfred
name: Unterasinger, Romed
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Veliidae
Velia
Velia rhadamantha
Velia rhadamantha cyrenaica tamanini, 1947

description: Velia rhadamantha cyrenaica TAMANINI, 1947
LBY L i b y e n: Cirenaica Cyrene, 1 Ex., 22.IV.1965, leg. Eckerlein H.
description: Published as part of Heiss, Ernst, Eckelt, Andreas, Lederwasch, Manfred & Unterasinger, Romed, 2022, Die Heteropterensammlung Ernst Heiss im Tiroler Landesmuseum Ferdinandeum. Teil IX: Gerromorpha II: Familien Mesoveliidae, Hebridae, Hydrometridae, Hermatobatidae, Veliidae, pp. 149-173 in Linzer biologische Beiträge 54 (1) on page 164, DOI: 10.5281/zenodo.7507258
Additional file 2: of Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer
Creators: name: H. Ali
name: Aliakbar Dariush
name: Provenzano, Elena
name: Bardwell, Helen
name: Abraham, Jean
name: Iddawela, Mahesh
name: Anne-Laure Vallier
name: Hiller, Louise
name: Janet. Dunn
name: Bowden, Sarah
name: Hickish, Tamas
name: McAdam, Karen
name: Houston, Stephen
name: Irwin, Mike
name: Pharoah, Paul
name: Brenton, James
name: Walton, Nicholas
name: Earl, Helena
name: Caldas, Carlos
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Plant Biology

description: CONSORT diagram illustrating the flow of patients at each analytical stage. (PDF 7Â kb)