cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6633341.v1
title: D. melanogaster predictions

description: About this dataset: These are the most reliable 100,000 PPI predictions for D. melanogaster. It is a CSV file.<br>Motivation: Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods. <br>Results: We extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae. Those data were the base to develop a PPI prediction method for each model organism. The method used evolutionary information through a profile-kernel Support Vector Machine (SVM). With the resulting eight models, we predicted all possible protein pairs in each organism and made the top predictions available through a web application. Almost all of the PPIs made available were predicted between proteins that have not been observed in any interaction, in particular for less well-studied organisms. Thus, our work complements existing resources and is particularly helpful for designing experiments because of its uniqueness. Experimental annotations and computational predictions are strongly influenced by the fact that some proteins have many partners and others few. To optimize machine learning, the newly methods explicitly ignored such a network-structure. This might be another strength of our approach. The database interface representing our results is accessible from https://rostlab.org/services/ppipair/.<br>Please cite us when you are using this data:<pre>@article{tran2018profppidb, title={ProfPPIdb: pairs of physical protein-protein interactions predicted for entire proteomes}, author={Tran, Linh and Hamp, Tobias and Rost, Burkhard}, journal={bioRxiv}, pages={332510}, year={2018}, publisher={Cold Spring Harbor Laboratory} }</pre>
DOI: 10.6084/m9.figshare.6633032
title: Data and code from "Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient"

description: This package contains data of mutualistic bird–fruit, bird–flower and insect–flower interaction networks and associated functional traits that have been sampled along a 3.5 km elevational gradient of near-natural and anthropogenic habitat on the southern slopes of Mt. Kilimanjaro.<br>Along with the raw data we provide R code to reproduce the analysis from the paper. For details about how to run the R code please have a look at the README file in the package. For details about the methods (e.g., field sampling, trait measurements or background of particular analyses) we refer to the original publication.<br>Due to the Data and Publication Policy of the Research Unit FOR1246, the figshare data are embargoed for public release until 1 January 2020. Until the embargo date for public release the data are available from the corresponding author upon reasonable request.<br>
DOI: 10.6084/m9.figshare.6633011
title: Random urine uric acid to creatinine and prediction of perinatal asphyxia: a meta-analysis

description: <b>Objective:</b> The purpose of the present review is to evaluate whether urine uric acid to creatinine ratio is increased in perinatal asphyxia and hypoxic-ischemic encephalopathy (HIE), as well as to assess its predictive accuracy in the disease. <b>Methods:</b> We used the Medline (1966–2017), Scopus (2004–2017), Clinicaltrials.gov (2008–2017), Embase (1980–2017), Cochrane Central Register of Controlled Trials CENTRAL (1999–2017), and Google Scholar (2004–2017) databases in our primary search along with the reference lists of electronically retrieved full-text papers. The hierarchical summary receiver operating characteristic (HSROC) model was used for the meta-analysis of diagnostic accuracy. <b>Results:</b> Fourteen studies were finally included in the present review, that investigated 1226 neonates. Urinary uric acid to creatinine ratio was significantly higher in neonates with perinatal asphyxia than in healthy controls (mean differences (MD): 1.43 95%CI [1.17, 1.69]). Specifically, the mean difference for Sarnat stage 1 was 0.70 (95%CI [0.28, 1.13]), for stage 2 1.41 (95%CI [0.99, 1.84]), and for stage 3 2.71 (95%CI [2.08, 3.35]). The estimated sensitivity for the summary point was 0.90 (95%CI (0.82–0.95)), the specificity was 0.88 (95%CI (0.73–0.95)) and the diagnostic odds ratio was calculated at 63.62 (95%CI (17.08–236.96)). <b>Conclusions:</b> Urinary uric acid to creatinine ratio is a rapid and an easily detected biomarker that may help physicians identify neonates at risk of developing perinatal asphyxia and HIE. However, large-scale prospective studies are still needed to determine its value in predicting mortality, as well as short- and long-term adverse neurological outcomes.
DOI: 10.6084/m9.figshare.6633011.v2
title: Random urine uric acid to creatinine and prediction of perinatal asphyxia: a meta-analysis

