cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5092225
title: Data from: Adaptive modulation of antibiotic resistance through intragenomic coevolution. Nature Ecology and Evolution

description: Figure_1_data Comma-separated files containing the data presented in Figure 1. conc = concentration antibiotic (μg/ml), od = Optical density (OD<sub>600</sub>). Separate files for ampicillin (AMP), tetracycline (TET) and chloramphenicol (CML) in each host/plasmid combination (evo = evolved, anc = ancestral).<br>Figure_2_S2_S3_dataComma-separated file containing the data presented in Figure 2, Figure S2 and Figure S3. rep = replication, chrom = chromosome, pos1 = first genomic position of feature, ref = nucleotide in reference, evo = nucleotide in evolved, HGVS.c = variation within coding sequence, HGVS.p = variation within protein sequence.<br>Figure_S1_dataComma-separated file containing the data presented in Figure S1. rep = replication.<br>Figure_S4_dataComma-separated files containing the data presented in Figure S4. rep = replication, conc = concentration tetracycline (μg/ml), od = optical density (OD<sub>600</sub>). Separate files for acrR, ompF and ychH knockouts.<br>Figure_S5_data Comma-separated file containing the data presented in Figure S5. rep = replication, rf = relative fitness of evolved strain vs ancestral plasmid free. Controls: ancestral plasmid containing vs ancestral plasmid free and ancestral plasmid free (GFP) vs ancestral plasmid free (mcherry).<br>Figure_S6_data Comma-separated file containing the data presented in Figure S6. rep = replication, plasmid (E = evolved, A = ancestral), host (E = evolved, A = ancestral), treatment = treatment evolved plasmid or host was sourced from. Columns there after are OD<sub>600</sub>; column headers are seconds from start of growth curve.<br>Figure_S7_data Comma-separated file containing the data presented in Figure S7. rep = replication, rf = relative fitness of evolved strain with either ancestral plasmid (EA) or evolved strain with evolved plasmid (EE) vs ancestral plasmid containing. Control ancestral plasmid containing (GFP) vs ancestral plasmid containing (mcherry).<br>Figure_S8_data Comma-separated file containing the data presented in Figure S8. Clone = ID of randomly selected clone from transfer, transfer = number of transfers (days) from start of evolution experiment. ompF::IS N = not present, Y = present identified through PCR. tetA = mutations within tetA observed in ompF::IS background, tetR = mutations within tetR observed in ompF::IS background.<br>Population codes represent selection treatment: C - no antibiotic, A - ampicillin, T - tetracycline, AT - ampicillin + tetracycline, and A/T - cycling treatment.
DOI: 10.6084/m9.figshare.5092225.v1
title: Data from: Adaptive modulation of antibiotic resistance through intragenomic coevolution. Nature Ecology and Evolution

