cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc253h71
title: CCDC 1999352: Experimental Crystal Structure Determination

description: Related Article: Naohiro Uemura, Momoka Hosaka, Aoi Washio, Yasushi Yoshida, Takashi Mino, Masami Sakamoto|2020|Cryst.Growth Des.|20|4898|doi:10.1021/acs.cgd.0c00829
DOI: 10.5517/ccdc.csd.cc253h82
title: CCDC 1999353: Experimental Crystal Structure Determination

description: Related Article: Naohiro Uemura, Momoka Hosaka, Aoi Washio, Yasushi Yoshida, Takashi Mino, Masami Sakamoto|2020|Cryst.Growth Des.|20|4898|doi:10.1021/acs.cgd.0c00829
DOI: 10.5517/ccdc.csd.cc1q0h4c
title: CCDC 1579392: Experimental Crystal Structure Determination

description: Related Article: Xiang Chen, Zhaoqi Guo, Cong Zhang, Rong Gao, Jianguo Zhang, Haixia Ma|2020|CrystEngComm|22|5436|doi:10.1039/D0CE00643B
DOI: 10.5517/ccdc.csd.cc248pgl
title: CCDC 1974559: Experimental Crystal Structure Determination

description: Related Article: Xiang Chen, Zhaoqi Guo, Cong Zhang, Rong Gao, Jianguo Zhang, Haixia Ma|2020|CrystEngComm|22|5436|doi:10.1039/D0CE00643B
DOI: 10.6084/m9.figshare.9746786
title: LSTM+GA data

description: These data sets are three types of data:<br>-Data used by the fuzzy logic simulation model such as temp_prices and temperatures.<br>-Data generated by the fuzzy simulator such as fuzzy_outxx.csv and used to train the LSTM models.<br>- Data related to the optimization process such as results and GA_pricing, optimized_prices_loads<br><br>
DOI: 10.6084/m9.figshare.9746786.v1
title: LSTM+GA data

description: These data sets are three types of data:<br>-Data used by the fuzzy logic simulation model such as temp_prices and temperatures.<br>-Data generated by the fuzzy simulator such as fuzzy_outxx.csv and used to train the LSTM models.<br>- Data related to the optimization process such as results and GA_pricing, optimized_prices_loads<br><br>
DOI: 10.5517/ccdc.csd.cc254wfn
title: CCDC 2000691: Experimental Crystal Structure Determination

description: Related Article: Rajendiran Kanagaraj, Ajay Kumar Jana, P.D. Babu, Vasudeva Siruguri, Pradip K. Maji, Swarup K. Panda, Avijit Kumar Paul|2021|J.Mol.Struct.|1224|129027|doi:10.1016/j.molstruc.2020.129027
DOI: 10.5517/ccdc.csd.cc254wgp
title: CCDC 2000692: Experimental Crystal Structure Determination

description: Related Article: Rajendiran Kanagaraj, Ajay Kumar Jana, P.D. Babu, Vasudeva Siruguri, Pradip K. Maji, Swarup K. Panda, Avijit Kumar Paul|2021|J.Mol.Struct.|1224|129027|doi:10.1016/j.molstruc.2020.129027
DOI: 10.5517/ccdc.csd.cc254whq
title: CCDC 2000693: Experimental Crystal Structure Determination

description: Related Article: Rajendiran Kanagaraj, Ajay Kumar Jana, P.D. Babu, Vasudeva Siruguri, Pradip K. Maji, Swarup K. Panda, Avijit Kumar Paul|2021|J.Mol.Struct.|1224|129027|doi:10.1016/j.molstruc.2020.129027
DOI: 10.6084/m9.figshare.9746630
title: Microbial community of fish eggs on the XuWen coral reef, China

description: The sequnence reads of microbial composition from Acanthopagrus schlegelii and Halichoeres nigrescens eggs<br>
DOI: 10.6084/m9.figshare.9746630.v1
title: Microbial community of fish eggs on the XuWen coral reef, China

description: The sequnence reads of microbial composition from Acanthopagrus schlegelii and Halichoeres nigrescens eggs<br>
DOI: 10.6084/m9.figshare.9746609
title: Insect DNA from bat faeces

