cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5142187
title: Genome annotation sugarcane cultivar SP80-3280 (Gene prediction)

description: Annotation of the draft genome sequence of the polyploid sugarcane cultivar SP80-3280. Evidence for gene prediction were: RNASeq data from Mattiello et al. 2015 (Strand-specific RNASeq short reads from the same cultivar) using BRAKER1, and a de novo transcriptome assembly (Trinity, see Mattiello et al. 2015) from the same data mapped to the genome using PASA, ESTs aligned to the genome using exonerate, and Sorghum bicolor proteins aligned to the genome using Exonerate. Evidences were combined using Evidence Modeller, generating this high quality gene prediction.
DOI: 10.6084/m9.figshare.5142172
title: Dataset for Habitat loss and fragmentation reduce effective gene flow by disrupting seed dispersal in a Neotropical palm

description: Habitat loss and fragmentation often reduce gene flow and genetic diversity in plants by disrupting the movement of pollen and seed. However, direct comparisons of the contributions of pollen vs. seed dispersal to genetic variation in fragmented landscapes are lacking. To address this knowledge gap, we partitioned the genetic diversity contributed by male gametes from pollen sources and female gametes from seed sources within established seedlings of the palm Oenocarpus bataua in forest fragments and continuous forest in northwest Ecuador. This approach allowed us to quantify the separate contributions of each of these two dispersal processes to genetic variation in a fragmented landscape. Compared to continuous forest, fragments had stronger spatial genetic structure, especially among female gametes, and reduced effective population sizes. We found that within and among fragments, allelic diversity was lower and genetic structure higher for female gametes than for male gametes. Moreover, female gametic allelic diversity in fragments co-varied with surrounding forest cover, while male gametic allelic diversity did not. These results indicate that limited seed dispersal restricts genetic diversity and strengthens genetic structure in this system. Although pollen movement may also be impacted by habitat loss and fragmentation, it nonetheless serves to promote gene flow and diversity within and among fragments. Pollen and seed dispersal play distinctive roles in determining patterns of genetic variation in fragmented landscapes, and maintaining the integrity of both dispersal processes will be critical to managing and conserving genetic variation in the face of continuing habitat loss and fragmentation in tropical landscapes.<br>
DOI: 10.6084/m9.figshare.5142229.v1
title: Images_M1_09

description: Image Set 9
DOI: 10.6084/m9.figshare.5142172.v1
title: Dataset for Habitat loss and fragmentation reduce effective gene flow by disrupting seed dispersal in a Neotropical palm

description: Habitat loss and fragmentation often reduce gene flow and genetic diversity in plants by disrupting the movement of pollen and seed. However, direct comparisons of the contributions of pollen vs. seed dispersal to genetic variation in fragmented landscapes are lacking. To address this knowledge gap, we partitioned the genetic diversity contributed by male gametes from pollen sources and female gametes from seed sources within established seedlings of the palm Oenocarpus bataua in forest fragments and continuous forest in northwest Ecuador. This approach allowed us to quantify the separate contributions of each of these two dispersal processes to genetic variation in a fragmented landscape. Compared to continuous forest, fragments had stronger spatial genetic structure, especially among female gametes, and reduced effective population sizes. We found that within and among fragments, allelic diversity was lower and genetic structure higher for female gametes than for male gametes. Moreover, female gametic allelic diversity in fragments co-varied with surrounding forest cover, while male gametic allelic diversity did not. These results indicate that limited seed dispersal restricts genetic diversity and strengthens genetic structure in this system. Although pollen movement may also be impacted by habitat loss and fragmentation, it nonetheless serves to promote gene flow and diversity within and among fragments. Pollen and seed dispersal play distinctive roles in determining patterns of genetic variation in fragmented landscapes, and maintaining the integrity of both dispersal processes will be critical to managing and conserving genetic variation in the face of continuing habitat loss and fragmentation in tropical landscapes.<br>
DOI: 10.6084/m9.figshare.5142154
title: High genetic differentiation of red gorgonian populations from the Atlantic Ocean and the Mediterranean Sea

