cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7484663.v1
title: "Cord leptin predicts neuropsychological development in childhood; “Rhea” Mother – Child Cohort, Crete, Greece" - Supplementary Material - Marked changes

description: Supplementary Material (Figures and Tables) - Marked changes
DOI: 10.7284/100963
title: pCO2 (Partial Pressure of Carbon Dioxide) data collected during research cruise MGL1002 using a LDEO pCO2 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484561
title: De novo transposable elements (TE) identification in Zosterops borbonicus genome.

description: De novo transposable elements (TE) identification in Zosterops borbonicus genome. See Leroy et al. 'A bird's white-eye shot: looking down on a new avian sex chromosome evolution'.'
DOI: 10.6084/m9.figshare.7484561.v1
title: De novo transposable elements (TE) identification in Zosterops borbonicus genome.

description: De novo transposable elements (TE) identification in Zosterops borbonicus genome. See Leroy et al. 'A bird's white-eye shot: looking down on a new avian sex chromosome evolution'.'
DOI: 10.6084/m9.figshare.7484657.v1
title: "Cord leptin predicts neuropsychological development in childhood; “Rhea” Mother – Child Cohort, Crete, Greece" - Supplementary Material - Clean

description: Supplementary Material (Figures and Tables) - Clean version
DOI: 10.7284/100962
title: Rain Gauge data collected during research cruise MGL1002 using a RM Young 50202 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484552
title: The proposed genome organization (“agp file”) of birds species obtained using DeCoSTAR approaches.

description: The proposed genome organization (“agp file”) of birds species obtained using DeCoSTAR approaches. See Leroy et al. A bird's white-eye shot: looking down on a new avian sex chromosome evolution.
DOI: 10.6084/m9.figshare.7484549
title: Supplementary Material for: Janus Kinase Inhibitors for the Treatment of Severe Alopecia Areata: An Open-Label Comparative Study

description: <b><i>Background:</i></b> Alopecia areata (AA) is a common autoimmune disorder characterized by patchy hair loss. There are many treatments available for AA. However, treatments of severe forms of AA are not satisfactory. Recently, oral Janus kinase (JAK) inhibitors were found to be effective for the treatment of severe AA variants. <b><i>Objective:</i></b> The aim of this work was to evaluate and compare the efficacy, side effects, and durability of two oral JAK inhibitor medications (ruxolitinib and tofacitinib) in the treatment of severe AA. <b><i>Methods:</i></b> This study included 75 patients with AA with more than 30% scalp hair loss, alopecia totalis, and alopecia universalis randomized into 2 groups. The first group (<i>n</i> = 38) received ruxolitinib 20 mg twice daily, and the second group (<i>n</i> = 37) received oral tofacitinib 5 mg twice daily. The treatment continued for 6 months followed by 3 months of follow-up off therapy. Efficacy of treatment was assessed by monitoring the change in the Severity of Alopecia Tool (SALT) score. <b><i>Results:</i></b> Both tofacitinib and ruxolitinib induced remarkable hair regrowth, with a mean change in SALT score of 93.8 ± 3.25 in the ruxolitinib group and 95.2 ± 2.69 in the tofacitinib group. However, the ruxolitinib group showed a shorter duration for initial hair regrowth. There was no statistically significant difference between the groups regarding hair regrowth at the end of the 6-month treatment and relapse rate at the end of the 3-month follow-up. Around two thirds of cases experienced relapse. Both drugs were well tolerated, with no reported serious adverse effects. <b><i>Conclusion:</i></b> Both ruxolitinib and tofacitinib could be considered effective and well-tolerated treatments for extensive AA.
DOI: 10.6084/m9.figshare.7484552.v1
title: The proposed genome organization (“agp file”) of birds species obtained using DeCoSTAR approaches.

