cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16650413
title: Additional file 2 of Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

description: Additional file 1. Supplementary tables.
DOI: 10.6084/m9.figshare.16650413.v1
title: Additional file 2 of Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

description: Additional file 1. Supplementary tables.
DOI: 10.6084/m9.figshare.16650425
title: Additional file 1 of Dentition and body condition: tooth wear as a correlate of weight loss in roe deer

description: Additional file 1. Dataset. Individual characteristics, tooth wear scores, M1 height and hypsodonty index of M1 data referred to 319 roe deer females legally shot during the regular annual harvest (1 Jan–15 Mar for females) between 2007 and 2017 in the Arezzo province (43° 28′ N, 11° 53′ E), Tuscany, Central Italy
DOI: 10.6084/m9.figshare.16650425.v1
title: Additional file 1 of Dentition and body condition: tooth wear as a correlate of weight loss in roe deer

description: Additional file 1. Dataset. Individual characteristics, tooth wear scores, M1 height and hypsodonty index of M1 data referred to 319 roe deer females legally shot during the regular annual harvest (1 Jan–15 Mar for females) between 2007 and 2017 in the Arezzo province (43° 28′ N, 11° 53′ E), Tuscany, Central Italy
DOI: 10.6084/m9.figshare.16650476
title: Additional file 1 of STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

description: Additional file 1. Microsoft Excel: The first sheet (S1) contains results from accessions using SARS-CoV-2 detection tool as described in Methods; the second sheet (S2) contains those accessions from S1 subject to verification using STAT as described in Methods. S1 SARS-CoV-2 Contamination. S2 SARS-CoV-2 Verification.
DOI: 10.6084/m9.figshare.16650476.v1
title: Additional file 1 of STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

description: Additional file 1. Microsoft Excel: The first sheet (S1) contains results from accessions using SARS-CoV-2 detection tool as described in Methods; the second sheet (S2) contains those accessions from S1 subject to verification using STAT as described in Methods. S1 SARS-CoV-2 Contamination. S2 SARS-CoV-2 Verification.
DOI: 10.6084/m9.figshare.16650482.v1
title: Additional file 2 of STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

description: Additional file 2. Microsoft Excel: The first four sheets (S1-S4) contain the top five NCBI BLAST® hits for each accession spot in which at least one of those hits was human. The last sheet contains summary STAT taxonomic data for each of the four accessions before and after human contamination removal tool treatment as described in Methods. S1 SRR11092056 BLAST® Results. S2 SRR11092057 BLAST® Results. S3 SRR13402847 BLAST® Results. S4 SRR13444106 BLAST® Results. S5 STAT Taxonomic Slices.
DOI: 10.6084/m9.figshare.16650482
title: Additional file 2 of STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

description: Additional file 2. Microsoft Excel: The first four sheets (S1-S4) contain the top five NCBI BLAST® hits for each accession spot in which at least one of those hits was human. The last sheet contains summary STAT taxonomic data for each of the four accessions before and after human contamination removal tool treatment as described in Methods. S1 SRR11092056 BLAST® Results. S2 SRR11092057 BLAST® Results. S3 SRR13402847 BLAST® Results. S4 SRR13444106 BLAST® Results. S5 STAT Taxonomic Slices.
DOI: 10.6084/m9.figshare.16650488
title: Additional file 3 of STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

description: Additional file 3. Microsoft Excel: The first sheet (S1) contains STAT accuracy test raw data; the next two sheets (S2, S3) contain viral false positive resolved taxa from each of two tests; the final sheet (S4) contains the TaxIds used in the accuracy test.
DOI: 10.6084/m9.figshare.16650488.v1
title: Additional file 3 of STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

description: Additional file 3. Microsoft Excel: The first sheet (S1) contains STAT accuracy test raw data; the next two sheets (S2, S3) contain viral false positive resolved taxa from each of two tests; the final sheet (S4) contains the TaxIds used in the accuracy test.
DOI: 10.6084/m9.figshare.16650503
title: Additional file 2 of Identifying homogeneous subgroups of patients and important features: a topological machine learning approach