description: FASTQ files from 178 bat faecal samples. Target DNA is the 158-bp minibarcode region for insects on the CO1 gene (ZBJ primers).
DOI: 10.6084/m9.figshare.9746573
title: Decoding the signature of molecular mechanism involved in mutation associated resistance to 1, 3-benzothiazin-4-ones (Btzs) based DprE1 inhibitors using BTZ043 as a reference drug

description: Different resistant strains of <i>M. tuberculosis</i> (Mtb) highlight the urgent need of novel anti-tubercular drugs. In mycobacteria, decaprenyl-phosphoryl-β-D-ribose 2’-oxidase (DprE1) is an appealing enzyme to target as it is involved in the biosynthesis of cell wall component arabinogalactan.1, 3-benzothiazin-4-ones (BTZs) based drugs are promising irreversible inhibitors of DprE1. However, a single point mutation of Cys387Ser in DprE1 results in the development of resistance to these drugs. Herein, we made an effort to decode the molecular mechanism of Cys387Ser DprE1 mutation associated resistance in Mtb against BTZs using different <i>in silico</i> techniques. Since the 3D crystal structure of mutant Cys387Ser protein is not yet been solved, thus the homology model was also developed using 4P8N as a template protein with 99.8% homology with the target protein. The computational results suggested that the factors like HOMO–LUMO energy gap, Burgi-Dunitz angle and distance support the covalent inhibition of wild DprE1 by 1, 3-benzothiazin-4-ones class of drugs, using BTZ043 as a reference drug and the same factors support the cause of resistance in case of Cys387Ser mutation. On the basis of these results, it was concluded that BTZ043 can efficiently inhibit the wild type DprE1 than mutant DprE1.
DOI: 10.6084/m9.figshare.9746573.v1
title: Decoding the signature of molecular mechanism involved in mutation associated resistance to 1, 3-benzothiazin-4-ones (Btzs) based DprE1 inhibitors using BTZ043 as a reference drug

description: Different resistant strains of <i>M. tuberculosis</i> (Mtb) highlight the urgent need of novel anti-tubercular drugs. In mycobacteria, decaprenyl-phosphoryl-β-D-ribose 2’-oxidase (DprE1) is an appealing enzyme to target as it is involved in the biosynthesis of cell wall component arabinogalactan.1, 3-benzothiazin-4-ones (BTZs) based drugs are promising irreversible inhibitors of DprE1. However, a single point mutation of Cys387Ser in DprE1 results in the development of resistance to these drugs. Herein, we made an effort to decode the molecular mechanism of Cys387Ser DprE1 mutation associated resistance in Mtb against BTZs using different <i>in silico</i> techniques. Since the 3D crystal structure of mutant Cys387Ser protein is not yet been solved, thus the homology model was also developed using 4P8N as a template protein with 99.8% homology with the target protein. The computational results suggested that the factors like HOMO–LUMO energy gap, Burgi-Dunitz angle and distance support the covalent inhibition of wild DprE1 by 1, 3-benzothiazin-4-ones class of drugs, using BTZ043 as a reference drug and the same factors support the cause of resistance in case of Cys387Ser mutation. On the basis of these results, it was concluded that BTZ043 can efficiently inhibit the wild type DprE1 than mutant DprE1.
DOI: 10.6084/m9.figshare.9746507
title: Single or double embryo transfer? Decision-making process in patients participating in an oocyte donation program

description: In IVF/ICSI programs, after receiving the information about the success results of single embryo transfer (SET) vs double embryo transfer (DET) and the risks of multiple pregnancy, a significant number of patients opt for SET. Up to date, no comparable studies have been published in oocyte recipients. The aim of this study was to evaluate if the counseling provided to oocyte recipients influence their decision on the number of embryos to be transferred. Fifty-five recipients expressed their preference and the relevance for the decision-making process that they attribute to certain factors through an anonymous questionnaire completed pre and post-counseling. Before counseling, 32 out of 55 recipients preferred DET, 13 preferred SET and 10 were undecided. From the 32 recipients who preferred DET, 16 (50%) maintained their preference after counseling, 13 (40.6%) changed their decision to SET and 3 (9.4%) changed to undecided (McNemar’s test: <i>p</i> p
DOI: 10.6084/m9.figshare.9746507.v1
title: Single or double embryo transfer? Decision-making process in patients participating in an oocyte donation program