description: <b>Objective:</b> The purpose of the present review is to evaluate whether urine uric acid to creatinine ratio is increased in perinatal asphyxia and hypoxic-ischemic encephalopathy (HIE), as well as to assess its predictive accuracy in the disease. <b>Methods:</b> We used the Medline (1966–2017), Scopus (2004–2017), Clinicaltrials.gov (2008–2017), Embase (1980–2017), Cochrane Central Register of Controlled Trials CENTRAL (1999–2017), and Google Scholar (2004–2017) databases in our primary search along with the reference lists of electronically retrieved full-text papers. The hierarchical summary receiver operating characteristic (HSROC) model was used for the meta-analysis of diagnostic accuracy. <b>Results:</b> Fourteen studies were finally included in the present review, that investigated 1226 neonates. Urinary uric acid to creatinine ratio was significantly higher in neonates with perinatal asphyxia than in healthy controls (mean differences (MD): 1.43 95%CI [1.17, 1.69]). Specifically, the mean difference for Sarnat stage 1 was 0.70 (95%CI [0.28, 1.13]), for stage 2 1.41 (95%CI [0.99, 1.84]), and for stage 3 2.71 (95%CI [2.08, 3.35]). The estimated sensitivity for the summary point was 0.90 (95%CI (0.82–0.95)), the specificity was 0.88 (95%CI (0.73–0.95)) and the diagnostic odds ratio was calculated at 63.62 (95%CI (17.08–236.96)). <b>Conclusions:</b> Urinary uric acid to creatinine ratio is a rapid and an easily detected biomarker that may help physicians identify neonates at risk of developing perinatal asphyxia and HIE. However, large-scale prospective studies are still needed to determine its value in predicting mortality, as well as short- and long-term adverse neurological outcomes.
DOI: 10.6084/m9.figshare.6633011.v1
title: Random urine uric acid to creatinine and prediction of perinatal asphyxia: a meta-analysis

description: <b>Objective:</b> The purpose of the present review is to evaluate whether urine uric acid to creatinine ratio is increased in perinatal asphyxia and hypoxic-ischemic encephalopathy (HIE), as well as to assess its predictive accuracy in the disease. <b>Methods:</b> We used the Medline (1966–2017), Scopus (2004–2017), Clinicaltrials.gov (2008–2017), Embase (1980–2017), Cochrane Central Register of Controlled Trials CENTRAL (1999–2017), and Google Scholar (2004–2017) databases in our primary search along with the reference lists of electronically retrieved full-text papers. The hierarchical summary receiver operating characteristic (HSROC) model was used for the meta-analysis of diagnostic accuracy. <b>Results:</b> Fourteen studies were finally included in the present review, that investigated 1226 neonates. Urinary uric acid to creatinine ratio was significantly higher in neonates with perinatal asphyxia than in healthy controls (mean differences (MD): 1.43 95%CI [1.17, 1.69]). Specifically, the mean difference for Sarnat stage 1 was 0.70 (95%CI [0.28, 1.13]), for stage 2 1.41 (95%CI [0.99, 1.84]), and for stage 3 2.71 (95%CI [2.08, 3.35]). The estimated sensitivity for the summary point was 0.90 (95%CI (0.82–0.95)), the specificity was 0.88 (95%CI (0.73–0.95)) and the diagnostic odds ratio was calculated at 63.62 (95%CI (17.08–236.96)). <b>Conclusions:</b> Urinary uric acid to creatinine ratio is a rapid and an easily detected biomarker that may help physicians identify neonates at risk of developing perinatal asphyxia and HIE. However, large-scale prospective studies are still needed to determine its value in predicting mortality, as well as short- and long-term adverse neurological outcomes.
DOI: 10.6084/m9.figshare.6633005
title: An artificial inoculation protocol for <i>Uromycladium acaciae</i>, cause of a serious disease of <i>Acacia mearnsii</i> in southern Africa