description: The proposed genome organization (“agp file”) of birds species obtained using DeCoSTAR approaches. See Leroy et al. A bird's white-eye shot: looking down on a new avian sex chromosome evolution.
DOI: 10.7284/100945
title: Singlebeam Echosounder data collected during research cruise MGL1002 using a Knudsen 3260 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484549.v1
title: Supplementary Material for: Janus Kinase Inhibitors for the Treatment of Severe Alopecia Areata: An Open-Label Comparative Study

description: <b><i>Background:</i></b> Alopecia areata (AA) is a common autoimmune disorder characterized by patchy hair loss. There are many treatments available for AA. However, treatments of severe forms of AA are not satisfactory. Recently, oral Janus kinase (JAK) inhibitors were found to be effective for the treatment of severe AA variants. <b><i>Objective:</i></b> The aim of this work was to evaluate and compare the efficacy, side effects, and durability of two oral JAK inhibitor medications (ruxolitinib and tofacitinib) in the treatment of severe AA. <b><i>Methods:</i></b> This study included 75 patients with AA with more than 30% scalp hair loss, alopecia totalis, and alopecia universalis randomized into 2 groups. The first group (<i>n</i> = 38) received ruxolitinib 20 mg twice daily, and the second group (<i>n</i> = 37) received oral tofacitinib 5 mg twice daily. The treatment continued for 6 months followed by 3 months of follow-up off therapy. Efficacy of treatment was assessed by monitoring the change in the Severity of Alopecia Tool (SALT) score. <b><i>Results:</i></b> Both tofacitinib and ruxolitinib induced remarkable hair regrowth, with a mean change in SALT score of 93.8 ± 3.25 in the ruxolitinib group and 95.2 ± 2.69 in the tofacitinib group. However, the ruxolitinib group showed a shorter duration for initial hair regrowth. There was no statistically significant difference between the groups regarding hair regrowth at the end of the 6-month treatment and relapse rate at the end of the 3-month follow-up. Around two thirds of cases experienced relapse. Both drugs were well tolerated, with no reported serious adverse effects. <b><i>Conclusion:</i></b> Both ruxolitinib and tofacitinib could be considered effective and well-tolerated treatments for extensive AA.
DOI: 10.7284/100960
title: SSV (Sound Speed Velocimeter) data collected during research cruise MGL1002 using a AML MicroSV instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484534
title: Supplementary Material for: Subunit Composition of Ribosome in the <b><i>yqgF</i></b> Mutant Is Deficient in pre-16S rRNA Processing of <b><i>Escherichia coli</i></b>

description: <i>Escherichia coli</i> 16S, 23S, and 5S ribosomal RNAs (rRNAs) are transcribed as a single primary transcript, which is subsequently processed into mature rRNAs by several RNases. Three RNases (RNase III, RNase E, and RNase G) were reported to function in processing the 5′-leader of precursor 16S rRNA (pre-16S rRNA). Previously, we showed that a novel essential YqgF is involved in that processing. Here we investigated the ribosome subunits of the <i>yqgF</i><sup>ts</sup> mutant by LC-MS/MS. The mutant ribosome had decreased copy numbers of ribosome protein S1, suggesting that the <i>yqgF</i> gene enables incorporation of ribosomal protein S1 into ribosome by processing of the 5′-end of pre-16S rRNA. The ribosome protein S1 is essential for translation in <i>E. coli</i>; therefore, our results suggest that YqgF converts the inactive form of newly synthesized ribosome into the active form at the final step of ribosome assembly.
DOI: 10.7284/100961
title: SSV (Sound Speed Velocimeter) data collected during research cruise MGL1002 using a AML MicroSV instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484531
title: Supplementary Material for: A Simple Method for Removal of the <b><i>Chlamydomonas reinhardtii</i></b> Cell Wall Using a Commercially Available Subtilisin (Alcalase)