description: In IVF/ICSI programs, after receiving the information about the success results of single embryo transfer (SET) vs double embryo transfer (DET) and the risks of multiple pregnancy, a significant number of patients opt for SET. Up to date, no comparable studies have been published in oocyte recipients. The aim of this study was to evaluate if the counseling provided to oocyte recipients influence their decision on the number of embryos to be transferred. Fifty-five recipients expressed their preference and the relevance for the decision-making process that they attribute to certain factors through an anonymous questionnaire completed pre and post-counseling. Before counseling, 32 out of 55 recipients preferred DET, 13 preferred SET and 10 were undecided. From the 32 recipients who preferred DET, 16 (50%) maintained their preference after counseling, 13 (40.6%) changed their decision to SET and 3 (9.4%) changed to undecided (McNemar’s test: <i>p</i> p
DOI: 10.6084/m9.figshare.9746492.v1
title: Supraglacial rivers and lakes on the southwest Greenland Ice Sheet

description: The data are GIS shapefiles of supraglacial rivers and lakes on the southwest Greenland Ice Sheet mapped using seven Landsat-8 satellite imagery acquired between July 13 and August 2, 2015.
DOI: 10.6084/m9.figshare.9746381
title: Raw data from A place for everything and everything in its place: spatial organization of individuals on nests of the primitively eusocial wasp <i>Ropalidia marginata</i>

description: Excel files with raw data for all R codes in ESM file 1
DOI: 10.6084/m9.figshare.9746375
title: Raw Data from Functional implications of dentition-based morphotypes in piscivorous fishes

description: Raw data used for analyses in our study
DOI: 10.6084/m9.figshare.9746360
title: Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina - Blastocystis Stramenopile Lineage

description: Full alignment, trimmed alignment and trees of the analyses used in "<b>Ancient Adaptive Lateral Gene Transfers in the Symbiotic <i>Opalina</i>- <i>Blastocystis </i>StramenopileLineage</b>"<b></b>
DOI: 10.6084/m9.figshare.9746348
title: Arkshell_mt_genome

description: Mitochondrial genes derived from transcriptomic data of ark shell species acquired from NCBI SRA Database.
DOI: 10.6084/m9.figshare.9746360.v1
title: Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina - Blastocystis Stramenopile Lineage

description: Full alignment, trimmed alignment and trees of the analyses used in "<b>Ancient Adaptive Lateral Gene Transfers in the Symbiotic <i>Opalina</i>- <i>Blastocystis </i>StramenopileLineage</b>"<b></b>
DOI: 10.11583/dtu.9746324
title: A room acoustics model and simulated impulse responses of a living room

description: A set of 21 room impulse responses simulated in ODEON (commercial and proprietary software, www.odeon.dk) and auralized for the audio-visual immersion lab (AVIL, 64 channels; Ahrens et al., 2019), using the LORA toolbox (Favrot et al., 2010).The dataset contains seven azimuth locations (-90:30:90 degrees) and three distances (1.4m, 2.4m, 3.4m).<br>Example:IR01 refers to -90degrees (left), 1.4m distance.IR07 refers to 90degrees (right), 1.4m distance.<br>IR08 refers to -90degrees (left), 2.4m distance.<br>IR21 refers to 90degrees (right), 3.4m distance.<br><br>This database contains the loudspeaker impulse responses, the ODEON room model as well as the raw ODEON output files.
DOI: 10.6084/m9.figshare.9746348.v1
title: Arkshell_mt_genome

description: Mitochondrial genes derived from transcriptomic data of ark shell species acquired from NCBI SRA Database.
DOI: 10.6084/m9.figshare.9746303
title: Paddy soil microbial functional genes

description: Paddy soil microbial functional genes, contains C, N, S, P etc. 429 paddy soil samples from 39 long-term paddy fields across China.
DOI: 10.6084/m9.figshare.9746312
title: Quantitative summary of abstracts from ialeUK conferences 1992-2017

