cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6945560.v1
title: Supplementary Material for: Variations in Oxygen Saturation Targeting, and Retinopathy of Prematurity Screening and Treatment Criteria in Neonatal Intensive Care Units: An International Survey

description: <b><i>Background:</i></b> Rates of retinopathy of prematurity (ROP) and ROP treatment vary between neonatal intensive care units (NICUs). Neonatal care practices, including oxygen saturation (SpO<sub>2</sub>) targets and criteria for the screening and treatment of ROP, are potential contributing factors to the variations. <b><i>Objectives:</i></b><i></i> To survey variations in SpO<sub>2</sub> targets in 2015 (and whether there had been recent changes) and criteria for ROP screening and treatment across the networks of the International Network for Evaluating Outcomes in Neonates (iNeo). <b><i>Methods:</i></b> Online prepiloted questionnaires on treatment practices for preterm infants were sent to the directors of 390 NICUs in 10 collaborating iNeo networks. Nine questions were asked and the results were summarized and compared. <b><i>Results:</i></b> Overall, 329/390 (84%) NICUs responded, and a majority (60%) recently made changes in upper and lower SpO<sub>2</sub> target limits, with the median set higher than previously by 2–3% in 8 of 10 networks. After the changes, fewer NICUs (15 vs. 28%) set an upper SpO<sub>2</sub> target limit &gt; 95% and fewer (3 vs. 5%) a lower limit &lt; 85%. There were variations in ROP screening criteria, and only in the Swedish network did all NICUs follow a single guideline. The initial retinal examination was carried out by an ophthalmologist in all but 6 NICUs, and retinal photography was used in 20% but most commonly as an adjunct to indirect ophthalmoscopy. <b><i>Conclusions:</i></b> There is considerable variation in SpO<sub>2</sub> targets and ROP screening and treatment criteria, both within networks and between countries.
DOI: 10.6084/m9.figshare.6945413
title: Supplementary Material for: Do Common Marmosets (<b><i>Callithrix jacchus</i></b>) Use Scent to Communicate Information about Food Resources?

description: Many animals use olfactory cues to signal information about food resources; however, this particular use of scent has received little attention in primates. Common<b><i></i></b> marmosets (<i>Callithrix jacchus</i>)<i></i> are exudativores that gouge bark to elicit exudate production and frequently deposit scent marks at gouge holes. We conducted preliminary tests of the hypothesis that common marmosets use olfactory cues to communicate information about exudate value, with more desirable resources targeted for marking. We performed choice experiments on two captive male marmosets. The animals were presented with: (1) a urine scent-marked and unmarked food resource, and (2) a high and low value food resource (i.e., greater/lesser food volumes). Marmosets placed more scent marks on high, compared to low, value food resources. Animals also spent more time gouging, removed more bark and more frequently revisited high versus low value food resources. Lastly, scent-marked foods were gouged more often than unmarked foods. Our findings support the hypothesis that marmosets use scent marking and olfaction to convey information about food resources, although verification in a larger sample is needed. Nonetheless, the demonstrated link between food value and scent marking suggests that olfactory signals may aid marmoset foraging decisions.
DOI: 10.6084/m9.figshare.6945341
title: Supplementary Material for: The MRI Sepsis Score: An Innovative Tool for the Evaluation of Septic Peritonitis in Mice Using 7-Tesla Small Animal MRI

