cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9989006.v1
title: Ecophysiology and genetic diversity in species of the bamboo <i>Chusquea</i> in the high Andes, Venezuela

description: <b>Background</b>: Woody bamboos of the genus <i>Chusquea</i> grow along a broad range of elevations in the Venezuelan Andes. Their growth-form and density vary along the cloud forest – páramo gradient. In this article, we related ecophysiological traits and population genetic diversity information to explain the distribution of growth-form patterns of <i>Chusquea</i> in the Merida Andes, Venezuela. <b>Aims</b>: We quantified differences in the ecophysiological response and genetic diversity of scandent cloud forest and shrub-like páramo bamboos of the genus <i>Chusquea</i>, taking in account the differences in their flowering patterns, growth-form and habitat. <b>Methods</b>: We related low temperature resistance, water relations and leaf gas exchange variables to the growth-form, habitat, flowering patterns and genetic diversity in species of <i>Chusquea</i>. The genetic diversity study was based on Inter Sequence Simple Repeats and Random Amplified Polymorphic DNA markers analysis of cloud forest and páramo populations. <b>Results</b>: Scandent cloud forest and shrub-like páramo species of <i>Chusquea</i> had a very similar ecophysiological response for all the variables analysed during wet and dry seasons and were capable of enduring freezing temperatures through moderate supercooling. Species associated with the cloud forest – páramo gradient maintained low stomatal conductance and transpiration rates that favoured high leaf water potentials, without limiting photosynthetic rates. Shrub-like bamboos growing above the continuous forest line had a small decline in net photosynthesis rates, associated with an increase in water use efficiency. Both scandent and shrub-like bamboos had a remarkably high genetic diversity, comparable to non-clonal species. <b>Conclusions</b>: Species of <i>Chusquea</i> in the Venezuelan Andes are a physiologically relatively homogeneous group across a broad elevation gradient. Population genetic diversity appears to be more related with their flowering pattern and habitat conditions than with their growth form.
DOI: 10.6084/m9.figshare.9988820
title: Supplementary Material for: <b><i>Ubiquitin-Specific Protease 8</i></b> Mutant Corticotrope Adenomas Present Unique Secretory and Molecular Features and Shed Light on the Role of Ubiquitylation on ACTH Processing

description: <b><i>Background:</i></b> Somatic mutations in the ubiquitin-specific protease 8 (USP8) gene have recently been shown to occur in ACTH-secreting pituitary adenomas, thus calling attention to the ubiquitin system in corticotrope adenomas. <b><i>Objectives:</i></b> Assess the consequences of <i>USP8</i> mutations and establish the role of ubiquitin on ACTH turnover in human ACTH-secreting pituitary adenomas. <b><i>Methods:</i></b> <i>USP8</i> mutation status was established in 126 ACTH-secreting adenomas. Differences in ACTH secretion and <i>POMC</i> expression from adenoma primary cultures and in microarray gene expression profiles from archival specimens were sought according to <i>USP8</i> sequence. Ubiquitin/ACTH coimmunoprecipitation and incubation with MG132, a proteasome inhibitor, were performed in order to establish whether ubiquitin plays a role in POMC/ACTH degradation in corticotrope adenomas. <b><i>Results:</i></b> <i>USP8</i> mutations were identified in 29 adenomas (23%). Adenomas presenting <i>USP8</i> mutations secreted greater amounts of ACTH and expressed <i>POMC</i> at higher levels compared to <i>USP</i> wild-type specimens. <i>USP8</i> mutant adenomas were also more sensitive to modulation by CRH and dexamethasone in vitro. At microarray analysis, genes associated with endosomal protein degradation and membrane components were downregulated in <i>USP8</i> mutant adenomas as were <i>AVPR1B</i>, <i>IL11RA</i>, and<i> PITX2</i>. Inhibition of the ubiquitin-proteasome pathway increased ACTH secretion and POMC itself proved a target of ubiquitylation, independently of <i>USP8</i> sequence status. <b><i>Conclusions:</i></b> Our study has shown that <i>USP8</i> mutant ACTH-secreting adenomas present a more “typical” corticotrope phenotype and reduced expression of several genes associated with protein degradation. Further, ubiquitylation is directly involved in intracellular ACTH turnover, suggesting that the ubiquitin-proteasome system may represent a target for treatment of human ACTH-secreting adenomas.
DOI: 10.6084/m9.figshare.9988784
title: Supplementary Material for: Increased Incidence of Thyroid Disease in Patients with Alopecia Areata: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Alopecia areata (AA) is a common, clinically heterogeneous, immune-mediated, nonscarring hair loss disease with a pathogenesis that is not fully understood. The prevalence of thyroid disease is likely increased among individuals with AA. However, this association remains controversial. <b><i>Objective:</i></b> To evaluate the risk of thyroid disease in patients with AA. <b><i>Methods:</i></b> We performed a systematic review by searching both English and Chinese literature databases. Random- or fixed-effects models were used to summarize the association between thyroid disease and AA. <b><i>Results:</i></b> In total, 17 articles were included in this meta-analysis, with 2,850 AA cases and 4,667 controls. Overall, the prevalence of thyroid disease in patients with AA was significantly increased compared with that in controls (odds ratios 3.66, 95% confidence intervals 2.90–4.61). <b><i>Conclusions:</i></b> The results suggest that AA patients should be screened for thyroid disease.
DOI: 10.6084/m9.figshare.9988610
title: ERP raw data