description: Summary of abstracts submitted to UK chapter of the International Association for Landscape Ecology (ialeUK) annual conferences 1992-2017. Abstracts were characterised using pre-defined classes within eight categories. See Young et al. (In Review) for full details.
DOI: 10.6084/m9.figshare.9746279
title: Supplementary Material for: Predicted Indirectly ReCognizable HLA Epitopes (PIRCHE) Are Associated with Poorer Outcome after Single Mismatch Unrelated Donor Stem Cell Transplantation: A Study of the Cooperative Transplant Study Group (KTS) of the German Group for Bone Marrow and Stem Cell Transplantation (DAG-KBT)

description: There is no established standard for selection of mismatched unrelated donors. Indirect recognition of HLA mismatches can be predicted using the model of “Predicted Indirectly ReCognizable HLA Epitopes” (PIRCHE). We performed a multicenter retrospective study evaluating the impact PIRCHE on outcome after allogeneic stem cell transplantation (allo-HSCT) from single mismatched (HLA 9/10 matched) unrelated donors. The study cohort included 424 adult recipients of HLA 9/10 matched unrelated donor transplants (9/10 MUD), treated for AML or MDS at 6 transplant centers across Germany. Detection of PIRCHE was associated with lower overall survival (OS) (47 vs. 57%, <i>p</i> = 0.04), higher non-relapse mortality (NRM) (32 vs. 20%, <i>p</i> = 0.05), and higher incidence of chronic graft-versus-host disease (GVHD) (49 vs. 31%, <i>p</i> = 0.04) at 2 years. Cumulative incidence of acute GVHD grade 2–4 at 6 months was not significantly different (30 vs. 23%, <i>p</i> = 0.2). OS for 9/10 MUD with no PIRCHE was similar to 10/10 MUD (57 vs. 55%). In multivariate analysis, PIRCHE retained negative impact on OS (RR 1.5, 95% CI 1.0–2.1, <i>p</i> = 0.03) and NRM (RR 1.7, 95% CI 1.0–2.9, <i>p</i> = 0.03). To the best of our knowledge, for the first time, we show the association of PIRCHE and survival outcome after allo-HSCT. The PIRCHE model, if validated in an independent cohort, may allow selection of permissible HLA mismatches that enable improved transplant outcome.
DOI: 10.6084/m9.figshare.9746303.v1
title: Paddy soil microbial functional genes

description: Paddy soil microbial functional genes, contains C, N, S, P etc. 429 paddy soil samples from 39 long-term paddy fields across China.
DOI: 10.6084/m9.figshare.9746312.v2
title: Quantitative summary of abstracts from ialeUK conferences 1992-2017

description: Summary of abstracts submitted to UK chapter of the International Association for Landscape Ecology (ialeUK) annual conferences 1992-2017. Abstracts were characterised using pre-defined classes within eight categories. See Young et al. (In Review) for full details.
DOI: 10.6084/m9.figshare.9746267
title: Supplementary Material for: DNA Ploidy Analysis and Cell Block Immunohistochemistry in the Diagnosis of Malignant Effusions