description: Additional file 2. Main characteristics of the top five clusters derived with our pipeline applied to the validation dataset
DOI: 10.6084/m9.figshare.16650503.v1
title: Additional file 2 of Identifying homogeneous subgroups of patients and important features: a topological machine learning approach

description: Additional file 2. Main characteristics of the top five clusters derived with our pipeline applied to the validation dataset
DOI: 10.6084/m9.figshare.16650536
title: Additional file 10 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 10: Table S5. Boundary cut-off values. A list of WSS cut-off values is provided for each species. These values were previously established based on the Human Microbiome Project (HMP) using our classifier and can be used to assess the relatedness of the strains in two separate samples in the same individual (Kumar et al., 2017).
DOI: 10.6084/m9.figshare.16650536.v1
title: Additional file 10 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 10: Table S5. Boundary cut-off values. A list of WSS cut-off values is provided for each species. These values were previously established based on the Human Microbiome Project (HMP) using our classifier and can be used to assess the relatedness of the strains in two separate samples in the same individual (Kumar et al., 2017).
DOI: 10.6084/m9.figshare.16650569
title: Additional file 6 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 6: Table S1. Sample and sequence read information. The original sequence files were sequenced and deposited by (A) James et al., (B) Davar et al., and (C) Baruch et al. The table represents the sample information along with sequence read information.
DOI: 10.6084/m9.figshare.16650569.v1
title: Additional file 6 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 6: Table S1. Sample and sequence read information. The original sequence files were sequenced and deposited by (A) James et al., (B) Davar et al., and (C) Baruch et al. The table represents the sample information along with sequence read information.
DOI: 10.6084/m9.figshare.16650572
title: Additional file 7 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 7: Table S2. WSS scores for Baruch et al. All pairwise comparisons were conducted between a donor-recipient paired sample from Baruch et al. The resultant scores (%) are shown as a numerical value. *CO indicates the cut-off value for each species
DOI: 10.6084/m9.figshare.16650572.v1
title: Additional file 7 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 7: Table S2. WSS scores for Baruch et al. All pairwise comparisons were conducted between a donor-recipient paired sample from Baruch et al. The resultant scores (%) are shown as a numerical value. *CO indicates the cut-off value for each species
DOI: 10.6084/m9.figshare.16650575
title: Additional file 8 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 8: Table S3. WSS scores for Davar et al. All pairwise comparisons were conducted between donor-recipient paired samples. The resultant scores (%) are shown as a numerical value. *CO indicates the cut-off value for each species.
DOI: 10.6084/m9.figshare.16650575.v1
title: Additional file 8 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 8: Table S3. WSS scores for Davar et al. All pairwise comparisons were conducted between donor-recipient paired samples. The resultant scores (%) are shown as a numerical value. *CO indicates the cut-off value for each species.
DOI: 10.6084/m9.figshare.16650581
title: Additional file 9 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 9: Table S4. WSS scores for James et al. All pairwise comparisons were conducted among colon segment samples. The resultant WSS scores (%) are shown as a numerical value under the ‘WSS’ column.
DOI: 10.6084/m9.figshare.16650581.v1
title: Additional file 9 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

description: Additional file 9: Table S4. WSS scores for James et al. All pairwise comparisons were conducted among colon segment samples. The resultant WSS scores (%) are shown as a numerical value under the ‘WSS’ column.
DOI: 10.6084/m9.figshare.16650596
title: Additional file 3 of ssvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors

description: Additional file 3: Table S1. CUT&RUN quality control on fresh versus frozen samples (XLSX 10 KB)
DOI: 10.6084/m9.figshare.16650596.v1
title: Additional file 3 of ssvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors

description: Additional file 3: Table S1. CUT&RUN quality control on fresh versus frozen samples (XLSX 10 KB)
DOI: 10.6084/m9.figshare.15134649.v1
title: Data and code for our article "speeding up quantum dissipative dynamics of open systems with kernel methods"

description: This dataset includes training data set, test dataset, already prepared input files and the code related to our paper on "speeding up quantum dissipative dynamics of open systems with kernel methods"<br>
DOI: 10.6084/m9.figshare.15134649
title: Data and code for our article "speeding up quantum dissipative dynamics of open systems with kernel methods"

