61 Works

Supply chain design during product development: a systematic literature review

Ewout Reitsma, Per Hilletofth & Eva Johansson
This paper explores how supply chains can be designed during product development (PD) through systematically reviewing 143 peer-reviewed journal articles written in English. The findings indicate that practitioners can perform 14 supply chain design (SCD) activities during PD. These activities are grouped into levels and areas, and a model is developed that interrelates SCD with nine product characteristics. Therewith, scholars are given a deep insight into the literature on SCD during PD. The paper also...

Additional file 9 of Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Maryam Rezaei Somee, Mohammad Ali Amoozegar, Seyed Mohammad Mehdi Dastgheib, Mahmoud Shavandi, Leila Ghanbari Maman, Stefan Bertilsson & Maliheh Mehrshad
Additional file 9: Supplementary Figure S1. Schematic representation of HC degradation pathways studied in this work. Purple circles show key HC degrading enzymes trigerring the degradation. Blue circles are other crucial enzymes. Important intermediate compounds are written in blue. Supplementary Figure S2. Distribution of 143512 genomes of the GTDB database release 89 in different phyla. Supplementary Figure S3. Distribution of aliphatic hydrocarbon-degrading genes across domain bacteria at the phylum level. In plot A, the color...

The Death Spiral of T Pyxidis

Joseph Patterson, Arto Oksanen, Berto Monard, Robert Rea, Franz-Josef Hambsch, Jennie McCormick, Peter Nelson, Jonathan Kemp, William Allen, Thomas Krajci, Simon Lowther, Shawn Dvorak, Thomas Richards, Gordon Myers & Greg Bolt
We report a long campaign to track the 1.8 hr photometric wave in the recurrent nova T Pyxidis, using the global telescope network of the Center for Backyard Astrophysics. During 1996-2011, that wave was highly stable in amplitude and waveform, resembling the orbital wave commonly seen in supersoft binaries. The period, however, was found to increase on a timescale P/P-dot=3x10^5 yr. This suggests a mass transfer rate of ~10^-7 M_sol/yr in quiescence. The orbital signal...

Additional file 10 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 10: Supplementary Figure S6. Reproducibility of alpha diversity between technical replicates. OTU/ASV richness was calculated for A) gut-16S, B) soil-16S, and C) soil-ITS datasets. Samples were rarefied to an equal number of reads per sample before calculating richness, and any samples whose replicate pair was removed after rarefaction (because of having lower number of reads than the rarefaction depth) were excluded from further analysis. LotuS1 results for soil-16S were removed due to too...

Additional file 11 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 11: Supplementary Figure S7. Observed composition of the mock community compared to the composition predicted by each pipeline. A) Relative abundances of the 16 orders having the highest abundance. B) Bray-Curtis distance based PCoA of the observed composition of the mock sample and composition predicted by each pipeline

Additional file 13 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 13: Supplementary Figure S9. Accuracy of each pipeline in predicting the mock community composition at species level. For benchmarking we compared the fraction of reads assigned to true taxa and both correctly and erroneously recovered taxa at the species level from the mock community.

Additional file 3 of Leptospira seroprevalence and associated risk factors in healthy Swedish dogs

Karolina Scahill, Ulrika Windahl, Sofia Boqvist & Lena Pelander
Additional file 3: Appendix 3. Shows the questionnaire that was answered by the dog owners (translated from Swedish).

Additional file 7 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 7: Supplementary Figure S3. Reproducibility of the technical replicates respective to different LotuS2 non-default parameters. Bray-Curtis distances between technical replicates of A) gut-16S, B) soil-16S, and C) soil-ITS datasets using default and non-default parameters (LotuS2 flags: -lulu 0, -xtalk 1, -keepUnclassified 1, -ITSx 0, where 1 means the option is activated; 0 means deactivated). When activated, -lulu option uses LULU R package [24] to merge OTUs/ASVs based on their co-occurrences; -xtalk option checks...

Additional file 6 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 6: Supplementary Figure S2. Reproducibility and data usage efficiency respective to dereplication filtering. A, D and G) Data usage efficiency of each tested pipeline at different dereplication parameters of LotuS2 (from strictest to least strict dereplication: 20:1,12:3,6:2; 15:1,9:3,12:2; 10:1,6:3,8:2; 8:1,4:2,3:3 (default); 4:1; 2:1, and 1:1) using DADA2 or CD-HIT clustering for 16S and ITS datasets, respectively, by comparing the number of sequence clusters (OTUs/ASVs) to retrieved read counts in final output matrix.The dereplication...