description: The algal cell wall is a potent barrier for delivery of transgenes for genetic engineering. Conventional methods developed for higher plant systems are often unable to penetrate or remove algal cell walls owing to their unique physical and chemical properties. Therefore, we developed a simple transformation method for <i>Chlamydomonas reinhardtii</i> using commercially available enzymes. Out of 7 enzymes screened for cell wall disruption, a commercial form of subtilisin (Alcalase) was the most effective at a low concentration (0.3 Anson units/mL). The efficiency was comparable to that of gamete lytic enzyme, a protease commonly used for the genetic transformation of <i>C. reinhardtii</i>. The transformation efficiency of our noninvasive method was similar to that of previous methods using autolysin as a cell wall-degrading enzyme in conjunction with glass bead transformation. Subtilisin showed approximately 35% sequence identity with sporangin, a hatching enzyme of <i>C. reinhardtii</i>, and shared conserved active domains, which may explain the effective cell wall degradation. Our trans­formation method using commercial subtilisin is more reliable and time saving than the conventional method using autolysin released from gametes for cell wall lysis.
DOI: 10.6084/m9.figshare.7484534.v1
title: Supplementary Material for: Subunit Composition of Ribosome in the <b><i>yqgF</i></b> Mutant Is Deficient in pre-16S rRNA Processing of <b><i>Escherichia coli</i></b>

description: <i>Escherichia coli</i> 16S, 23S, and 5S ribosomal RNAs (rRNAs) are transcribed as a single primary transcript, which is subsequently processed into mature rRNAs by several RNases. Three RNases (RNase III, RNase E, and RNase G) were reported to function in processing the 5′-leader of precursor 16S rRNA (pre-16S rRNA). Previously, we showed that a novel essential YqgF is involved in that processing. Here we investigated the ribosome subunits of the <i>yqgF</i><sup>ts</sup> mutant by LC-MS/MS. The mutant ribosome had decreased copy numbers of ribosome protein S1, suggesting that the <i>yqgF</i> gene enables incorporation of ribosomal protein S1 into ribosome by processing of the 5′-end of pre-16S rRNA. The ribosome protein S1 is essential for translation in <i>E. coli</i>; therefore, our results suggest that YqgF converts the inactive form of newly synthesized ribosome into the active form at the final step of ribosome assembly.
DOI: 10.6084/m9.figshare.7484525
title: Supplementary Material for: Perception of Risk for Older Adults: Differences in Evaluations for Self versus Others and across Risk Domains

description: <b><i>Background and Objectives:</i></b> Proxy decision-making may be flawed by inaccurate perceptions of risk. This may be particularly true when older adults are the targets of the decisions, given the pervasive negative stereotypes about older adults. <b><i>Methods:</i></b> In study 1, individuals aged 18- to 87 years (as target persons) as well as one of their close social partners (as informants) reported on the risks they perceived for the target person in various life domains. Study 2 additionally explored potential differences in how people make risky decisions on behalf of younger and older adult targets. Younger (age 18–35 years) and older (age 60–81 years) adults (as target persons of the risk evaluations) as well as informants reported on risk perceptions and the likelihood of risk-taking for health, financial, and social scenarios concerning the target persons. Congruence between self-rated and informant-rated risk perceptions and risk-taking were computed on a dyadic as well as a group level. <b><i>Results:</i></b> Informants’ risk perceptions were positively associated with the risks their partners perceived for themselves. Informants and their partners agreed that social risks vary little across adulthood, but they disagreed in terms of recreational, financial, and health risks, and in terms of the decisions they would make. <b><i>Conclusion:</i></b> Family members, partners, and close friends are sensitive to vulnerabilities of their social partners, but in some domains and according to their partners’ age they perceive a greater (or smaller) risk than their partners perceive for themselves. In situations requiring surrogate decision-making, people may decide differently from how their social partners would decide for themselves.
DOI: 10.7284/100957
title: Water Temperature data collected during research cruise MGL1002 using a Sea-Bird SBE-38 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/100956
title: TSG (Thermosalinograph) data collected during research cruise MGL1002 using a Sea-Bird SBE-21 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484495
title: <i>Drosophila</i> p53 integrates the antagonism between autophagy and apoptosis in response to stress