description: This dataset includes training data set, test dataset, already prepared input files and the code related to our paper on "speeding up quantum dissipative dynamics of open systems with kernel methods"<br>
DOI: 10.5281/zenodo.5518294
title: NMR dataset for metallo-B-lactamase IMP-1

description: NMR dataset to support publication: Localising individual atoms of tryptophan side chains in the metallo-B-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites NMR data are in Bruker format and pulse programs are contained within each dataset with the name "pulprog" Table of contents Experiment number Experiment 1 IMP1 A53C with C2-Y tag (figure S3-a)<br> 2 IMP1 A53C with C2-Tb tag (figure S3-a)<br> 3 IMP1 A53C with C2-Tm tag (figure S3-a)<br> 4 captopril bound IMP1 A53C with C2-Y tag (figure S4-a)<br> 5 captopril bound IMP1 A53C with C2-Tb tag (figure S4-a)<br> 6 captopril bound IMP1 A53C with C2-Tm tag (figure S4-a)<br> 7 IMP1 N172C with C2-Y tag (figure S3-b)<br> 8 IMP1 N172C with C2-Tb tag (figure S3-b)<br> 9 IMP1 N172C with C2-Tm tag (figure S3-b)<br> 10 captopril bound IMP1 N172C with C2-Y tag (figure S4-b)<br> 11 captopril bound IMP1 N172C with C2-Tb tag (figure S4-b)<br> 12 captopril bound IMP1 N172C with C2-Tm tag (figure S4-b)<br> 13 IMP1 S204C with C2-Y tag (figure S3-c)<br> 14 IMP1 S204C with C2-Tb tag (figure S3-c)<br> 15 IMP1 S204C with C2-Tm tag (figure S3-c) <br> 16 captopril bound IMP1 S204C with C2-Y tag (figure S4-c)<br> 17 captopril bound IMP1 S204C with C2-Tb tag (figure S4-c)<br> 18 captopril bound IMP1 S204C with C2-Tm tag (figure S4-c)<br> 19 IMP1 N172C with C2-Y tag (figure 2-B)<br> 20 IMP1 N172C with C2-Tb tag (figure 2-E)<br> 21 IMP1 S204C with C2-Y tag (figure 2-F) <br> 22 IMP1 N172C with C2-Y tag (figure 2-E)<br> 23 IMP1 N172C with C12-Y tag (figure S5-a)<br> 24 IMP1 N172C with C12-Tb tag (figure S5-a)<br> 25 IMP1 N172C with C12-Tm tag (figure S5-a)<br> 26 captopril bound IMP1 N172C with C12-Y tag (figure S5-b)<br> 27 captopril bound IMP1 N172C with C12-Tb tag (figure S5-b)<br> 28 captopril bound IMP1 N172C with C12-Tm tag (figure S5-b)
DOI: 10.5281/zenodo.5518293
title: NMR dataset for metallo-B-lactamase IMP-1