description: Figure_1_data Comma-separated files containing the data presented in Figure 1. conc = concentration antibiotic (μg/ml), od = Optical density (OD<sub>600</sub>). Separate files for ampicillin (AMP), tetracycline (TET) and chloramphenicol (CML) in each host/plasmid combination (evo = evolved, anc = ancestral).<br>Figure_2_S2_S3_dataComma-separated file containing the data presented in Figure 2, Figure S2 and Figure S3. rep = replication, chrom = chromosome, pos1 = first genomic position of feature, ref = nucleotide in reference, evo = nucleotide in evolved, HGVS.c = variation within coding sequence, HGVS.p = variation within protein sequence.<br>Figure_S1_dataComma-separated file containing the data presented in Figure S1. rep = replication.<br>Figure_S4_dataComma-separated files containing the data presented in Figure S4. rep = replication, conc = concentration tetracycline (μg/ml), od = optical density (OD<sub>600</sub>). Separate files for acrR, ompF and ychH knockouts.<br>Figure_S5_data Comma-separated file containing the data presented in Figure S5. rep = replication, rf = relative fitness of evolved strain vs ancestral plasmid free. Controls: ancestral plasmid containing vs ancestral plasmid free and ancestral plasmid free (GFP) vs ancestral plasmid free (mcherry).<br>Figure_S6_data Comma-separated file containing the data presented in Figure S6. rep = replication, plasmid (E = evolved, A = ancestral), host (E = evolved, A = ancestral), treatment = treatment evolved plasmid or host was sourced from. Columns there after are OD<sub>600</sub>; column headers are seconds from start of growth curve.<br>Figure_S7_data Comma-separated file containing the data presented in Figure S7. rep = replication, rf = relative fitness of evolved strain with either ancestral plasmid (EA) or evolved strain with evolved plasmid (EE) vs ancestral plasmid containing. Control ancestral plasmid containing (GFP) vs ancestral plasmid containing (mcherry).<br>Figure_S8_data Comma-separated file containing the data presented in Figure S8. Clone = ID of randomly selected clone from transfer, transfer = number of transfers (days) from start of evolution experiment. ompF::IS N = not present, Y = present identified through PCR. tetA = mutations within tetA observed in ompF::IS background, tetR = mutations within tetR observed in ompF::IS background.<br>Population codes represent selection treatment: C - no antibiotic, A - ampicillin, T - tetracycline, AT - ampicillin + tetracycline, and A/T - cycling treatment.
DOI: 10.6084/m9.figshare.5092213
title: Assessment of Keratinase and Other Hydrolytic Enzymes in Thermophilic Bacteria Isolated from Geothermal Areas in Patagonia Argentina

description: Thermophilic aerobic bacteria were isolated from two geothermal areas in Neuquén province using two different enrichment methods and a total of 30 isolates were obtained. From chicken feather enrichment cultures, strains affiliated to <i>Bacillus cytotoxicus</i> and <i>Bacillus licheniformis</i> were isolated and all of them demonstrated the capability to degrade completely chicken feather. A preliminary research on biotechnological enzymes' potential demonstrated that all the isolates displayed at least one of the extracellular hydrolytic enzymes tested. Most of the isolates showed protease, inulinase and/or pectinase activities, while cellulase and xylanase activities were less common. In light of these findings, geothermal areas of Argentina may be considered as a potential source of thermophilic bacteria able to produce many industrially relevant enzymes.
DOI: 10.6084/m9.figshare.5092213.v2
title: Assessment of Keratinase and Other Hydrolytic Enzymes in Thermophilic Bacteria Isolated from Geothermal Areas in Patagonia Argentina

description: Thermophilic aerobic bacteria were isolated from two geothermal areas in Neuquén province using two different enrichment methods and a total of 30 isolates were obtained. From chicken feather enrichment cultures, strains affiliated to <i>Bacillus cytotoxicus</i> and <i>Bacillus licheniformis</i> were isolated and all of them demonstrated the capability to degrade completely chicken feather. A preliminary research on biotechnological enzymes' potential demonstrated that all the isolates displayed at least one of the extracellular hydrolytic enzymes tested. Most of the isolates showed protease, inulinase and/or pectinase activities, while cellulase and xylanase activities were less common. In light of these findings, geothermal areas of Argentina may be considered as a potential source of thermophilic bacteria able to produce many industrially relevant enzymes.
DOI: 10.6084/m9.figshare.5092159
title: Gender context effects in noun recognition: grammatical cues or co-occurrence effects?

description: Determiners with congruent gender facilitate the recognition of the following noun. We examine two explanations of this effect: either gender information is retrieved and influences lexical access, or gender effects are due to the determiner-noun co-occurrence. French nouns are either feminine or masculine and are preceded by feminine or masculine determiners in the singular. Plural articles are unmarked for gender. Because some nouns (peanuts) occur more frequently in the plural than in their singular, they frequently co-occur with determiners that do not provide gender information. Conversely, nouns that occur more frequently in their singular form (cathedral) co-occur more frequently with gender-marked determiners. We examined the recognition of plural- and singular-oriented nouns preceded by gender-marked and unmarked determiners. Singular-oriented nouns were recognised faster after gender-marked (singular) articles than after gender-unmarked (plural) ones. However, plural-oriented nouns were recognised faster after gender-unmarked (plural) articles, suggesting that articles/nouns co-occurrence outweigh abstract gender cue.
DOI: 10.6084/m9.figshare.5092213.v1
title: Assessment of keratinase and other hydrolytic enzymes in thermophilic bacteria isolated from geothermal areas in Patagonia Argentina