description: This is the raw data for the part 2 (ERP, recognition test) for Fantasmas_EEG project
DOI: 10.6084/m9.figshare.9988559
title: Supplementary Material for: Mechanisms and Risk Factors Contributing to Visual Field Deficits following Stereotactic Laser Amygdalohippocampotomy

description: Selective laser amygdalohippocampotomy (SLAH) is a minimally invasive surgical treatment for medial temporal lobe epilepsy. Visual field deficits (VFDs) are a significant potential complication. The objective of this study was to determine the relationship between VFDs and potential mechanisms of injury to the optic radiations and lateral geniculate nucleus. We performed a retrospective cross-sectional analysis of 3 patients (5.2%) who developed persistent VFDs after SLAH within our larger series (<i>n</i> = 58), 15 healthy individuals and 10 SLAH patients without visual complications. Diffusion tractography was used to evaluate laser catheter penetration of the optic radiations. Using a complementary approach, we evaluated evidence for focal microstructural tissue damage within the optic radiations and lateral geniculate nucleus. Overablation and potential heat radiation were assessed by quantifying ablation and choroidal fissure CSF volumes as well as energy deposited during SLAH.<i></i>SLAH treatment parameters did not distinguish VFD patients. Atypically high overlap between the laser catheter and optic radiations was found in 1/3 VFD patients and was accompanied by focal reductions in fractional anisotropy where the catheter entered the lateral occipital white matter. Surprisingly, lateral geniculate tissue diffusivity was abnormal following, but also preceding, SLAH in patients who subsequently developed a VFD (all <i>p</i> = 0.005).<i></i>In our series, vision-related complications following SLAH, which appear to occur less frequently than following open temporal lobe ­surgery, were not directly explained by SLAH treatment parameters. Instead, our data suggest that variations in lateral geniculate structure may influence susceptibility to indirect heat injury from transoccipital SLAH.
DOI: 10.6084/m9.figshare.9988553
title: MySQL dump of analysed projects

description: database holding all data for the OO vs Authors study
DOI: 10.6084/m9.figshare.9988358
title: most forked github projects

description: list of the top 200 most FORKED projects off gitHub as of Sept2019
DOI: 10.6084/m9.figshare.9988553.v1
title: MySQL dump of analysed projects

description: database holding all data for the OO vs Authors study
DOI: 10.6084/m9.figshare.9988559.v1
title: Supplementary Material for: Mechanisms and Risk Factors Contributing to Visual Field Deficits following Stereotactic Laser Amygdalohippocampotomy