description: Patterns of genetic variation within a species may be used to infer past events in the evolutionary history of marine species. In the present study we aimed to compare the genetic diversity of the red gorgonian <i>Paramuricea clavata</i> in the Atlantic Ocean and the Mediterranean Sea. For genetic markers we used microsatellites and a mitochondrial gene fragment. Our results revealed a distinct genetic composition and diversity between the Mediterranean and the Atlantic. The Mediterranean samples had higher microsatellite heterozygosity, allelic richness and private allelic richness. The hypotheses that can explain these patterns are the isolation of Atlantic populations and/or a founder effect. Additionally, a clear difference was obtained from the mitochondrial locus, since sequences from Atlantic and Mediterranean samples diverged by 1%, which is high for soft corals.
DOI: 10.6084/m9.figshare.5142154.v1
title: High genetic differentiation of red gorgonian populations from the Atlantic Ocean and the Mediterranean Sea

description: Patterns of genetic variation within a species may be used to infer past events in the evolutionary history of marine species. In the present study we aimed to compare the genetic diversity of the red gorgonian <i>Paramuricea clavata</i> in the Atlantic Ocean and the Mediterranean Sea. For genetic markers we used microsatellites and a mitochondrial gene fragment. Our results revealed a distinct genetic composition and diversity between the Mediterranean and the Atlantic. The Mediterranean samples had higher microsatellite heterozygosity, allelic richness and private allelic richness. The hypotheses that can explain these patterns are the isolation of Atlantic populations and/or a founder effect. Additionally, a clear difference was obtained from the mitochondrial locus, since sequences from Atlantic and Mediterranean samples diverged by 1%, which is high for soft corals.
DOI: 10.6084/m9.figshare.5142187.v2
title: Genome annotation sugarcane cultivar SP80-3280 (Gene prediction)

description: Annotation of the draft genome sequence of the polyploid sugarcane cultivar SP80-3280. Evidence for gene prediction were: RNASeq data from Mattiello et al. 2015 (Strand-specific RNASeq short reads from the same cultivar) using BRAKER1, and a de novo transcriptome assembly (Trinity, see Mattiello et al. 2015) from the same data mapped to the genome using PASA, ESTs aligned to the genome using exonerate, and Sorghum bicolor proteins aligned to the genome using Exonerate. Evidences were combined using Evidence Modeller, generating this high quality gene prediction.
DOI: 10.6084/m9.figshare.5142187.v1
title: Genome annotation SP80-3280 (Gene prediction)

description: Annotation of the draft genome sequence of the polyploid sugarcane cultivar SP80-3280. Evidence for gene prediction were: RNASeq data from Mattiello et al. 2015 (Strand-specific RNASeq short reads from the same cultivar) using BRAKER1, and a de novo transcriptome assembly (Trinity, see Mattiello et al. 2015) from the same data mapped to the genome using PASA, ESTs aligned to the genome using exonerate, and Sorghum bicolor proteins aligned to the genome using Exonerate. Evidences were combined using Evidence Modeller, generating this high quality gene prediction.
DOI: 10.6084/m9.figshare.5140291
title: Shaping of Reach-to-Grasp Kinematics by Intentions: A Meta-Analysis

description: When we reach to grasp something, we need to take into account both the properties of the object we are grasping and the intention we have in mind. Previous research has found these constraints to be visible in the reach-to-grasp kinematics, but there is no consensus on which kinematic parameters are the most sensitive. To examine this, a systematic literature search and meta-analyses were performed. The search identified studies assessing how changes in either an object property or a prior intention affect reach-to-grasp kinematics in healthy participants. Hereafter, meta-analyses were conducted using a restricted maximum likelihood random effect model. The meta-analyses showed that changes in both object properties and prior intentions affected reach-to-grasp kinematics. Based on these results, the authors argue for a tripartition of the reach-to-grasp movement in which the accelerating part of the reach is primarily associated with transporting the hand to the object (i.e., extrinsic object properties), the decelerating part of the reach is used as a preparation for object manipulation (i.e., prepare the grasp or the subsequent action), and the grasp is associated with manipulating the object's intrinsic properties, especially object size.
DOI: 10.6084/m9.figshare.5140291.v1
title: Shaping of Reach-to-Grasp Kinematics by Intentions: A Meta-Analysis