description: The tumor suppressor TP53/p53 is a known regulator of apoptosis and macroautophagy/autophagy. However, the molecular mechanism by which TP53 regulates 2 apparently incompatible processes remains unknown. We found that <i>Drosophila</i> lacking <i>p53</i> displayed impaired autophagic flux, higher caspase activation and mortality in response to oxidative stress compared with wild-type flies. Moreover, autophagy and apoptosis were differentially regulated by the p53 (p53B) and ΔNp53 (p53A) isoforms: while the former induced autophagy in differentiated neurons, which protected against cell death, the latter inhibited autophagy by activating the caspases Dronc, Drice, and Dcp-1. Our results demonstrate that the differential use of p53 isoforms combined with the antagonism between apoptosis and autophagy ensures the generation of an appropriate p53 biological response to stress.
DOI: 10.6084/m9.figshare.7484495.v1
title: <i>Drosophila</i> p53 integrates the antagonism between autophagy and apoptosis in response to stress

description: The tumor suppressor TP53/p53 is a known regulator of apoptosis and macroautophagy/autophagy. However, the molecular mechanism by which TP53 regulates 2 apparently incompatible processes remains unknown. We found that <i>Drosophila</i> lacking <i>p53</i> displayed impaired autophagic flux, higher caspase activation and mortality in response to oxidative stress compared with wild-type flies. Moreover, autophagy and apoptosis were differentially regulated by the p53 (p53B) and ΔNp53 (p53A) isoforms: while the former induced autophagy in differentiated neurons, which protected against cell death, the latter inhibited autophagy by activating the caspases Dronc, Drice, and Dcp-1. Our results demonstrate that the differential use of p53 isoforms combined with the antagonism between apoptosis and autophagy ensures the generation of an appropriate p53 biological response to stress.
DOI: 10.7284/100964
title: Winch data collected during research cruise MGL1002 using a Lebus CTD instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484480
title: New robust weighted averaging- and model-based methods for assessing trait-environment relationships: R-code

description: This is the R-code belonging to the paper <br>New robust weighted averaging- and model-based methods for assessing trait-environment relationships. <br>It contains two new methods, a new weighted averaging method and a new model-based method: 1. The new weighted averaging method combines site-level CWM with a species-level regression of Species Niche Centroids (SNC) on to the trait. The regressions are weighted by Hill's effective number (<i>N</i><sub>2</sub>) of occurrences of each species and the <i>N</i><sub>2</sub>-diversity of a site, and are subsequently combined in a sequential test procedure known as the max-test.2. Using the test statistics of these new methods, the permutation-based max test provides strong statistical evidence for trait-environment association in a plant community dataset, where existing methods show (very) weak evidence. The powers of the two new methods were similar in a simulation study based on this dataset.<br>
DOI: 10.6084/m9.figshare.7484462
title: Supplementary Material for: The Association of Echocardiographic Peak Systolic Strain Rate with Cardiovascular Outcomes in Haemodialysis Patients

description: <b><i>Background/Aims:</i></b> Echocardiographic abnormalities of systolic function can be detected earlier with advancing echocardiographic technologies. Given the high prevalence of left ventricular hypertrophy in dialysis patients, we hypothesised that one such marker of strain, peak systolic strain rate (SR) would demonstrate association with cardiovascular outcome in a haemodialysis cohort. <b><i>Methods:</i></b> Recruited prevalent haemodialysis patients underwent standard transthoracic echocardiography as part of a detailed cardiovascular assessment on a non-dialysis day during a short inter-dialytic midweek break. Patients were followed up to mortality and cardiovascular end points. Multivariate Cox proportional hazard models were built to determine the association of above versus below median SR in a model adjusted for confounding factors. <b><i>Results:</i></b> 183 patients were enrolled and followed up for a median 925 days. Median age was 64.9 years, prevalence of LVH 55%, and median SR -0.86 (-1.00 to -0.72). An SR greater than -0.86 S<sup>-1</sup> (less negative) had a hazard ratio (HR) of 2.32 (1.36 to 3.95) in association with all-cause mortality after adjustment for EF, age, smoking history, MI, previous transplant, albumin and systolic blood pressure. For cardiovascular mortality, the HR was 2.343 (0.99 to 5.553) p =0.046. The only echocardiographic parameter independently associated with MACE was above median E/e (HR 2.09 [1.03 to 4.24], p=0.04). No echocardiographic parameter was associated with heart failure episodes. <b><i>Conclusion:</i></b> SR demonstrates association with outcome in this population and highlights the consideration that such sub-clinical cardiac changes should be routinely sought when referring haemodialysis patients for cardiac assessments.
DOI: 10.6084/m9.figshare.7484471
title: Supplementary Material for: Preoperative Enteral Nutrition and Surgical Outcomes in Adults with Crohn’s Disease: A Systematic Review