description: Selective laser amygdalohippocampotomy (SLAH) is a minimally invasive surgical treatment for medial temporal lobe epilepsy. Visual field deficits (VFDs) are a significant potential complication. The objective of this study was to determine the relationship between VFDs and potential mechanisms of injury to the optic radiations and lateral geniculate nucleus. We performed a retrospective cross-sectional analysis of 3 patients (5.2%) who developed persistent VFDs after SLAH within our larger series (<i>n</i> = 58), 15 healthy individuals and 10 SLAH patients without visual complications. Diffusion tractography was used to evaluate laser catheter penetration of the optic radiations. Using a complementary approach, we evaluated evidence for focal microstructural tissue damage within the optic radiations and lateral geniculate nucleus. Overablation and potential heat radiation were assessed by quantifying ablation and choroidal fissure CSF volumes as well as energy deposited during SLAH.<i></i>SLAH treatment parameters did not distinguish VFD patients. Atypically high overlap between the laser catheter and optic radiations was found in 1/3 VFD patients and was accompanied by focal reductions in fractional anisotropy where the catheter entered the lateral occipital white matter. Surprisingly, lateral geniculate tissue diffusivity was abnormal following, but also preceding, SLAH in patients who subsequently developed a VFD (all <i>p</i> = 0.005).<i></i>In our series, vision-related complications following SLAH, which appear to occur less frequently than following open temporal lobe ­surgery, were not directly explained by SLAH treatment parameters. Instead, our data suggest that variations in lateral geniculate structure may influence susceptibility to indirect heat injury from transoccipital SLAH.
DOI: 10.6084/m9.figshare.9988319
title: Analysis code to reproduce the results from Multi-modal communication: song sparrows increase signal redundancy in noise

description: Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multi-modal communication is affected by anthropogenic noise is relatively poor understood. Here, we ask whether song sparrows (<i>Melospiza melodia</i>) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (i) that song sparrows will shift signalling effort to the visual modality (the multi-modal shift hypothesis) and (ii) that they will increase redundancy of their multi-modal signalling (the back-up signal hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signalling effort to visual modality (i.e. wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase the redundancy of their multi-modal signals, which may aid in the robustness of the communication system.
DOI: 10.6084/m9.figshare.9988319.v1
title: Analysis code to reproduce the results from Multi-modal communication: song sparrows increase signal redundancy in noise

description: Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multi-modal communication is affected by anthropogenic noise is relatively poor understood. Here, we ask whether song sparrows (<i>Melospiza melodia</i>) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (i) that song sparrows will shift signalling effort to the visual modality (the multi-modal shift hypothesis) and (ii) that they will increase redundancy of their multi-modal signalling (the back-up signal hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signalling effort to visual modality (i.e. wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase the redundancy of their multi-modal signals, which may aid in the robustness of the communication system.
DOI: 10.6084/m9.figshare.9988313
title: Data to reproduce the results from Multi-modal communication: song sparrows increase signal redundancy in noise

description: Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multi-modal communication is affected by anthropogenic noise is relatively poor understood. Here, we ask whether song sparrows (<i>Melospiza melodia</i>) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (i) that song sparrows will shift signalling effort to the visual modality (the multi-modal shift hypothesis) and (ii) that they will increase redundancy of their multi-modal signalling (the back-up signal hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signalling effort to visual modality (i.e. wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase the redundancy of their multi-modal signals, which may aid in the robustness of the communication system.
DOI: 10.6084/m9.figshare.9988313.v1
title: Data to reproduce the results from Multi-modal communication: song sparrows increase signal redundancy in noise