description: <b><i>Background:</i></b> Effusion cytology is a major diagnostic tool in medicine and has both therapeutic and prognostic implications. One of the dilemmas encountered is the differentiation between atypical cells and reactive mesothelial cells. The use of ancillary tools can reduce this grey zone and help to achieve a definitive diagnosis. <b><i>Objectives:</i></b> The main objective of this study was to evaluate the role of flow cytometry (FCM) and cell block with immunohistochemistry (IHC), along with the clinicoradiological investigations, to achieve a final diagnosis in effusion cytology to the maximum extent possible. <b><i>Method:</i></b> A prospective study was conducted. Effusion fluids, showing adequate amount and cellularity, were processed for conventional cytology, ploidy analysis by FCM, and cell block analysis, followed by IHC wherever required. Conventional cytological analysis was done by 2 independent pathologists, to look for interobserver variation, if any. The final result was achieved on the basis of integration of the results of the aforementioned studies, cytological details, clinicoradiological information, tissue biopsy findings, and follow-up. <b><i>Result:</i></b> A total of 90 samples were analyzed. On cytological examination, observer I categorized 60% samples as benign and 18.8% (<i>n</i> = 17) as malignant versus 58% categorized as benign and 23.3% (<i>n</i> = 21) as malignant by observer II. Observer I reported 19 (21.1%) equivocal cases and observer II reported 16 (17.7%). When both pathologists were considered together, the number of equivocal cases increased to 20. Sensitivity and specificity of FCM were 96.67 and 100%, respectively, and 100% for the cell block. On combining all techniques, the equivocal cases were resolved and a total of 33 cases were reported as malignant. However, 3 cases could still not be categorized and were labeled inconclusive. <b><i>Conclusion:</i></b> Conventional cytology combined with cell block IHC and FCM has the potential to minimize the requirement of tissue biopsy for confirmation. If the first sample is used judiciously for all the techniques, this may reduce the requirement for a second sample and possibly also the time required for a definite diagnosis and the initiation of therapy.
DOI: 10.6084/m9.figshare.9746312.v1
title: Quantitative summary of abstracts from ialeUK conferences 1992-2017

description: Summary of abstracts submitted to UK chapter of the International Association for Landscape Ecology (ialeUK) annual conferences 1992-2017. Abstracts were characterised using pre-defined classes within eight categories. See Young et al. (In Review) for full details.
DOI: 10.6084/m9.figshare.9746225
title: research data.rar

description: research data
DOI: 10.6084/m9.figshare.9746225.v1
title: research data.rar

description: research data
DOI: 10.6084/m9.figshare.9746198
title: Supplementary Material for: Early Relative Change in Hepatic Function with Lenvatinib for Unresectable Hepatocellular Carcinoma

description: <b><i>Background/Aim:</i></b> Lenvatinib (LEN) has been developed for the treatment of unresectable hepatocellular carcinoma (u-HCC). We aimed to elucidate the relative change in hepatic reserve function early following LEN treatment in affected patients. <b><i>Materials/Methods:</i></b> From March 2018 to April 2019, 123 u-HCC patients (median age 71 years; male:female ratio 95:28; Child-Pugh score 5:6:7 = 65:50:8; modified albumin-bilirubin [mALBI] grade 1:2a:2b:3 = 44:28:50:1, Barcelona Clinic Liver Cancer stage A:B:C = 1:49:73) were enrolled. Relative changes in hepatic reserve function at 2 and 4 weeks after starting LEN were retrospectively evaluated. <b><i>Results:</i></b> The median survival was 11.3 months. The Child-Pugh score declined from the start to 4 weeks after commencing LEN (score 5:6:7:8:9:≥10 = 65:50:8:0:0:0 vs. 50:39:22:8:0:4, <i>p</i> &lt; 0.001). A comparison among ALBI scores at the start of LEN and those at 2 and 4 weeks revealed significant relative changes (–2.36 ± 0.45 to –2.20 ± 0.49 at 2 weeks, –2.15 ± 0.50 at 4 weeks, <i>p</i> &lt; 0.001, Bonferroni method), while there was no significant difference between those at 2 and 4 weeks (<i>p</i>= 0.210, Bonferroni method). Assessments of relative changes of ALBI score in patients divided by mALBI grade 1, 2a, and 2b or more showed a significant decline in score regardless of grade (–2.82 ± 0.17 to –2.53 ± 0.34, <i>p</i> &lt; 0.001; –2.46 ± 0.10 to –2.31 ± 0.33, <i>p</i> = 0.017; and –1.90 ± 0.26 to –1.75 ± 0.42, <i>p</i>= 0.009, respectively). <b><i>Conclusion:</i></b> Decline in hepatic function is common in the early stage (≤4 weeks, especially within 2 weeks) after introducing LEN. It is important to introduce molecular targeting agent drugs for u-HCC in patients with better hepatic function, who show transarterial catheter chemoembolization failure, as much as possible, along with consideration of the negative influence of LEN on the early response of hepatic function.
DOI: 10.6084/m9.figshare.9746198.v1
title: Supplementary Material for: Early Relative Change in Hepatic Function with Lenvatinib for Unresectable Hepatocellular Carcinoma