description: When we reach to grasp something, we need to take into account both the properties of the object we are grasping and the intention we have in mind. Previous research has found these constraints to be visible in the reach-to-grasp kinematics, but there is no consensus on which kinematic parameters are the most sensitive. To examine this, a systematic literature search and meta-analyses were performed. The search identified studies assessing how changes in either an object property or a prior intention affect reach-to-grasp kinematics in healthy participants. Hereafter, meta-analyses were conducted using a restricted maximum likelihood random effect model. The meta-analyses showed that changes in both object properties and prior intentions affected reach-to-grasp kinematics. Based on these results, the authors argue for a tripartition of the reach-to-grasp movement in which the accelerating part of the reach is primarily associated with transporting the hand to the object (i.e., extrinsic object properties), the decelerating part of the reach is used as a preparation for object manipulation (i.e., prepare the grasp or the subsequent action), and the grasp is associated with manipulating the object's intrinsic properties, especially object size.
DOI: 10.6084/m9.figshare.5140174
title: Experimental support that natural selection has shaped the latitudinal distribution of mitochondrial haplotypes in Australian Drosophila melanogaster

description: Thermal Traits - data used to make figures in the paper plus the alignment of the Australian haplotypes
DOI: 10.6084/m9.figshare.5140174.v1
title: Experimental support that natural selection has shaped the latitudinal distribution of mitochondrial haplotypes in Australian Drosophila melanogaster

description: Thermal Traits - data used to make figures in the paper plus the alignment of the Australian haplotypes
DOI: 10.6084/m9.figshare.5140099
title: Validating Fin Ray Microchemistry as a Tool to Reconstruct the Migratory History of White Sturgeon

description: The objective of this study was to validate the use of fin ray strontium isotope ratios (<sup>87</sup>Sr:<sup>86</sup>Sr) via laser ablation (LA) to resolve fine-scale movement patterns in sturgeons (Acipenseridae) during freshwater rearing in early life stages. We conducted a laboratory experiment in which juvenile White Sturgeon <i>Acipenser transmontanus</i> were exposed to two water sources exhibiting distinctive <sup>87</sup>Sr:<sup>86</sup>Sr isotope values (American River and Putah Creek, California) over weekly time periods to understand how water exposure histories are archived in pectoral fin rays. Using LA multicollector inductively coupled plasma mass spectrometry with a laser diameter of 65 µm, we detected distinct shifts in fin ray <sup>87</sup>Sr:<sup>86</sup>Sr values to match a water source in fish that were exposed for 2, 4, 6, and 12 weeks. Fin ray <sup>87</sup>Sr:<sup>86</sup>Sr values matched the new water source after 21.7 d (SD = 7.8; range = 11–36 d) of exposure. The lower limit of this estimate was constrained by the rate of fin ray growth as well as the LA spot size. Additionally, we assessed how diet affected fin ray <sup>87</sup>Sr:<sup>86</sup>Sr values by feeding a marine-derived pellet feed commonly used in aquaculture to a subset of White Sturgeon, while others were fed a diet consisting of fish with <sup>87</sup>Sr:<sup>86</sup>Sr values that matched their respective water source. Generally, we observed only a minor influence of diet, but there was some variability across individual fish in the effect of diet on the resulting fin ray <sup>87</sup>Sr:<sup>86</sup>Sr value. As with any geochemical analytical technique, fin ray microchemistry has some limitations related to individual variability in fin ray growth and development; however, it is a promising approach to reconstructing sturgeon migratory history by using a nonlethal sampling method. Received December 16, 2016; accepted April 13, 2017 Published online June 23, 2017
DOI: 10.6084/m9.figshare.5140099.v1
title: Validating Fin Ray Microchemistry as a Tool to Reconstruct the Migratory History of White Sturgeon