description: <b><i>Background:</i></b> Magnetic resonance imaging (MRI) techniques are rarely used in the context of abdominal sepsis and in sepsis research. This study investigates the impact of MRI for monitoring septic peritonitis in an animal model (colon ascendens stent-induced peritonitis, CASP). The CASP model closely mimics that of human disease and is highly standardized. The most frequently employed readout parameter in mouse CASP studies is prolonged or decreased rate of survival. Monitoring the progression of peritonitis via MRI could provide a helpful tool in the evaluation of severity. The use of alternative readout systems could very well reduce the number of research animals. Perspectively, clinical improvement after certain treatment could be classified. <b><i>Methods:</i></b> This study describes for the first time MRI findings following the induction of septic peritonitis in mice using the CASP model. Two sublethal groups of mice with septic peritonitis were investigated. Each had received one of two differing stent diameters in order to control the leakage of feces into the abdominal cavity. Each mouse served as its own control. Imaging and analyses were performed blinded. Gut diameters, stomach volume, abdominal organ wall diameters, and volume of the adrenal glands were measured. Serum corticosterone levels were detected using ELISA. Serum IL-6, TNF-α, IL-1β, and IL-10 levels were screened by cytometric bead array. Statistical analysis was performed using the Mann-Whitney U test for nonparametric probes and the Kruskal-Wallis and <i>t</i> tests. <b><i>Results:</i></b> Using a 7-tesla MRI scanner 24 and 48 h after induction of septic peritonitis, interenteric fluid, organ swelling of spleen and adrenal glands, as well as dilatation of the stomach were compared to nonseptic conditions. Swelling of adrenal glands resulted in an increased serum corticosterone level. In addition, the wall of the intestine bowel was thickened. Based upon these findings, an MRI score (MRI sepsis score, MSS) for abdominal sepsis in mice was established. Reduced stent sizes led to reduced severity of the abdominal sepsis, which could be reproduced in the MSS, which is described here for the first time. <b><i>Conclusions:</i></b> Intraabdominal variations during septic peritonitis are detectable by MRI techniques. MRI methods should become a more important tool for the evaluation of abdominal peritonitis. MSS could provide an interesting tool for the evaluation of therapeutic strategies.
DOI: 10.6084/m9.figshare.6945332
title: Limited evidence for differential reproductive fitness of wild Atlantic cod in areas of high and low salmon farming density

description: ABSTRACT: Sea cage fish aquaculture attracts large aggregations of wild fish that feed on farm waste. Fish that associate closely with farms undergo physiological changes, and captive feeding trials indicate possible negative effects on reproductive fitness. However, little is known about the significance of this phenomenon for reproduction in wild fish over larger spatial scales. To assess if coastal areas with intensive aquaculture impact the fitness of wild fish, we collected Atlantic cod <i>Gadus morhua</i> from 2 areas, one with high and and one with low salmon farming density (HFD and LFD respectively) in south-western Norway, a region that hosts the world’s largest coastal fish aquaculture industry. We conducted a captive spawning trial and compared a range of reproductive fitness metrics. Two fatty acids that occur at high levels in commercial feed, oleic and lineoleic acid, were strongly correlated in the ovaries of HFD fish, but a comparison of lipid profiles between HFD and LFD fish showed no differences in total lipids or essential fatty acids. Although HFD fish were slightly larger than LFD fish and had similar body condition, the volume of eggs produced did not differ, indicating relatively lower reproductive investment by HFD fish. HFD eggs were 5% smaller than LFD eggs, which did not lead to differential hatching success but may have contributed to HFD larvae being 8% smaller than their LFD counterparts at 40 days post spawning. The potential for cumulative effects of smaller eggs and larvae on fitness at later life stages warrants further investigation.
DOI: 10.6084/m9.figshare.6945320
title: Mild drying of sandy soil can physically limit the uptake of phosphorus by rainfed lowland rice in northeast Thailand

description: Poor response of rice to phosphorus (P) fertilization and low phytoavailability of soil P have been reported in sandy rainfed fields in northeast Thailand. In order to evaluate the effects of mild soil drying on the uptake of P by rainfed lowland rice, we carried out nutrient omission trials for nitrogen (N) and P at Ubon Ratchathani Rice Research Center under rainfed and flooded conditions. The surface soil was classified as sandy loam. To avoid severe soil drying and drought stress in the rainfed field, soil water potential at a depth of 20 cm was maintained at the field capacity (&gt; −20 kPa) by flush irrigation. The effects of flooding and drying on the soil properties were also evaluated in the laboratory using soils with diverse textures in and around the center. In the field experiments, the above-ground biomass of rice plants (RD6) did not respond significantly to P fertilization in the rainfed field, although it responded positively to N fertilization. Root length in the surface 10 cm under the rainfed condition was significantly smaller than that under the flooded condition due partly to the increased soil hardness upon drying, but this could not quantitatively explain the large discrepancy of P uptake observed between the rainfed and flooded conditions. Under the rainfed condition, the P uptake did not increase significantly, even when the concentration of soil Bray P was tripled by transferring the surface soil from the flooded to the rainfed field. From the laboratory experiments, it was further suggested that soil P was supplied mainly by diffusion and that the effective diffusion coefficient for P can become less than one-tenth of the value in the flooded field when the sandy soil with clay at around 10% dried to −100 kPa. Our results suggest that the uptake of P by the rainfed lowland rice grown in sandy soil can be limited physically by mild soil drying that reduces the supply of P to roots by diffusion rather than the chemical extractability of soil P.
DOI: 10.6084/m9.figshare.6945320.v1
title: Mild drying of sandy soil can physically limit the uptake of phosphorus by rainfed lowland rice in northeast Thailand