description: NMR dataset to support publication: Localising individual atoms of tryptophan side chains in the metallo-B-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites NMR data are in Bruker format and pulse programs are contained within each dataset with the name "pulprog" Table of contents Experiment number Experiment 1 IMP1 A53C with C2-Y tag (figure S3-a)<br> 2 IMP1 A53C with C2-Tb tag (figure S3-a)<br> 3 IMP1 A53C with C2-Tm tag (figure S3-a)<br> 4 captopril bound IMP1 A53C with C2-Y tag (figure S4-a)<br> 5 captopril bound IMP1 A53C with C2-Tb tag (figure S4-a)<br> 6 captopril bound IMP1 A53C with C2-Tm tag (figure S4-a)<br> 7 IMP1 N172C with C2-Y tag (figure S3-b)<br> 8 IMP1 N172C with C2-Tb tag (figure S3-b)<br> 9 IMP1 N172C with C2-Tm tag (figure S3-b)<br> 10 captopril bound IMP1 N172C with C2-Y tag (figure S4-b)<br> 11 captopril bound IMP1 N172C with C2-Tb tag (figure S4-b)<br> 12 captopril bound IMP1 N172C with C2-Tm tag (figure S4-b)<br> 13 IMP1 S204C with C2-Y tag (figure S3-c)<br> 14 IMP1 S204C with C2-Tb tag (figure S3-c)<br> 15 IMP1 S204C with C2-Tm tag (figure S3-c) <br> 16 captopril bound IMP1 S204C with C2-Y tag (figure S4-c)<br> 17 captopril bound IMP1 S204C with C2-Tb tag (figure S4-c)<br> 18 captopril bound IMP1 S204C with C2-Tm tag (figure S4-c)<br> 19 IMP1 N172C with C2-Y tag (figure 2-B)<br> 20 IMP1 N172C with C2-Tb tag (figure 2-E)<br> 21 IMP1 S204C with C2-Y tag (figure 2-F) <br> 22 IMP1 N172C with C2-Y tag (figure 2-E)<br> 23 IMP1 N172C with C12-Y tag (figure S5-a)<br> 24 IMP1 N172C with C12-Tb tag (figure S5-a)<br> 25 IMP1 N172C with C12-Tm tag (figure S5-a)<br> 26 captopril bound IMP1 N172C with C12-Y tag (figure S5-b)<br> 27 captopril bound IMP1 N172C with C12-Tb tag (figure S5-b)<br> 28 captopril bound IMP1 N172C with C12-Tm tag (figure S5-b)
DOI: 10.6084/m9.figshare.16649800
title: Native herbivores indirectly facilitate the growth of invasive Spartina in a eutrophic saltmarsh

description: These data were collected to explain how eutrophication interact with native herbivores to facilitate the growth of a globally invasive species <i>Spartina alterniflora</i> in coastal China by using a two year field nitrogen (N)-enrichment X crab exclusion experiment.
DOI: 10.6084/m9.figshare.16649800.v5
title: Native herbivores indirectly facilitate the growth of invasive Spartina in a eutrophic saltmarsh

description: These data were collected to explain how eutrophication interact with native herbivores to facilitate the growth of a globally invasive species <i>Spartina alterniflora</i> in coastal China by using a two year field nitrogen (N)-enrichment X crab exclusion experiment.
DOI: 10.6084/m9.figshare.16649800.v4
title: Native herbivores indirectly facilitate the growth of invasive Spartina in a eutrophic saltmarsh

description: These data were collected to explain how eutrophication interact with native herbivores to facilitate the growth of a globally invasive species <i>Spartina alterniflora</i> in coastal China by using a two year field nitrogen (N)-enrichment X crab exclusion experiment.
DOI: 10.6084/m9.figshare.16651723
title: Supplementary Material for: Immune Checkpoint Inhibitors: The Emerging Cornerstone in Cholangiocarcinoma Therapy?

description: <b><i>Background:</i></b> Cholangiocarcinoma (CCA) encompasses a heterogeneous group of malignant tumors with dismal prognosis and increasing incidence worldwide. Both late diagnosis due to the lack of early symptoms and the refractory nature of these tumors seriously compromise patients’ welfare and outcomes. <b><i>Summary:</i></b> During the last decade, immunotherapy and, more specifically, modulation of immune checkpoints-mediated signaling pathways have been under the spotlight in the field of oncology, emerging as a potential therapeutic approach for the treatment of several cancers, including CCA. Generally, high expression levels of immune checkpoints in patients with CCA have been associated with worse clinical outcomes, particularly with shorter overall survival and relapse-free survival. Thus, immune checkpoint inhibitors (ICIs), which mainly constitute different monoclonal antibodies, have been developed in order to hamper the immune checkpoint-mediated pathways. Interestingly, chemotherapy may increase the expression of immune checkpoints, while other therapeutic approaches such as ablative and targeted therapies may enhance their antitumor activity. In this sense, several clinical trials evaluated the safety and efficacy of ICIs for CCA, both as a monotherapy and in combination with other ICIs or loco-regional and systemic therapies. Additionally, many other clinical trials are currently ongoing and results are eagerly awaited. Here, we summarize the key aspects of immune checkpoint molecules as prognostic factors and therapeutic targets in CCA, highlighting the most recent advances in the field and future research directions. <b><i>Key Messages:</i></b> (1) Effective therapeutic approaches for CCA are urgently needed. (2) Expression levels of immune checkpoints in patients with CCA have been proposed to be related with clinical outcomes. (3) Combination of different ICIs may outperform the efficacy of ICI monotherapy for CCA treatment. (4) Recent studies point toward the combination of ICIs and other common therapies, especially chemotherapy, as a promising strategy for treatment of CCA patients.
DOI: 10.6084/m9.figshare.16651738
title: Supplementary Material for: Vitreous Noise on Optical Coherence Tomography as an Early Finding of Brolucizumab-Related Intraocular Inflammation