description: <i>Uromycladium acaciae</i> is the cause of a severe wattle rust epidemic in plantations of <i>Acacia mearnsii</i> (black wattle) in southern Africa. Research on the biology of this damaging rust is assisting in the development of control strategies. One strategy under investigation is the identification and deployment of resistant lines of <i>A. mearnsii</i>. Selection of resistant families currently relies on large-scale, time-consuming and expensive field trials. In this study, we present a detailed artificial inoculation protocol for <i>U. acaciae</i>, which can be used to screen for resistance. The results of an experiment that used the protocol to screen the relative resistance of 12 families of <i>A. mearnsii</i> to <i>U. acaciae</i> are also presented. The developed artificial inoculation protocol can also be used to investigate several other aspects of this host–pathogen system.
DOI: 10.6084/m9.figshare.6633005.v2
title: An artificial inoculation protocol for <i>Uromycladium acaciae</i>, cause of a serious disease of <i>Acacia mearnsii</i> in southern Africa

description: <i>Uromycladium acaciae</i> is the cause of a severe wattle rust epidemic in plantations of <i>Acacia mearnsii</i> (black wattle) in southern Africa. Research on the biology of this damaging rust is assisting in the development of control strategies. One strategy under investigation is the identification and deployment of resistant lines of <i>A. mearnsii</i>. Selection of resistant families currently relies on large-scale, time-consuming and expensive field trials. In this study, we present a detailed artificial inoculation protocol for <i>U. acaciae</i>, which can be used to screen for resistance. The results of an experiment that used the protocol to screen the relative resistance of 12 families of <i>A. mearnsii</i> to <i>U. acaciae</i> are also presented. The developed artificial inoculation protocol can also be used to investigate several other aspects of this host–pathogen system.
DOI: 10.6084/m9.figshare.6632999
title: Survival of Douglas-fir provenances in Austria: site-specific late and early frost events are more important than provenance origin.

description: These trials were established between 1973 and 1993 by the Austrian Research Centre for Forests BFW across a wide spectrum of site conditions (Fig. 1). The provenance trials were designed as randomized blocks. Within each block (replication) three to four-year-old pre-cultivated seedlings of selected provenances were planted in plots of 20-100 individuals with a spacing of 2m x 2m. The number of alive and dead trees /seedlings was recorded for each trial in ages between 3 and 10 years before any management measures were implemented
DOI: 10.6084/m9.figshare.6632999.v2
title: Survival of Douglas-fir provenances in Austria: site-specific late and early frost events are more important than provenance origin.

description: These trials were established between 1973 and 1993 by the Austrian Research Centre for Forests BFW across a wide spectrum of site conditions (Fig. 1). The provenance trials were designed as randomized blocks. Within each block (replication) three to four-year-old pre-cultivated seedlings of selected provenances were planted in plots of 20-100 individuals with a spacing of 2m x 2m. The number of alive and dead trees /seedlings was recorded for each trial in ages between 3 and 10 years before any management measures were implemented
DOI: 10.6084/m9.figshare.6632999.v1
title: Response of Douglas fir provenances to spring and autumn frost in Austria

description: These trials were established between 1973 and 1993 by the Austrian Research Centre for Forests BFW across a wide spectrum of site conditions (Fig. 1). The provenance trials were designed as randomized blocks. Within each block (replication) three to four-year-old pre-cultivated seedlings of selected provenances were planted in plots of 20-100 individuals with a spacing of 2m x 2m. The number of alive and dead trees /seedlings was recorded for each trial in ages between 3 and 10 years before any management measures were implemented
DOI: 10.6084/m9.figshare.6632942
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632942.v1
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632942.v2
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632942.v3
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632942.v4
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632942.v6
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632942.v5
title: the vertical movement of dissolved organic carbon through two distinct soil types under Castanopsis fargesii Franch. and C. carlesii (Hemsl.) Hayata forests