description: Poor response of rice to phosphorus (P) fertilization and low phytoavailability of soil P have been reported in sandy rainfed fields in northeast Thailand. In order to evaluate the effects of mild soil drying on the uptake of P by rainfed lowland rice, we carried out nutrient omission trials for nitrogen (N) and P at Ubon Ratchathani Rice Research Center under rainfed and flooded conditions. The surface soil was classified as sandy loam. To avoid severe soil drying and drought stress in the rainfed field, soil water potential at a depth of 20 cm was maintained at the field capacity (&gt; −20 kPa) by flush irrigation. The effects of flooding and drying on the soil properties were also evaluated in the laboratory using soils with diverse textures in and around the center. In the field experiments, the above-ground biomass of rice plants (RD6) did not respond significantly to P fertilization in the rainfed field, although it responded positively to N fertilization. Root length in the surface 10 cm under the rainfed condition was significantly smaller than that under the flooded condition due partly to the increased soil hardness upon drying, but this could not quantitatively explain the large discrepancy of P uptake observed between the rainfed and flooded conditions. Under the rainfed condition, the P uptake did not increase significantly, even when the concentration of soil Bray P was tripled by transferring the surface soil from the flooded to the rainfed field. From the laboratory experiments, it was further suggested that soil P was supplied mainly by diffusion and that the effective diffusion coefficient for P can become less than one-tenth of the value in the flooded field when the sandy soil with clay at around 10% dried to −100 kPa. Our results suggest that the uptake of P by the rainfed lowland rice grown in sandy soil can be limited physically by mild soil drying that reduces the supply of P to roots by diffusion rather than the chemical extractability of soil P.
DOI: 10.6084/m9.figshare.6945332.v1
title: Limited evidence for differential reproductive fitness of wild Atlantic cod in two areas of high and low salmon farming density

description: ABSTRACT: Sea cage fish aquaculture attracts large aggregations of wild fish that feed on farm waste. Fish that associate closely with farms undergo physiological changes, and captive feeding trials indicate possible negative effects on reproductive fitness. However, little is known about the significance of this phenomenon for reproduction in wild fish over larger spatial scales. To assess if coastal areas with intensive aquaculture impact the fitness of wild fish, we collected Atlantic cod <i>Gadus morhua</i> from 2 areas, one with high and and one with low salmon farming density (HFD and LFD respectively) in south-western Norway, a region that hosts the world’s largest coastal fish aquaculture industry. We conducted a captive spawning trial and compared a range of reproductive fitness metrics. Two fatty acids that occur at high levels in commercial feed, oleic and lineoleic acid, were strongly correlated in the ovaries of HFD fish, but a comparison of lipid profiles between HFD and LFD fish showed no differences in total lipids or essential fatty acids. Although HFD fish were slightly larger than LFD fish and had similar body condition, the volume of eggs produced did not differ, indicating relatively lower reproductive investment by HFD fish. HFD eggs were 5% smaller than LFD eggs, which did not lead to differential hatching success but may have contributed to HFD larvae being 8% smaller than their LFD counterparts at 40 days post spawning. The potential for cumulative effects of smaller eggs and larvae on fitness at later life stages warrants further investigation.
DOI: 10.17028/rd.lboro.6945311
title: UK-wide Typical Meteorological Year Global Horizontal Irradiance Data for Photovoltaic Systems