description: Although the effects of anthropogenic noise on animal communication have been studied widely, most research on the effect of noise in communication has been on communication in a single modality. Consequently, how multi-modal communication is affected by anthropogenic noise is relatively poor understood. Here, we ask whether song sparrows (<i>Melospiza melodia</i>) show evidence of plasticity in response to noise in two aggressive signals in acoustic and visual modalities. We test two hypotheses: (i) that song sparrows will shift signalling effort to the visual modality (the multi-modal shift hypothesis) and (ii) that they will increase redundancy of their multi-modal signalling (the back-up signal hypothesis). We presented male song sparrows with song playback and a taxidermic mount with or without a low-frequency acoustic noise from a nearby speaker. We found that males did not switch their signalling effort to visual modality (i.e. wing waves) in response to the noise. However, the correlation between warbled soft songs and wing waves increased in the noise treatment, i.e. signals became more redundant. These results suggest that when faced with anthropogenic noise, song sparrows can increase the redundancy of their multi-modal signals, which may aid in the robustness of the communication system.
DOI: 10.6084/m9.figshare.9988247
title: Supplementary Material for: Infarct Patterns in Patients with Atherosclerotic Vertebrobasilar Disease in Relation to Hemodynamics

description: <b><i>Introduction:</i></b> Distal territory blood flow is independently associated with subsequent strokes in symptomatic vertebrobasilar atherosclerotic disease. We aimed to assess infarct patterns in relation to hemodynamic status in the prospective Vertebrobasilar Flow Evaluation and Risk of Transient Ischemic Attack and Stroke (VERiTAS) study. <b><i>Methods:</i></b> Distal territory blood flow was measured using quantitative magnetic resonance angiography (MRA) in 72 patients with symptomatic atherosclerotic vertebrobasilar disease, and then dichotomized into normal (<i>n</i> = 54) and low (<i>n</i> = 18) flow. Patients were followed longitudinally on standard medical management. Two observers blinded to flow status independently reviewed the imaging performed at the time of subsequent strokes, in order to adjudicate the likely mechanism based on infarct patterns. The frequency of stroke mechanisms was qualitatively compared based on flow status. <b><i>Results:</i></b> During a median follow-up period of 23 months, 10/72 patients had a subsequent stroke; 5 of these had low distal flow. Infarct patterns were adjudicated to be consistent with hemodynamic (<i>n</i> = 2), embolic (<i>n</i> = 4), and junctional plaque/perforator (<i>n</i> = 4) infarcts. Hemodynamic infarcts were seen in 40% (2/5) low-flow patients, in comparison to 0% (0/5) normal-flow patients. <b><i>Conclusion:</i></b> In contrast to normal-flow patients, those with low distal flow seem to be uniquely susceptible to hemodynamic infarctions, although other patterns of infarction can also be seen in these hemodynamically impaired patients.
DOI: 10.6084/m9.figshare.9988232
title: Intellagama egg development_Func.Ecol.Pezaro.2019.xlsx

description: The data was used for publication in the journal Functional Ecology
DOI: 10.6084/m9.figshare.9988247.v1
title: Supplementary Material for: Infarct Patterns in Patients with Atherosclerotic Vertebrobasilar Disease in Relation to Hemodynamics

description: <b><i>Introduction:</i></b> Distal territory blood flow is independently associated with subsequent strokes in symptomatic vertebrobasilar atherosclerotic disease. We aimed to assess infarct patterns in relation to hemodynamic status in the prospective Vertebrobasilar Flow Evaluation and Risk of Transient Ischemic Attack and Stroke (VERiTAS) study. <b><i>Methods:</i></b> Distal territory blood flow was measured using quantitative magnetic resonance angiography (MRA) in 72 patients with symptomatic atherosclerotic vertebrobasilar disease, and then dichotomized into normal (<i>n</i> = 54) and low (<i>n</i> = 18) flow. Patients were followed longitudinally on standard medical management. Two observers blinded to flow status independently reviewed the imaging performed at the time of subsequent strokes, in order to adjudicate the likely mechanism based on infarct patterns. The frequency of stroke mechanisms was qualitatively compared based on flow status. <b><i>Results:</i></b> During a median follow-up period of 23 months, 10/72 patients had a subsequent stroke; 5 of these had low distal flow. Infarct patterns were adjudicated to be consistent with hemodynamic (<i>n</i> = 2), embolic (<i>n</i> = 4), and junctional plaque/perforator (<i>n</i> = 4) infarcts. Hemodynamic infarcts were seen in 40% (2/5) low-flow patients, in comparison to 0% (0/5) normal-flow patients. <b><i>Conclusion:</i></b> In contrast to normal-flow patients, those with low distal flow seem to be uniquely susceptible to hemodynamic infarctions, although other patterns of infarction can also be seen in these hemodynamically impaired patients.
DOI: 10.6084/m9.figshare.9988220
title: Nonlocal correlation in a Weyl semimetal slab