description: We describe a case of brolucizumab-related intraocular inflammation (IOI) detected using vitreous haze on optical coherence tomography (OCT) at an early stage before the patient was aware of any symptom. A 69-year-old female presented with decreased right vision. The patient was diagnosed with pachychoroidal neovasculopathy and started intravitreal aflibercept (IVA) with a 3+ treat-and-extend strategy (TAE). Although the serous retinal detachment (SRD) disappeared after IVA treatment, the patient was managed with treatment every 4 weeks without extending the treatment interval To shorten the treatment interval, intravitreal brolucizumab (IVBr) was started 44 weeks after starting IVA treatment. After initiating IVBr treatment, the SRD completely disappeared. However, 16 weeks after starting IVBr, OCT showed noise in the vitreous cavity, which had not been seen before, and infrared images showed a black smoke-like shadow over the macula. Despite these findings, the patient had no subjective symptoms, and so IVBr was re-administered with an 8-week TAE interval. Five days after IVBr treatment, vitreous inflammatory cells were observed, and the noise in the vitreous cavity and the smoke-like shadow in the infrared image were further enhanced. We diagnosed the patient with brolucizumab-related IOI, and anti-inflammatory treatment was initiated. After extensive treatment, the vitreous opacity gradually disappeared, and the vitreous noise on OCT and the black smoke-like shadow on infrared images disappeared. IOI may have already been present 16 weeks after starting IVBr treatment, when we judged that there was no inflammation and IVBr was re-administered. When following patients receiving IVBr, IOI may be detected by OCT at an earlier stage by evaluating vitreous haze.
DOI: 10.6084/m9.figshare.16651738.v1
title: Supplementary Material for: Vitreous Noise on Optical Coherence Tomography as an Early Finding of Brolucizumab-Related Intraocular Inflammation

description: We describe a case of brolucizumab-related intraocular inflammation (IOI) detected using vitreous haze on optical coherence tomography (OCT) at an early stage before the patient was aware of any symptom. A 69-year-old female presented with decreased right vision. The patient was diagnosed with pachychoroidal neovasculopathy and started intravitreal aflibercept (IVA) with a 3+ treat-and-extend strategy (TAE). Although the serous retinal detachment (SRD) disappeared after IVA treatment, the patient was managed with treatment every 4 weeks without extending the treatment interval To shorten the treatment interval, intravitreal brolucizumab (IVBr) was started 44 weeks after starting IVA treatment. After initiating IVBr treatment, the SRD completely disappeared. However, 16 weeks after starting IVBr, OCT showed noise in the vitreous cavity, which had not been seen before, and infrared images showed a black smoke-like shadow over the macula. Despite these findings, the patient had no subjective symptoms, and so IVBr was re-administered with an 8-week TAE interval. Five days after IVBr treatment, vitreous inflammatory cells were observed, and the noise in the vitreous cavity and the smoke-like shadow in the infrared image were further enhanced. We diagnosed the patient with brolucizumab-related IOI, and anti-inflammatory treatment was initiated. After extensive treatment, the vitreous opacity gradually disappeared, and the vitreous noise on OCT and the black smoke-like shadow on infrared images disappeared. IOI may have already been present 16 weeks after starting IVBr treatment, when we judged that there was no inflammation and IVBr was re-administered. When following patients receiving IVBr, IOI may be detected by OCT at an earlier stage by evaluating vitreous haze.