description: Thermophilic aerobic bacteria were isolated from two geothermal areas in Neuquén province using two different enrichment methods and a total of 30 isolates were obtained. From chicken feather enrichment cultures, strains affiliated to <i>Bacillus cytotoxicus</i> and <i>B. licheniformis</i> were isolated and all of them demonstrated the capability to degrade completely chicken feather. A preliminary research on biotechnological enzymes potential demonstrated that all the isolates displayed at least one of the extracellular hydrolytic enzyme tested. Most of the isolates showed protease, inulinase and/or pectinase activities while cellulase and xylanase activities were less common. In light of these findings, geothermal areas of Argentina may be considered a potential source of thermophilic bacteria able to produce many industrially relevant enzymes.
DOI: 10.6084/m9.figshare.5092144
title: Airborne vs. radio-transmitted vocalizations in two primates: a technical report

description: Elucidating the structure and function of joint vocal displays (e.g. duet, chorus) recorded with a conventional microphone has proved difficult in some animals owing to the complex acoustic properties of the combined signal, a problem reminiscent of multi-speaker conversations in humans. Towards this goal, we set out to simultaneously compare air-transmitted (AT) with radio-transmitted (RT) vocalizations in one pair of humans and one pair of captive Bolivian grey titi monkeys (<i>Plecturocebus donacophilus</i>) all equipped with an accelerometer – or vibration transducer – closely apposed to the larynx. First, we observed no crosstalk between the two radio transmitters when subjects produced vocalizations at the same time close to each other. Second, compared with AT acoustic recordings, sound segmentation and pitch tracking of the RT signal was more accurate, particularly in a noisy and reverberating environment. Third, RT signals were less noisy than AT signals and displayed more stable amplitude regardless of distance, orientation and environment of the animal. The microphone outperformed the accelerometer with respect to sound spectral bandwidth and speech intelligibility: the sounds of RT speech were more attenuated and dampened as compared to AT speech. Importantly, we show that vocal telemetry allows reliable separation of the subjects’ voices during production of joint vocalizations, which has great potential for future applications of this technique with free-ranging animals.
DOI: 10.6084/m9.figshare.5092159.v1
title: Gender context effects in noun recognition: grammatical cues or co-occurrence effects?

description: Determiners with congruent gender facilitate the recognition of the following noun. We examine two explanations of this effect: either gender information is retrieved and influences lexical access, or gender effects are due to the determiner-noun co-occurrence. French nouns are either feminine or masculine and are preceded by feminine or masculine determiners in the singular. Plural articles are unmarked for gender. Because some nouns (peanuts) occur more frequently in the plural than in their singular, they frequently co-occur with determiners that do not provide gender information. Conversely, nouns that occur more frequently in their singular form (cathedral) co-occur more frequently with gender-marked determiners. We examined the recognition of plural- and singular-oriented nouns preceded by gender-marked and unmarked determiners. Singular-oriented nouns were recognised faster after gender-marked (singular) articles than after gender-unmarked (plural) ones. However, plural-oriented nouns were recognised faster after gender-unmarked (plural) articles, suggesting that articles/nouns co-occurrence outweigh abstract gender cue.
DOI: 10.6084/m9.figshare.5092144.v1
title: Airborne vs. radio-transmitted vocalizations in two primates: a technical report