description: <b><i>Background/Aim:</i></b> Lenvatinib (LEN) has been developed for the treatment of unresectable hepatocellular carcinoma (u-HCC). We aimed to elucidate the relative change in hepatic reserve function early following LEN treatment in affected patients. <b><i>Materials/Methods:</i></b> From March 2018 to April 2019, 123 u-HCC patients (median age 71 years; male:female ratio 95:28; Child-Pugh score 5:6:7 = 65:50:8; modified albumin-bilirubin [mALBI] grade 1:2a:2b:3 = 44:28:50:1, Barcelona Clinic Liver Cancer stage A:B:C = 1:49:73) were enrolled. Relative changes in hepatic reserve function at 2 and 4 weeks after starting LEN were retrospectively evaluated. <b><i>Results:</i></b> The median survival was 11.3 months. The Child-Pugh score declined from the start to 4 weeks after commencing LEN (score 5:6:7:8:9:≥10 = 65:50:8:0:0:0 vs. 50:39:22:8:0:4, <i>p</i> &lt; 0.001). A comparison among ALBI scores at the start of LEN and those at 2 and 4 weeks revealed significant relative changes (–2.36 ± 0.45 to –2.20 ± 0.49 at 2 weeks, –2.15 ± 0.50 at 4 weeks, <i>p</i> &lt; 0.001, Bonferroni method), while there was no significant difference between those at 2 and 4 weeks (<i>p</i>= 0.210, Bonferroni method). Assessments of relative changes of ALBI score in patients divided by mALBI grade 1, 2a, and 2b or more showed a significant decline in score regardless of grade (–2.82 ± 0.17 to –2.53 ± 0.34, <i>p</i> &lt; 0.001; –2.46 ± 0.10 to –2.31 ± 0.33, <i>p</i> = 0.017; and –1.90 ± 0.26 to –1.75 ± 0.42, <i>p</i>= 0.009, respectively). <b><i>Conclusion:</i></b> Decline in hepatic function is common in the early stage (≤4 weeks, especially within 2 weeks) after introducing LEN. It is important to introduce molecular targeting agent drugs for u-HCC in patients with better hepatic function, who show transarterial catheter chemoembolization failure, as much as possible, along with consideration of the negative influence of LEN on the early response of hepatic function.
DOI: 10.6084/m9.figshare.9746162
title: The impact of neutrophil-lymphocyte ratio on risk reclassification of patients with advanced renal cell cancer to guide risk-directed therapy

description: <b>Background:</b> An elevated neutrophil-lymphocyte ratio (NLR) is associated with poor prognosis in advanced renal cell carcinoma (RCC). We examined whether the addition of NLR improves the risk reclassification of advanced RCC using current prognostic tools from the Memorial Sloan Kettering Cancer Center (MSKCC) and International Metastatic Renal Cell Carcinoma Database Consortium (IMDC). <b>Methods:</b> Using randomised data from the COMPARZ trial of first-line pazopanib vs. sunitinib in advanced RCC, we constructed multivariable models containing MSKCC and IMDC predictor variables with and without NLR. We evaluated model discrimination using the concordance index (C-index). We computed net reclassification improvement to quantify patient reclassification into low/intermediate/poor risk groups with the addition of NLR. <b>Results:</b> Of 1102 patients, NLR ≥ 5 (16%) was associated with shorter survival adjusting for MSKCC variables (adjusted HR 1.89, <i>p</i> &lt; .001). Adding NLR to MSKCC variables increased the C-index by 0.01. Among patients who died before 24 months (<i>N</i> = 415), adding NLR reclassified 8% and 2% to a higher and lower risk category, respectively. Among those alive at 24 months (<i>N</i> = 636), adding NLR reclassified 4% and 1% to a higher and lower risk category, respectively. This finding translates to a net benefit of eight additional patients who die within 24 months correctly identified as poor risk per 1000 patients tested. We obtained similar results when evaluating NLR with IMDC variables. <b>Conclusions:</b> NLR does not substantially improve risk reclassification over pre-existing prognostic tools. MSKCC and IMDC classifications remain the standard for guiding risk-directed therapy and trial stratification of patients with advanced RCC.