description: The objective of this study was to validate the use of fin ray strontium isotope ratios (<sup>87</sup>Sr:<sup>86</sup>Sr) via laser ablation (LA) to resolve fine-scale movement patterns in sturgeons (Acipenseridae) during freshwater rearing in early life stages. We conducted a laboratory experiment in which juvenile White Sturgeon <i>Acipenser transmontanus</i> were exposed to two water sources exhibiting distinctive <sup>87</sup>Sr:<sup>86</sup>Sr isotope values (American River and Putah Creek, California) over weekly time periods to understand how water exposure histories are archived in pectoral fin rays. Using LA multicollector inductively coupled plasma mass spectrometry with a laser diameter of 65 µm, we detected distinct shifts in fin ray <sup>87</sup>Sr:<sup>86</sup>Sr values to match a water source in fish that were exposed for 2, 4, 6, and 12 weeks. Fin ray <sup>87</sup>Sr:<sup>86</sup>Sr values matched the new water source after 21.7 d (SD = 7.8; range = 11–36 d) of exposure. The lower limit of this estimate was constrained by the rate of fin ray growth as well as the LA spot size. Additionally, we assessed how diet affected fin ray <sup>87</sup>Sr:<sup>86</sup>Sr values by feeding a marine-derived pellet feed commonly used in aquaculture to a subset of White Sturgeon, while others were fed a diet consisting of fish with <sup>87</sup>Sr:<sup>86</sup>Sr values that matched their respective water source. Generally, we observed only a minor influence of diet, but there was some variability across individual fish in the effect of diet on the resulting fin ray <sup>87</sup>Sr:<sup>86</sup>Sr value. As with any geochemical analytical technique, fin ray microchemistry has some limitations related to individual variability in fin ray growth and development; however, it is a promising approach to reconstructing sturgeon migratory history by using a nonlethal sampling method. Received December 16, 2016; accepted April 13, 2017 Published online June 23, 2017
DOI: 10.6084/m9.figshare.5140057
title: Correction of copy number induced false positives in CRISPR screens

description: Data and scripts necessary to reproduce the results and figures presented in:<br><br>Correction of copy number induced false positives in CRISPR screensAntoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. Robert McDonald III, Tobias Schmelzle, Hans Bitter, Audrey KauffmannPLOS Computational Biology, 2018.<br>
DOI: 10.6084/m9.figshare.5140057.v1
title: Correction of copy number induced false positives in CRISPR screens

description: !!! This repository is currently being updated !!!Updated scripts and data will be added soon<br><br>These are the data and scripts necessary to reproduce the results and figures presented in:Correction of copy number induced false positives in CRISPR screensAntoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. RobertMcDonald III, Tobias Schmelzle, Hans Bitter, Audrey KauffmannbioRxiv 151985; doi: https://doi.org/10.1101/151985
DOI: 10.6084/m9.figshare.5140057.v2
title: Correction of copy number induced false positives in CRISPR screens

description: Updated scripts and data<br><br>These are the data and scripts necessary to reproduce the results and figures presented in:Correction of copy number induced false positives in CRISPR screensAntoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. RobertMcDonald III, Tobias Schmelzle, Hans Bitter, Audrey Kauffmann<br>
DOI: 10.6084/m9.figshare.5139946
title: Images_M1_08

description: Image Set 8
DOI: 10.6084/m9.figshare.5139946.v1
title: Images_M1_08

description: Image Set 8
DOI: 10.6084/m9.figshare.5139874
title: Supplementary Material for: Perioperative Strokes Following Surgical Correction of Mitral Valves: A Systematic Review and Meta-Analysis

description: <b><i>Objective:</i></b> The primary aim of this meta-analysis was to quantify the impact of perioperative strokes on stroke-related mortality after open mitral valve (MV) procedures were performed. <b><i>Methods:</i></b> An electronic search of the PubMed, Embase, and the Web of Science databases was performed to retrieve articles published up to December 2015, relevant to patients undergoing MV procedures. Data were extracted from the final list of 25 studies to calculate a summary OR for 30-day stroke-related mortality. <b><i>Results:</i></b> The stroke rate in the total sample population was 1.62% (73/4,498). The 30-day all-cause mortality rate was 3.51% (158/4,498). The percentage of total deaths caused by stroke was 6.87%. The summary OR of stroke-related mortality following MV procedures was estimated to be 7.22 (95% CI 4.13-12.63, <i>p</i> &lt; 0.0001). A subgroup analysis was done for studies involving concomitant MV surgery and coronary artery bypass grafting. The summary estimate of the subgroup showed an OR of 8.508 (95% CI 1.552-46.622, <i>p</i> = 0.0136). <b><i>Conclusion:</i></b> Perioperative strokes following open MV procedures may be associated with more than 7 times greater odds of 30-day stroke-related mortality. They appear to be more commonly occurring than what is reported by current literature, making further studies investigating possible mechanisms and preventive measures a priority.
DOI: 10.6084/m9.figshare.5139856
title: A stand-level model derived from National Forest Inventory data to predict periodic annual volume increment of forests in Italy