description: <b><i>Background and Aim:</i></b> Enteral nutrition (EN) is applicable to adult Crohn’s disease (CD) in treating malnutrition and in inducing remission – here as a less effective alternative than corticosteroids. The purpose of this review is to determine whether preoperative EN impacts postoperative complications of adult CD, either by means of nutritional or therapeutic effects. <b><i>Summary:</i></b> A systematic review of English written full-text research articles published between January 1990 and November 2017, including adult patients undergoing abdominal surgery for complicated CD after EN, was performed. Four studies out of 22 were selected, all of which institutional, retrospective, case-control cohorts, one classified as “good quality” and three as “poor quality,” as rated by the Newcastle-Ottawa Scale. The application of inclusion and exclusion criteria resulted in a non-intentional absence of studies referring to supplemental EN among those reviewed. The reduced number of heterogeneous eligible studies impeded meta-analysis. In all studies, exclusive EN (EEN) was used and well tolerated, allowing to defer or even avoid surgery altogether, improving patients’ global state. The two studies with the greatest number of patients found preoperative EEN to be an independent factor against infectious and non-infectious complications in 219 patients and against anastomotic leaks or abscesses in 38 patients. Also, in univariate analysis, EEN was found to increase preop­erative immunosuppressant-free intervals and to protect against anastomotic dehiscences, intra-abdominal abscesses, surgical wound infections, ileus, stomas, and reoperations in the largest study; in another study it was related to fewer intra-abdominal septic complications. <b><i>Key Messages:</i></b> All reviewed studies are retrospective and, consequently, of limited relevance. Nonetheless, all of them call the attention of the scientific community to the potential benefits of preoperative EEN on postoperative outcomes in adult CD, calling for prospective multi-institutional studies and randomized controlled trials.
DOI: 10.7284/100989
title: Expendable Probe data collected during research cruise MGL1004 using a Sippican MK21 instrument system onboard the platform RV Marcus G. Langseth

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7484462.v1
title: Supplementary Material for: The Association of Echocardiographic Peak Systolic Strain Rate with Cardiovascular Outcomes in Haemodialysis Patients

description: <b><i>Background/Aims:</i></b> Echocardiographic abnormalities of systolic function can be detected earlier with advancing echocardiographic technologies. Given the high prevalence of left ventricular hypertrophy in dialysis patients, we hypothesised that one such marker of strain, peak systolic strain rate (SR) would demonstrate association with cardiovascular outcome in a haemodialysis cohort. <b><i>Methods:</i></b> Recruited prevalent haemodialysis patients underwent standard transthoracic echocardiography as part of a detailed cardiovascular assessment on a non-dialysis day during a short inter-dialytic midweek break. Patients were followed up to mortality and cardiovascular end points. Multivariate Cox proportional hazard models were built to determine the association of above versus below median SR in a model adjusted for confounding factors. <b><i>Results:</i></b> 183 patients were enrolled and followed up for a median 925 days. Median age was 64.9 years, prevalence of LVH 55%, and median SR -0.86 (-1.00 to -0.72). An SR greater than -0.86 S<sup>-1</sup> (less negative) had a hazard ratio (HR) of 2.32 (1.36 to 3.95) in association with all-cause mortality after adjustment for EF, age, smoking history, MI, previous transplant, albumin and systolic blood pressure. For cardiovascular mortality, the HR was 2.343 (0.99 to 5.553) p =0.046. The only echocardiographic parameter independently associated with MACE was above median E/e (HR 2.09 [1.03 to 4.24], p=0.04). No echocardiographic parameter was associated with heart failure episodes. <b><i>Conclusion:</i></b> SR demonstrates association with outcome in this population and highlights the consideration that such sub-clinical cardiac changes should be routinely sought when referring haemodialysis patients for cardiac assessments.