description: Elucidating the structure and function of joint vocal displays (e.g. duet, chorus) recorded with a conventional microphone has proved difficult in some animals owing to the complex acoustic properties of the combined signal, a problem reminiscent of multi-speaker conversations in humans. Towards this goal, we set out to simultaneously compare air-transmitted (AT) with radio-transmitted (RT) vocalizations in one pair of humans and one pair of captive Bolivian grey titi monkeys (<i>Plecturocebus donacophilus</i>) all equipped with an accelerometer – or vibration transducer – closely apposed to the larynx. First, we observed no crosstalk between the two radio transmitters when subjects produced vocalizations at the same time close to each other. Second, compared with AT acoustic recordings, sound segmentation and pitch tracking of the RT signal was more accurate, particularly in a noisy and reverberating environment. Third, RT signals were less noisy than AT signals and displayed more stable amplitude regardless of distance, orientation and environment of the animal. The microphone outperformed the accelerometer with respect to sound spectral bandwidth and speech intelligibility: the sounds of RT speech were more attenuated and dampened as compared to AT speech. Importantly, we show that vocal telemetry allows reliable separation of the subjects’ voices during production of joint vocalizations, which has great potential for future applications of this technique with free-ranging animals.
DOI: 10.6084/m9.figshare.5092099
title: How Many Methods Covered By Tests Are Pseudo-Tested?

description: Dataset of the <b>ICTSS 2017 paper by Niedermayr et al.</b><br><br>We analyzed test cases of 19 open-source projects using mutation testing. We determined for each covered method whether at least one test case can detect if the method’s whole logic is removed. We studied method characteristics and relations to test cases to find indicators for covered methods that are pseudo-tested.<br><br>The SQL dump requires a MySQL database (version &gt;= 5.7).
DOI: 10.6084/m9.figshare.5092099.v1
title: How Many Methods Covered By Tests Are Pseudo-Tested?

description: Dataset of the <b>ICTSS 2017 paper by Niedermayr et al.</b><br><br>We analyzed test cases of 19 open-source projects using mutation testing. We determined for each covered method whether at least one test case can detect if the method’s whole logic is removed. We studied method characteristics and relations to test cases to find indicators for covered methods that are pseudo-tested.<br><br>The SQL dump requires a MySQL database (version &gt;= 5.7).
DOI: 10.6084/m9.figshare.5092060
title: Supplementary Material for: Effects of Weight Loss with and without Exercise on Regional Body Fat Distribution in Postmenopausal Women

description: <strong><em>Background/Aims:</em></strong> The purpose was to determine whether lifestyle interventions have different effects on regional fat in women with normal glucose tolerance vs. impaired glucose tolerance (NGT vs. IGT). <b><i>Methods:</i></b> Changes in glucose metabolism (2-h oral glucose-tolerance tests), android to gynoid fat mass ratio (dual energy X-ray absorptiometry [DXA]), visceral to subcutaneous abdominal fat area ratio (CT), and abdominal to gluteal subcutaneous fat cell weight (FCW; adipose tissue biopsies) were determined in 60 overweight postmenopausal women (45-80 years) following 6 months of weight loss alone (WL; <i>n</i> = 28) or with aerobic exercise (AEX + WL; <i>n</i> = 32). <b><i>Results:</i></b> The interventions led to ∼8% decrease in weight, but only the AEX + WL group improved fitness (↑11% in VO<sub>2</sub>max) and reduced the android-to-gynoid fat mass ratio (↓5%; <i>p</i> &lt; 0.05). Both NGT and IGT groups reduced visceral and subcutaneous abdominal fat areas and abdominal and gluteal FCWs, which related to improvements in homeostatic model assessment (<i>r</i> = 0.34-0.42) and 2-h glucose (<i>r</i> = 0.34-0.35), respectively (<i>p</i> &lt; 0.05). The decline in FCW was 2× greater in women with IGT following WL (<i>p</i> &lt; 0.05). The ratios of abdominal-to-gluteal FCW did not change following either intervention. <b><i>Conclusions:</i></b> The mechanisms by which WL with and without exercise impact regional fat loss should be explored as reductions in abdominal fat area and subcutaneous FCW appear to influence glucose metabolism.
DOI: 10.6084/m9.figshare.5091985
title: Parental occupation

description: Parental occupation " Childhood social class and cognitive aging in the Swedish Adoption/Twin Study of Aging"
DOI: 10.6084/m9.figshare.5091985.v1
title: Parental occupation