description: We leached a standard DOC solution extracted from C. carlesii litter through two distinct soil types, using two leaching strategies: single leaching and sequential leaching. The two soil types under a natural Castanopsis carlesii (Hemsl.) Hayata forest (FC soils) and a natural Castanopsis fargesii Franch. forest (HA soils), respectively. Single leaching is each of six soil layers making up an entire 0-100 cm soil depth profile received single doses of standard DOC solution. Sequential leaching is a 6-fold larger amount of standard DOC solution sequentially percolated through the six soil layers. This file contains 3 sheet. The retention sheet is about DOC amount retained by each soil layer. The AI sheet is about aromaticity index of leachates out of each soil layer. The HIX sheet is humification index of leachates out of each soil layer. <br>
DOI: 10.6084/m9.figshare.6632936
title: McDonald versus Shirodkar cervical cerclage for the prevention of preterm birth: impact of body mass index

description: <b>Objective:</b> To compare obstetrical outcomes on women undergoing a McDonald or Shirodkar cerclage and to estimate the impact of maternal body mass index (BMI) on these outcomes. <b>Methods:</b> We conducted a retrospective review of the medical records of all women with singleton pregnancies who underwent placement of a McDonald or Shirodkar cerclage at St. Francis Hospital from January 2008 to October 2013. The subjects were categorized based on BMI groups (normal: less than 25 kg/m<sup>2</sup>, overweight: 25–29 kg/m<sup>2</sup>, obese: 30 kg/m<sup>2</sup> or more). The primary outcome was gestational age at delivery. Statistical analyses included chi-square, Student’s <i>t</i>-test, and multivariable regression analysis. <b>Results:</b> Of 95 women, 47 (49.5%) received a Shirodkar, and 48 (50.5%) a McDonald cerclage. 16 women (16.8%) were categorized as normal weight, 35 (36.8%) as overweight, and 44 (46.3%) as obese. Gestational age at delivery differed significantly by group, decreasing with each categorical increase in BMI (normal: 39.0 ± 0.3 weeks; overweight: 36.6 ± 0.7 weeks; obese: 33.0 ± 1.1 weeks; <i>p</i> p = .02). However, analysis showed a significant interaction between weight status and gestational age at delivery. Obese women had significantly longer pregnancies when they received a Shirodkar cerclage versus a McDonald cerclage (32.6 ± 1.0 weeks versus 28.8 ± 0.9 weeks; <i>p</i> p = .63). <b>Conclusions:</b> Compared to obese women receiving a McDonald cerclage, obese women receiving a Shirodkar cerclage had significantly longer pregnancies. No significant differences in pregnancy duration were found in normal/overweight women regardless of cerclage technique. Pregnancy duration in obese women receiving a Shirodkar cerclage was similar to the pregnancy duration of normal/overweight women.
DOI: 10.6084/m9.figshare.6632903
title: Medically indicated late preterm delivery and its impact on perinatal morbidity and mortality: a retrospective population-based cohort study

description: <b>Objective:</b> In the last few decades, attention has been focused on morbidity and mortality associated with late preterm delivery (34–36 + 6/7 weeks), accounting for 60–70% of all preterm births. This study is aimed to determine (1) the prevalence of late preterm deliveries (spontaneous and medically indicated) in our population; and (2) the rate of neonatal morbidity and mortality as well as maternal complications associated with the different phenotypes of late preterm deliveries. <b>Study design:</b> This retrospective population-based cohort study, included 96,176 women who had 257,182 deliveries, occurred between 1988 and 2011, allocated into three groups: term (<i>n</i> = 242,286), spontaneous (<i>n</i> = 10,063), and medically indicated (<i>n</i> = 4833) late preterm deliveries. <b>Results:</b> (1) Medically indicated late preterm deliveries were associated with increased maternal morbidity, as well as neonatal morbidity and mortality, in comparison with other study groups (<i>p</i> <b>Conclusions:</b> (1) Medically indicated late preterm deliveries were independently associated with adverse composite neonatal outcome; and (2) to benefit in term of neonatal outcome from the tool of medically indicated late preterm birth, their proportion should be kept below 35% of all late preterm deliveries, while exceeding this threshold increases the risk of neonatal mortality.