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opencc-by-4.0Dec 2017View details →

Technique de transplantation microchirurgicale de sporocystes de schistosomes.

Video instructions on the technique of microsurgical transplantation of schistosome sporocysts from a donor snail to a recipient snail (in French). Produced at IHPE (http://ihpe.univ-perp.fr/)

Fig. 2 in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 2. Index map (A) and release points of transplanted substrates in southwest Kochi Prefecture (B). a and b: this study, c and d: Nagamune (1918), and Kuno (1922). respectively. Table 1. Release and collection dates of transplanted substrates

Fig. 4 in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 4. Examples of the coral fragments showing substantial growth. Coenenchyme and branch growth, cross-section repair, and polyp increase were confirmed. Left side with capital letters: Before the release. Right side with small letters: After the collection. A and a: 215 days (Jul. 26, 2016, to Feb. 26, 2017), B and b: 328 days (Feb. 26, 2017, to Jan. 20, 2018), C and c: 340 days (Jul. 26, 2016, to Jul. 1, 2017), D and d: 363 days (Jun. 9, 2017, to Jun. 7, 2018), E and e: 461 days (Feb. 26, 2017, to Jun. 2, 2018), F and f: 936 days (Jul. 1, 2017, to Jan. 22, 2020). Scale bars = 10 mm. A–B is based on Koido and Toshino (2022).

Fig. 3 in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 3. An example of living broken and dead fragments. A: Coenenchyme had spread over the mount with the formation of many tiny polyps. Blue arrow: cross section was covered with coenenchyme, and a polyp had formed. Green arrow: Newly growing branch. B: Comparison of the dead specimen. Left: Before the release (Jun. 9, 2017). Right: After the collection (Jun. 7, 2018). Scale bars = 10 mm.

Fig. 1. Precious coral colonies used for transplantation. A in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 1. Precious coral colonies used for transplantation. A: Before cutting. The broken yellow line shows the separation line. B: After cutting. C: Precious coral fragments were transplanted on the concrete part of substrate (Kaiso-kun). D: Pre-release substrate. Blue arrows show fragments detached along with epoxy mount. E: Recovered substrate. C–E is based on Koido and Toshino (2022).

opencc-by-4.0Aug 2024View details →

Genome Sizes of Bacterial Species Detected in Cell-Free DNA of Patients with Acute Leukemia and Sepsis, Including Those Undergoing Bone Marrow Transplantation

Next Generation Sequencing (NGS) analysis of Cell-Free DNA provides valuable insights into a spectrum of pathogenic species (particularly bacterial) in blood. Patients with Sepsis often face problems like delays in treatment regimens (combination or cocktail of antibiotics) due to the long turnaround time (TAT) of classical and standard blood culture procedures. NGS gives results with lower TAT along with high-depth coverage. The use of NGS may be a possible solution to deciding treatment regimens for patients without losing precious time and more accurately possibly saving lives. Our curated dataset is of bacterial species or strains detected along with their genome size in 107 AML patients diagnosed with Sepsis clinically. Cell-free DNA profiles of patients were built and sequencing was done in Illumina (NovaSeq and NextSeq). Bioinformatic analysis was performed using two classification algorithms namely kraken2 and kaiju. For kraken2  based classification reference bacterial index developed by Carlo Ferravante et al (Zenodo 2020)  (link: https://zenodo.org/records/4055180) was used, while for kaiju-based classification reference database named "nr_euk" dated "2023-05-10" (link: https://bioinformatics-centre.github.io/kaiju/downloads.html) was used. Genome size annotation is important in metagenomics since for the use of depth of coverage (abundance), genome size is required. In metagenomic classification algorithms like kraken/kraken2 and kaiju output computes reads assigned only and not abundance. In kaiju, the problem is more complicated since the reference database does not have a fasta file but only an index file from which alignment is done.  To address the above challenges to compute "depth of coverage" or simply abundance, we build a Genome size annotator tool (https://github.com/patkarlab/Genome-Size-Annotation) which provides genome size for each species detected given its taxid is available. In this tool, the NCBI Datasets tool, NCBI Genome API check tool, and Data Mining from AI search engines like perplexity.ai are used.  We have curated two datasets Kraken2 dataset named "FINAL METAGENOMIC DATA MASTERSHEET - kraken_genome_annotation" Kaiju dataset named "FINAL METAGENOMIC DATA MASTERSHEET - kaiju_genome_annotation" *Please note that for kraken2 curated dataset, we used data mining from the AI search engine perplexity.ai while for kaiju we did not use perplexity, ai, and any species whose genome size was not found was labeled "NA"