description: A model was developed for predicting the periodic annual volume increment (PAI) of forests using variables commonly recorded through field surveys or the remote sensing. The model was developed using the Italian National Forest Inventory (INFC2005) data, publicly available at www.inventarioforestale.org. Data from 5707 plots were split into two groups. The first was used for fitting the model; the second was used for cross validation. Model reliability for applications at the local, in the Alpine and Mediterranean regions, and at the country level was tested. A sensitivity analysis was carried out to investigate the effects of entering inaccurate values of the number of trees per hectare, one of the predictors of the final model, that may occur in case of biased estimates from the remote sensing. During model calibration, the highest proportion of increment variation was captured using forest category (FC) as dummy variable and, in this respect, this study supports the classification of forests on ecological basis as a stratification criterion in environmental sampling. The model explained 72% of PAI and it predicted annual increment at plot level with no statistical difference to the observed value in any FC, at the country level.
DOI: 10.6084/m9.figshare.5139844
title: Supplementary Material for: Uniparental Disomy of Chromosome 15 in Two Cases by Chromosome Microarray: A Lesson Worth Thinking

description: Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurogenetic disorders caused by loss of function of the imprinted genes at 15q11q13. A 5-7 Mb paternal/maternal deletion of chromosomal region 15q11.2q13 is the major genetic cause of PWS/AS, but in a small group of patients, the PWS/AS phenotype can result from maternal/paternal uniparental disomy (UPD) of chromosome 15. Various mechanisms leading to UPD include gametic complementation, trisomy rescue, and compensatory UPD, which can be inferred from the pattern of uniparental heterodisomy (heteroUPD) or uniparental isodisomy (isoUPD). However, heteroUPD and isoUPD, especially mixed heteroUPD and isoUPD, are very rare in patients with PWS/AS. Here, we report 2 children with PWS/AS caused by mixed segmental heteroUPD 15 and isoUPD 15 which failed to be identified by chromosome microarray (CMA) but could be detected by other molecular genetic methods. The present report unravels the mechanism of mixed iso/heteroUPD 15 in PWS/AS and phenotype-genotype correlations. Moreover, our study suggests that CMA is prone to misdiagnosis for imprinting disorders such as PWS/AS, though it is considered a highly useful tool for copy number variations. As a result, other molecular detection methods, such as methylation analysis and STR marker analysis for UPD, should be supplementary used in this situation.
DOI: 10.6084/m9.figshare.5139850
title: Supplementary Material for: Comparing the Effects of Mindfulness-Based Cognitive Therapy and Sleep Psycho-Education with Exercise on Chronic Insomnia: A Randomised Controlled Trial

description: <b><i>Background:</i></b> Mindfulness-based cognitive therapy (MBCT) is a potential treatment for chronic insomnia. We evaluated the efficacy of MBCT for insomnia (MBCT-I) by comparing it with a sleep psycho-education with exercise control (PEEC) group. <b><i>Methods:</i></b> Adults with chronic primary insomnia (<i>n</i> = 216) were randomly allocated to the MBCT-I or PEEC group. The MBCT-I included mindfulness and psycho-education with cognitive and behavioural components under cognitive behavioural therapy for insomnia. PEEC included psycho-education of sleep hygiene and stimulus control, and exercises. Any change in insomnia severity was measured by the Insomnia Severity Index (ISI). Secondary outcomes included sleep parameters measured by a sleep diary, health service utilisation, absence from work and mindfulness measured by the Five Facet Mindfulness Questionnaire. <b><i>Results:</i></b> The ISI score significantly decreased in the MBCT-I group compared with the PEEC group at 2 months (i.e., post-intervention) (<i>p</i> = 0.023, effect size [95% CI] -0.360 [-0.675, -0.046]) but not at 5 or 8 months. Treatment response rates and remission rates based on the ISI cut-off scores were not significantly different between groups. Wake time after sleep onset (WASO) was less in the MBCT-I group at 2 and 5 months. At 8 months, both groups showed a reduced ISI score, sleep onset latency and WASO, and increased sleep efficiency and total sleep time; however, no group differences were seen. Other outcome measures did not significantly improve in either group. <b><i>Conclusions:</i></b> Long-term benefits were not seen in MBCT-I when compared with PEEC, although short-term benefits were seen.