description: Parental occupation " Childhood social class and cognitive aging in the Swedish Adoption/Twin Study of Aging"
DOI: 10.6084/m9.figshare.5091973
title: Supplementary Material for: Informant-Reported Cognitive Decline and Activity Engagement across Four Years in a Community Sample

description: <b><i>Background:</i></b> Subtle age-related cognitive decline may be associated with the capacity to remain engaged in mental, physical, and social activities. Informant reports of cognitive decline potentially provide additional information to psychometric tests on change in everyday cognitive function relevant to activity engagement. <b><i>Objective:</i></b> To investigate relations between decline in everyday cognitive function as assessed by informant report and activity engagement in community-dwelling older adults. <b><i>Methods:</i></b> A sample of cognitively normal older adults was drawn from the 2 latest waves of the PATH Through Life Study (<i>n</i> = 1,391; mean age 74.5 ± 1.5, 48.4% female). PATH is a 16-year longitudinal cohort study set in the Canberra/Queanbeyan district, Australia. Assessments were carried out at baseline, and at 3 subsequent time-points 4 years apart. At wave-4, the IQCODE, an informant measure of 4-year cognitive decline was provided by a spouse, family member, or friend of each participant. Activity engagement was assessed by the abbreviated RIASEC Mental Activity List, self-reported frequency and duration of physical activity (Whitehall Questionnaire) and the Lubben Social Network Scale that assessed interaction with family/friends. Participants provided demographic information, self-reported health status (SF-12), and responses to the Goldberg Depression Scale. The Symbol Digit Modalities Test (SDMT) and California Verbal Learning Test (CVLT) were used to measure objective 4-year cognitive change. Those with MMSE score of ≤27 were excluded. <b><i>Results:</i></b> IQCODE score predicted disengagement from mental activities over 4 years in cognitively healthy adults (β = -0.056, standard error [SE] = 0.019, <i>p</i> = 0.004). This association was robust to covariate control and change on the SDMT which was also significantly related to mental activity disengagement. In models adjusted for change scores on the SDMT and the CVLT, the IQCODE was associated with less physical (β = -0.692, SE = 0.24, <i>p</i> = 0.004) and social engagement (β -0.046, SE = 0.021, <i>p</i> = 0.032), but relationships were attenuated with the inclusion of covariates. <b><i>Conclusion:</i></b> Informant-reported cognitive decline in a non-clinical sample was linked to activities that support cognitive health. Associations were robust to adjustment for cognitive change scores. Utilising informant reports prior to the manifestation of clinically relevant decline may identify those who would benefit most from personalised activity interventions.
DOI: 10.6084/m9.figshare.5091940
title: Database completo LES e AR

description: database containing clinical and laboratory data of patients with rheumatoid arthrtitis and systemic lupus erythematosus
DOI: 10.6084/m9.figshare.5091934
title: Supplementary Material for: Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

description: Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to <i>Brettanomyces bruxellensis </i>contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 <i>B. bruxellensis </i>annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of <i>B. bruxellensis</i> LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of <i>B. bruxellensis</i> LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of <i>B. bruxellensis</i> LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast <i>B. bruxellensis</i>.
DOI: 10.6084/m9.figshare.5091940.v1
title: Database completo LES e AR

description: database containing clinical and laboratory data of patients with rheumatoid arthrtitis and systemic lupus erythematosus
DOI: 10.6084/m9.figshare.5091934.v1
title: Supplementary Material for: Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

description: Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to <i>Brettanomyces bruxellensis </i>contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 <i>B. bruxellensis </i>annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of <i>B. bruxellensis</i> LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of <i>B. bruxellensis</i> LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of <i>B. bruxellensis</i> LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast <i>B. bruxellensis</i>.
DOI: 10.6084/m9.figshare.5091904
title: cgm_min

description: Prospective cohort of patients with clinical time-based TIA with baseline and 8-week follow-up MRI for lesion evolution. 3T-MRI imaging was acquired in standard clinical TIA workflow. The set holds information per patient and per lesion.