Additional file 4 of Cerebellar abiotrophy in an Icelandic horse

Sanni Hansen, Emil Olsen, Marie Raundal & Jørgen Steen Agerholm
Additional file 4: Overview of biochemical and hematological analyses and examination for respiratory pathogens.

Appendix 1.; Appendix 2.; Appendix 3.; Appendix 4.; Figure S1.; Figure S2. from Birds differentially prioritize visual and olfactory foraging cues depending on habitat of origin and sex

Diana Rubene, Matthew Low & Anders Brodin
Supplementary methods. Detailed description of bird housing, experimental setup and preparation of foraging cues.; Summarised data for all bird individuals included in the study. Individual ID, sex, origin, learning cues and performance (Table S1) and STRANGE assessment of individual-related potential sources of bias (Table S2).; Model structures and model code for R and Jags.; Supplementary results. Estimated levels of preference with confidence intervals for the different types of cues from the performed analyses (Tables S3-S6).;...

Epidemiology and clinical course of COVID-19 in Shanghai, China

Yinzhong Shen, Fang Zheng, Danfeng Sun, Yun Ling, Jun Chen, Feng Li, Tao Li, Zhiping Qian, Yuyi Zhang, Qingnian Xu, Li Liu, Qin Huang, Fei Shan, Lie Xu, Jun Wu, Zhaoqin Zhu, Zhigang Song, Shenyang Li, Yuxin Shi, Jianliang Zhang, Xueyun Wu, Joshua B. Mendelsohn, Tongyu Zhu & Hongzhou Lu
Background: Novel coronavirus pneumonia (COVID-19) is prevalent around the world. We aimed to describe epidemiological features and clinical course in Shanghai. Methods: We retrospectively analysed 325 cases admitted at Shanghai Public Health Clinical Center, between January 20 and February 29, 2020. Results: 47.4% (154/325) had visited Wuhan within 2 weeks of illness onset. 57.2% occurred in 67 clusters; 40% were situated within 53 family clusters. 83.7% developed fever during the disease course. Median times from...

Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] in Ethiopia as revealed by microsatellite markers

Bethlehem Nemera, Mulugeta Kebede, Muluken Enyew & Tileye Feyissa
Ethiopia is the center of origin of sorghum (Sorghum bicolor L.). Understanding of the genetic diversity of the species is fundamental to design appropriate conservation and management strategies. The present study addressed the genetic diversity of sorghum accessions collected from major growing regions of Ethiopia. Eighty sorghum accessions representing five populations namely Amhara, Dire Dawa, Oromia, Southern Nations, Nationalities and Peoples (SNNP) and Tigray were analyzed with 11 simple sequence repeat (SSR) markers. Analysis of...

Genetic diversity and population structure of sorghum [Sorghum bicolor (L.) Moench] in Ethiopia as revealed by microsatellite markers

Bethlehem Nemera, Mulugeta Kebede, Muluken Enyew & Tileye Feyissa
Ethiopia is the center of origin of sorghum (Sorghum bicolor L.). Understanding of the genetic diversity of the species is fundamental to design appropriate conservation and management strategies. The present study addressed the genetic diversity of sorghum accessions collected from major growing regions of Ethiopia. Eighty sorghum accessions representing five populations namely Amhara, Dire Dawa, Oromia, Southern Nations, Nationalities and Peoples (SNNP) and Tigray were analyzed with 11 simple sequence repeat (SSR) markers. Analysis of...

Additional file 1 of Leptospira seroprevalence and associated risk factors in healthy Swedish dogs

Karolina Scahill, Ulrika Windahl, Sofia Boqvist & Lena Pelander
Additional file 1: Appendix 1. Shows number of reported dogs to the Swedish Board of Agriculture (2010-2020) [42]. All laboratory positive samples (antibodies (>1:100) and PCR) are reported regardless of clinical suspicion of disease. Travel and vaccination history is not known in tested dogs.

Additional file 11 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 11: Supplementary Figure S7. Observed composition of the mock community compared to the composition predicted by each pipeline. A) Relative abundances of the 16 orders having the highest abundance. B) Bray-Curtis distance based PCoA of the observed composition of the mock sample and composition predicted by each pipeline

Additional file 12 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 12: Supplementary Figure S8. Number of reads and OTUs/ASVs and those assigned true taxa at genus level by each pipeline in the analysis of the mock community. Total number of A) reads retrieved by each pipeline and those assigned to true taxa at genus level B) OTUs/ASVs generated by each pipeline and those assigned to true taxa at genus level. Blue and red line indicates number of 16S gene copies and species, respectively,...

Additional file 13 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 13: Supplementary Figure S9. Accuracy of each pipeline in predicting the mock community composition at species level. For benchmarking we compared the fraction of reads assigned to true taxa and both correctly and erroneously recovered taxa at the species level from the mock community.