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Data from: Reciprocal transplants reveal asymmetric local adaptation of Himalayan Rhododendron approaching elevational range limit

As plant species expand their upper limit of distribution under current warming, some retain both traditional climate space and biotic environment while others encounter novel conditions. The latter is the case for Rhododendron campanulatum,a woody shrub that grows both above and below treeline at our study site in the Eastern Himalaya where a very conspicuous, stable treeline was defined by a nearly contiguous canopy of tall Abies spectabilis trees, many of them over a century old. Prior work showed that treeline had remained static in this region while R. campanulatum expanded its elevational range limit. We tested local adaptation of R. campanulatum by performing reciprocal transplants between the species' current elevational range limit (4023masl) and just above treeline (3876 masl). Contrary to expectation, the coldest temperatures of late winter and early-mid spring were experienced by plants at the lower elevation: R. campanulatum at species' limit (upper site) were covered by snow for a longer period (40 more days) and escaped the coldest temperatures suffered by conspecifics at treeline (lower site). The harsher spring conditions at treeline likely explains why leaves were smaller at treeline (15.3 cm2) than at species-limit (21.3 cm2). Contrary to results from equivalent studies in other regions, survival was reduced more by downslope than by upslope movement, again potentially due to extreme cold temperatures observed at treeline in spring. Upslope transplantation had no effect on mortality, but mortality of species-limit saplings transplanted downslope was three times higher than that of residents at both sites. A general expectation is that locals should survive better than foreign transplants, but survival of locals and immigrants at our species-limit site was identical. However, those species-limit saplings that survive the transplant to treeline grew faster than both locals at treeline and the transplants at species-limit. Overall, we found asymmetric adaptation: compared to treeline saplings, those at species-limit (147 m above treeline) were more tolerant of extremes in the growing season but less tolerant of extremes in winter and early-mid spring, displaying local adaptation in a more complex manner than simply home advantage, and complicating predictions about impacts of future regional climate change.

opencc-zeroApr 2023View details →

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Tissue-specific features of the T cell repertoire following allogeneic hematopoietic cell transplantation in human and mouse

T cells are the central drivers of many inflammatory diseases, but the repertoire of tissue-resident T cells at sites of pathology in human organs remains poorly understood. We examined the site-specificity of T cell receptor (TCR) repertoires across tissues (5-18 tissues per patient) in prospectively collected autopsies of patients with and without graft-versus-host disease (GVHD), a potentially lethal tissue-targeting complication of allogeneic hematopoietic cell transplantation, as well as in mouse models of GVHD. Anatomic similarity between tissues was a key determinant of TCR repertoire composition within patients, independent of disease or transplant status. The T cells recovered from peripheral blood and spleen in patients and mice captured a limited portion of the TCR repertoire detected in tissues. Whereas few T cell clones were shared across patients, motif-based clustering revealed shared repertoire signatures across patients in a tissue-specific fashion. T cells at disease sites had a tissue-resident phenotype and were of donor origin based on single-cell chimerism analysis. These data demonstrate the complex composition of T cell populations that persist in human tissues at the end-stage of an inflammatory disorder following lymphocyte-directed therapy. These findings also underscore the importance of studying T cells in tissues rather than blood for tissue-based pathologies and suggest the tissue-specific nature of both the endogenous and post-transplant T cell landscape.

opencc-zeroJul 2023View details →

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Source height and contact with terrestrial soil drive transplanted epiphyte performance

<ol> <li class="MsoNormal">Epiphytes are characterized by their ability to survive without a root connection to the ground, but many basic life-history traits and ecological trade-offs of this unique aerial growth habit remain largely uncharacterized. Mortality causes are still not well understood, but falling from the host tree has been suggested as a leading cause of epiphyte mortality and community dynamics. Little empirical evidence exists for why epiphytes do not survive when forced to become terrestrial, and few studies exist that transplant epiphytes between high- and low-forest strata to test trade-offs between thriving in canopy environments and survival in the forest understory.</li> <li class="MsoNormal">Here, we experimentally test two hypotheses regarding the drivers of epiphyte mortality in a cloud forest of central Panama. We test whether simple contact with terrestrial soil is deleterious to epiphytes, preliminarily testing the Epiphyte Enemy Escape Hypothesis, and test the Vertical Niche Differentiation Hypothesis, wherein epiphytes are specifically adapted for microsites throughout the vertical forest strata. By monitoring survival, leaf loss, and health status of 270 transplanted epiphytes for a year and a half, we pinpoint the extent to which soil contact and height of origin regulate epiphyte performance. </li> <li class="MsoNormal">We found that contact with terrestrial soil itself was detrimental to epiphytes in situ, providing some of the first empirical data to explain why falling onto the ground, versus falling into the understory, is particularly fatal to epiphytes. However, we also found that mortality rates vary substantially among taxonomic groups and among epiphytes that originally came from different height strata.</li> <li class="MsoNormal"> Synthesis. Plants that are adapted for the canopy experience a trade-off with higher mortality when in contact with terrestrial soil. Follow-up studies should explore the role of terrestrial soil microbes and physiological constraints as potential drivers of decreased grounded epiphyte survival. </li> </ol>