description: TYPICAL METEOROLOGICAL YEAR DATA FOR PHOTOVOLTAIC SYSTEMS IN THE UK The data available for download comprises hourly TMY Global Horizontal Irradiance values generated from the 2008-2016 decade for a 10 x 10 km resolution grid covering the UK and Northern Ireland. Global Horizontal Irradiance in Wh/m^2. The data is initially interpolated to each grid point from UK Meteorological Office measured values. The TMY for each point is calculated as follows: For each month in the year (i.e., Jan., Feb., March, etc.), the ten-year monthly mean of irradiance data is obtained for the period 2004-2015.The historic month that most closely matches the ten-year mean for that month is identified i.e. the most “typical” month.The hourly data values from the twelve typical months are combined to create the typical year file. This might comprise e.g. January from 2010, February from 2005, March from 2007 etc. This simple method has been shown to perform well compared to other free-to-download TMY datasets.<br> If you make use of this data, please: 1. E-mail juice-centre@lboro.ac.uk with details of your employer/institution and a brief description of the project for which you require the data. 2. Cite this journal paper in any publications: http://www.mdpi.com/1996-1073/10/2/181 / https://doi.org/10.3390/en10020181.<br> INSTRUCTIONS: Open the kml file in Google Earth or software of your choice and locate the grid point nearest to the location you are interested in. Look up the coordinates of the point in the grid info file. Unzip folder and use Windows Explorer to open the csv containing TMY data for your selected point.<br>Please note that the KML file is released under a CC BY-SA licence as described in the file.
DOI: 10.6084/m9.figshare.6945332.v3
title: Limited evidence for differential reproductive fitness of wild Atlantic cod in areas of high and low salmon farming density

description: ABSTRACT: Sea cage fish aquaculture attracts large aggregations of wild fish that feed on farm waste. Fish that associate closely with farms undergo physiological changes, and captive feeding trials indicate possible negative effects on reproductive fitness. However, little is known about the significance of this phenomenon for reproduction in wild fish over larger spatial scales. To assess if coastal areas with intensive aquaculture impact the fitness of wild fish, we collected Atlantic cod <i>Gadus morhua</i> from 2 areas, one with high and and one with low salmon farming density (HFD and LFD respectively) in south-western Norway, a region that hosts the world’s largest coastal fish aquaculture industry. We conducted a captive spawning trial and compared a range of reproductive fitness metrics. Two fatty acids that occur at high levels in commercial feed, oleic and lineoleic acid, were strongly correlated in the ovaries of HFD fish, but a comparison of lipid profiles between HFD and LFD fish showed no differences in total lipids or essential fatty acids. Although HFD fish were slightly larger than LFD fish and had similar body condition, the volume of eggs produced did not differ, indicating relatively lower reproductive investment by HFD fish. HFD eggs were 5% smaller than LFD eggs, which did not lead to differential hatching success but may have contributed to HFD larvae being 8% smaller than their LFD counterparts at 40 days post spawning. The potential for cumulative effects of smaller eggs and larvae on fitness at later life stages warrants further investigation.
DOI: 10.6084/m9.figshare.6945332.v2
title: Limited evidence for differential reproductive fitness of wild Atlantic cod in two areas of high and low salmon farming density

description: ABSTRACT: Sea cage fish aquaculture attracts large aggregations of wild fish that feed on farm waste. Fish that associate closely with farms undergo physiological changes, and captive feeding trials indicate possible negative effects on reproductive fitness. However, little is known about the significance of this phenomenon for reproduction in wild fish over larger spatial scales. To assess if coastal areas with intensive aquaculture impact the fitness of wild fish, we collected Atlantic cod <i>Gadus morhua</i> from 2 areas, one with high and and one with low salmon farming density (HFD and LFD respectively) in south-western Norway, a region that hosts the world’s largest coastal fish aquaculture industry. We conducted a captive spawning trial and compared a range of reproductive fitness metrics. Two fatty acids that occur at high levels in commercial feed, oleic and lineoleic acid, were strongly correlated in the ovaries of HFD fish, but a comparison of lipid profiles between HFD and LFD fish showed no differences in total lipids or essential fatty acids. Although HFD fish were slightly larger than LFD fish and had similar body condition, the volume of eggs produced did not differ, indicating relatively lower reproductive investment by HFD fish. HFD eggs were 5% smaller than LFD eggs, which did not lead to differential hatching success but may have contributed to HFD larvae being 8% smaller than their LFD counterparts at 40 days post spawning. The potential for cumulative effects of smaller eggs and larvae on fitness at later life stages warrants further investigation.
DOI: 10.6084/m9.figshare.6945266
title: Aligned sequences in genus level for newick tree