Additional file 8 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 8: Supplementary Figure S4. Data usage efficiency of different amplicon sequence data analysis pipelines. Data usage efficiency on gut 16S rRNA (gut- 16S) and soil 16S rRNA (soil-16S) amplicons tested with different pipelines at different read truncation lengths (170, 200, and 230 & 170, 200, and 220 bases for the gut and soil datasets, respectively), by comparing the number of sequence clusters (ASVs /OTUs) to retrieved read counts in the final output matrix...

Additional file 9 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 9: Supplementary Figure S5. Reproducibility of beta diversity at different read truncation lengths. Reproducibility of sequenced technical replicates by measuring the Bray-Curtis (A and C) and Jaccard distances (B and D) of the microbiome composition among technical replicate samples. Two datasets were used to represent different biomes and amplicon technologies using (A, B) human faecal samples (16S rRNA primer, N=40 replicates) and (C, D) soil samples (16S rRNA, V4-V5 region primers, N=50 replicates)....

Additional file 1 of To what extent does surrounding landscape explain stand-level occurrence of conservation-relevant species in fragmented boreal and hemi-boreal forest?–a systematic review protocol

Malin Undin, Anita Atrena, Fredrik Carlsson, Mattias Edman, Bengt Gunnar Jonsson & Jennie Sandström
Additional file 1: Roses form The filled in ROSES reporting standards form for systematic review protocols.

Compiled notes from SORTEE discussion from Why don't we share data and code? Perceived barriers and benefits to public archiving practices

Dylan G. E. Gomes, Patrice Pottier, Robert Crystal-Ornelas, Emma J. Hudgins, Vivienne Foroughirad, Luna L. Sánchez-Reyes, Rachel Turba, Paula Andrea Martinez, David Moreau, Michael G. Bertram, Cooper A. Smout & Kaitlyn M. Gaynor
Our collective notes document during the initial SORTEE discussion and the 3 follow-up meetings with agendas and attendance of authors.

The Death Spiral of T Pyxidis

Joseph Patterson, Arto Oksanen, Berto Monard, Robert Rea, Franz-Josef Hambsch, Jennie McCormick, Peter Nelson, Jonathan Kemp, William Allen, Thomas Krajci, Simon Lowther, Shawn Dvorak, Thomas Richards, Gordon Myers & Greg Bolt
We report a long campaign to track the 1.8 hr photometric wave in the recurrent nova T Pyxidis, using the global telescope network of the Center for Backyard Astrophysics. During 1996-2011, that wave was highly stable in amplitude and waveform, resembling the orbital wave commonly seen in supersoft binaries. The period, however, was found to increase on a timescale P/P-dot=3x10^5 yr. This suggests a mass transfer rate of ~10^-7 M_sol/yr in quiescence. The orbital signal...

Circadian rhythms of vital signs are associated with in-hospital mortality in critically ill patients: A retrospective observational study

Zhengning Yang, Xiaoxia Xie, Xu Zhang, Lan Li, Ruoxue Bai, Hui Long, Yanna Ma, Zhenliang Hui, Yujie Qi & Jun Chen
Vital signs have been widely used to assess the disease severity of patients, but there is still a lack of research on their circadian rhythms. The objective is to explore the circadian rhythms of vital signs in critically ill patients and establish an in-hospital mortality prediction model. Study patients from the recorded eICU Collaborative Research Database were included in the present analyses. The circadian rhythms of vital signs are analyzed in critically ill patients using...

Circadian rhythms of vital signs are associated with in-hospital mortality in critically ill patients: A retrospective observational study

Zhengning Yang, Xiaoxia Xie, Xu Zhang, Lan Li, Ruoxue Bai, Hui Long, Yanna Ma, Zhenliang Hui, Yujie Qi & Jun Chen
Vital signs have been widely used to assess the disease severity of patients, but there is still a lack of research on their circadian rhythms. The objective is to explore the circadian rhythms of vital signs in critically ill patients and establish an in-hospital mortality prediction model. Study patients from the recorded eICU Collaborative Research Database were included in the present analyses. The circadian rhythms of vital signs are analyzed in critically ill patients using...

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Affiliations

  • Swedish University of Agricultural Sciences
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  • Earlham Institute
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  • University of Tartu
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  • Quadram Institute
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  • Zhejiang University
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  • Huazhong University of Science and Technology
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  • Shanghai Jiao Tong University
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  • Tianjin Medical University General Hospital
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  • Sun Yat-sen University
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  • West China Hospital of Sichuan University
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