opencc-zeroAug 2023View details →

opencc-by-4.0Dec 2022View details →

Data for: Greening the dike revetment with historic sod transplantation technique in a Living Lab.

Data from an in-situ experiment on a dike in Living Lab Hedwige Prosperpolder. In the experiment we applied a historic sod transplantation technique. We tested the erosion resistance of the adapted vegetated dike revetment after one growth season.  Dataset contains measurements in sods plot S1, S2, S3, S4 and in reference plots R1-R4. In addition, two section were only milled (K1 and F). These sections are not described in the publication, however some data is available and thus included in this dataset.  This dataset contains files from the following research steps:  1.    Visual observation (vegetation) 2.    Soil moisture content & Soil penetration resistance  3.    Root indication (doorwortelling) 4.    Sod pulling method (grastrek proef) 5.    Wave impact test (golfklap proef) & Overflow test (overloop proef) The data is described in the following publication: Kim van den Hoven, K., Grashof-Bokdam, C.J., Slim, P.A., Wentholt, L., Peeters, P., Depreiter, D., Koelewijn, A.R., Stoorvogel, M.M., van den Berg, M., Kroeze, C., van Loon-Steensma, J.M. (2024) Greening the dike revetment with historic sod transplantation technique in a Living Lab. Journal of Flood Risk Management. DOI:10.1111/jfr3.12968

A Study of Oral Ixazomib Maintenance Therapy in Participants With Newly Diagnosed Multiple Myeloma (NDMM) Not Treated With Stem Cell Transplantation (SCT)

ClinicalTrials.gov study NCT02312258. IPD Sharing: YES. Countries: 35. Publications: 2.

The De-novo Use of Eculizumab in Presensitized Patients Receiving Cardiac Transplantation

ClinicalTrials.gov study NCT02013037. IPD Sharing: YES. Countries: 1. Publications: 14.

restrictedIPD-UNDECIDEDFeb 2026View details →

Efficacy and Safety of Everolimus in Liver Transplant Recipients of Living Donor Liver Transplants

ClinicalTrials.gov study NCT01888432. IPD Sharing: UNDECIDED. Countries: 13. Publications: 1.

Efficacy and Safety Study of Maribavir Treatment Compared to Investigator-assigned Treatment in Transplant Recipients With Cytomegalovirus (CMV) Infections That Are Refractory or Resistant to Treatmen

ClinicalTrials.gov study NCT02931539. IPD Sharing: YES. Countries: 14. Publications: 6.

KRDI in Transplant-Eligible MM

ClinicalTrials.gov study NCT04430894. IPD Sharing: YES. Countries: 1. Publications: 1.

Efficacy and Safety Study of CSJ148 in Stem Cell Transplant Patients

ClinicalTrials.gov study NCT02268526. IPD Sharing: YES. Countries: 6. Publications: 1.

Maribavir for Treatment of Resistant or Refractory CMV Infections in Transplant Recipients

ClinicalTrials.gov study NCT01611974. IPD Sharing: YES. Countries: 1. Publications: 5.

Safety, Pharmacokinetics, and Preliminary Efficacy of Isatuximab in Patients Awaiting Kidney Transplantation

ClinicalTrials.gov study NCT04294459. IPD Sharing: YES. Countries: 2. Publications: 2.

Clazakizumab for the Treatment of Chronic Active Antibody Mediated Rejection in Kidney Transplant Recipients

ClinicalTrials.gov study NCT03744910. IPD Sharing: YES. Countries: 15. Publications: 4.

Study on Efficacy and Safety of LNP023 in C3 Glomerulopathy Patients Transplanted and Not Transplanted

ClinicalTrials.gov study NCT03832114. IPD Sharing: YES. Countries: 6. Publications: 1.