description: Aligned bacterial sequences in genus level, obtained from 16S rRNA sequencing of silkworm gut microbiota. This fasta file is used to generate the newick tree.
DOI: 10.6084/m9.figshare.6945266.v1
title: Aligned sequences in genus level for newick tree

description: Aligned bacterial sequences in genus level, obtained from 16S rRNA sequencing of silkworm gut microbiota. This fasta file is used to generate the newick tree.
DOI: 10.6084/m9.figshare.6945224
title: Supplementary Material for: Association between a New Sugar Index and Caries Experience: Results of a Cross-Sectional Field Study

description: <b><i>Objectives:</i></b> The aim of this study was to test the relationship between a newly developed sugar index and caries experience in 4th- and 6th-graders. <b><i>Materials and Methods:</i></b> A total of 1,019 fourth-graders and 925 sixth-graders from 2 regions in Northern Germany participated in the study. Caries experience was recorded by applying the ICDAS criteria. Tooth-brushing habits and other independent variables were examined psychometrically. Structured questions were formulated that were related to specific everyday eating situations, especially between main meals, which proved to be relevant for a higher caries risk. To compare mean caries scores, nonparametric tests were applied. The Pearson coefficient was calculated in order to verify the correlation between the sugar index and the caries experience. The influence of various independent variables on caries experience was assessed by stepwise backward logistic regression analysis. <b><i>Results:</i></b> With regard to the primary teeth of the 4th-graders, significant correlations with values &gt; 0.1 were found for all ICDAS outcome variables. With regard to the permanent teeth of the 6th-graders, the only significant correlations with the sugar index were for the ICDAS outcome variables D<sub>3–6</sub>MFT and D<sub>3–6</sub>FS. <b><i>Conclusion:</i></b> The results of our study show that not only the correlation between the sugar index and caries experience was stronger for 4th-graders than for 6th-graders, but also more distinctly visible differences were observed when comparing extreme groups. This indicates that protective factors, such as fluoridation and the preventive sealing of fissures, help level out the differences in caries occurrence in older children when compared to younger children.
DOI: 10.6084/m9.figshare.6945206
title: Taxonomy analysis of shotgun sequencing results

description: Taxonomy analysis of silkworm gut microbiota based on shotgun metagenomic sequencing data.
DOI: 10.6084/m9.figshare.6945224.v1
title: Supplementary Material for: Association between a New Sugar Index and Caries Experience: Results of a Cross-Sectional Field Study

description: <b><i>Objectives:</i></b> The aim of this study was to test the relationship between a newly developed sugar index and caries experience in 4th- and 6th-graders. <b><i>Materials and Methods:</i></b> A total of 1,019 fourth-graders and 925 sixth-graders from 2 regions in Northern Germany participated in the study. Caries experience was recorded by applying the ICDAS criteria. Tooth-brushing habits and other independent variables were examined psychometrically. Structured questions were formulated that were related to specific everyday eating situations, especially between main meals, which proved to be relevant for a higher caries risk. To compare mean caries scores, nonparametric tests were applied. The Pearson coefficient was calculated in order to verify the correlation between the sugar index and the caries experience. The influence of various independent variables on caries experience was assessed by stepwise backward logistic regression analysis. <b><i>Results:</i></b> With regard to the primary teeth of the 4th-graders, significant correlations with values &gt; 0.1 were found for all ICDAS outcome variables. With regard to the permanent teeth of the 6th-graders, the only significant correlations with the sugar index were for the ICDAS outcome variables D<sub>3–6</sub>MFT and D<sub>3–6</sub>FS. <b><i>Conclusion:</i></b> The results of our study show that not only the correlation between the sugar index and caries experience was stronger for 4th-graders than for 6th-graders, but also more distinctly visible differences were observed when comparing extreme groups. This indicates that protective factors, such as fluoridation and the preventive sealing of fissures, help level out the differences in caries occurrence in older children when compared to younger children.
DOI: 10.6084/m9.figshare.6945152
title: 16S rRNA sequencing result: bacteria abundance in genus level

description: Bacteria abundance of silkworm (strain QB and P50) in genus level