description: The programs are written for calculating the density of states in a Weyl semimetal slab, and all the transmission coefficients in a six-terminal system.
DOI: 10.6084/m9.figshare.9988220.v1
title: Nonlocal correlation in a Weyl semimetal slab

description: The programs are written for calculating the density of states in a Weyl semimetal slab, and all the transmission coefficients in a six-terminal system.
DOI: 10.6084/m9.figshare.9988232.v1
title: Intellagama egg development_Func.Ecol.Pezaro.2019.xlsx

description: The data was used for publication in the journal Functional Ecology
DOI: 10.6084/m9.figshare.9988103
title: Muscle2View CellProfiler Supplemental Table 1

description: We provide supplemental files for the manuscipt: "Muscle2View, a CellProfiler pipeline for detection of the capillary-to-muscle fiber interface and high-content quantification of fiber-type specific histology".<br><b>Supplemental Table 1</b>Mean ± standard deviation (SD) values obtained for each fiber-morphological variables analyzed in this study.<br>
DOI: 10.26180/5da6d06389bc5
title: Imports and Wage Inequality, Reexamined

description: Data and regression code for paper "Imports and Wage Inequality, Reexamined"<b> </b>
DOI: 10.6084/m9.figshare.9987968
title: Effect of Hot Electrons

description: The refractive indices and electric fields of chorus waves vary along latitude. The dimensionless parameter R varies with pitch angle and kinetic energy of electrons. The pitch angle and kinetic energy evolution of electrons interact with chorus waves.
DOI: 10.6084/m9.figshare.9987959
title: Data supporting the results in the paper: Sheng-Hsin Su, Biing T. Guan, Chia-Hao Chang-Yang, I-Fang Sun, Hsiang-Hua Wang, Chang-Fu Hsieh. 2020. "Multi-stemming and size enhance survival of dominant tree species in a frequently typhoon-disturbed forest". Journal of Vegetation Science 31(3):429-39.

description: Data supporting the results in the paper:Sheng-Hsin Su, Biing T. Guan, Chia-Hao Chang-Yang, I-Fang Sun, Hsiang-Hua Wang, Chang-Fu Hsieh. 2020<i>.</i> "Multi-stemming and size enhance survival of dominant tree species in a frequently typhoon-disturbed forest". <i>Journal of Vegetation Science</i> 31(3):429-39 (https://doi.org/10.1111/jvs.12858).<br>
DOI: 10.6084/m9.figshare.9988172
title: Genetic characteristics of non-familial epilepsy

description: Whole exome sequencing data (read depth= or &gt; 30) from 400 non-familial epilepsy with Korean ancestry.
DOI: 10.6084/m9.figshare.9987968.v1
title: Effect of Hot Electrons

description: The refractive indices and electric fields of chorus waves vary along latitude. The dimensionless parameter R varies with pitch angle and kinetic energy of electrons. The pitch angle and kinetic energy evolution of electrons interact with chorus waves.
DOI: 10.6084/m9.figshare.9988103.v1
title: Muscle2View CellProfiler Supplemental Table 1

description: We provide supplemental files for the manuscipt: "Muscle2View, a CellProfiler pipeline for detection of the capillary-to-muscle fiber interface and high-content quantification of fiber-type specific histology".<br><b>Supplemental Table 1</b>Mean ± standard deviation (SD) values obtained for each fiber-morphological variables analyzed in this study.<br>