cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11309249.v2
title: Differential DNA methylation following chemotherapy for breast cancer is associated with lack of memory improvement at one year

description: The biological basis underlying cognitive dysfunction in women with early-stage breast cancer (BC) remains unclear, but could reflect gene expression changes that arise from the acquisition and long-term retention of soma-wide alterations in DNA methylation in response to chemotherapy. In this longitudinal study, we identified differences in peripheral methylation patterns present in women prior to treatment (T1) and 1 year after receiving chemotherapy (T4) and evaluated relationships among the differential methylation (DM) ratios with changes in cognitive function. A total of 58 paired (T1 and T4) blood specimens were evaluated. Methylation values were determined for DNA isolated from whole blood using a genome-wide array . Cognitive function was measured using the validated, computerized <i>CNS Vital Signs</i> platform. Relationships between methylation patterns and cognitive domain scores were compared using a stepwise linear regression analysis, with demographic variables as covariates. The symptom comparison analysis was restricted to 2,199 CpG positions showing significant methylation ratio changes between T1 and T4. The positions with DM were enriched for genes involved in the modulation of cytokine concentrations. Significant DM ratios were associated with memory domain (56 CpGs). Eight of the ten largest DM ratio changes associated with lack of memory improvement were localized to genes involved in either neural function (<i>ECE2, PPFIBP2</i>) or signalling processes (<i>USP6NL, RIPOR2, KLF5, UBE2V1, DGKA, RPS6KA1</i>). These results suggest that epigenetic changes acquired and retained for at least one year in non-tumour cells following chemotherapy may be associated with a lack of memory improvement following treatment in BC survivors.
DOI: 10.17028/rd.lboro.3969093.v1
title: New multiple target tracking strategy using domain knowledge and optimisation - supporting data (multiple target tracking scenario)

description: Related data for SMC paper 'New Multiple Target Tracking Strategy Using Domain Knowledge and Optimisation'. This data related to the multiple target tracking scenario.
DOI: 10.6084/m9.figshare.8163692
title: MOESM3 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 3. Gene distribution of LCT-EC001 in the GO database.
DOI: 10.6084/m9.figshare.8163554.v1
title: Additional file 1: of Endometrioid endometrial cancer â recurringâ as high-grade serous adenocarcinoma in the inguinal lymph nodes in a patient with germline MLH1 mutated Lynch syndrome: consequence or coincidence?

description: The raw data of sequencing results of primary tumors. (XLSX 1198 kb)
DOI: 10.6084/m9.figshare.8163704
title: MOESM5 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 5. Gene distribution of LCT-EC001 in the KEGG database.
DOI: 10.6084/m9.figshare.8163716.v1
title: MOESM7 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 7. Location and database source of 68 antibiotic resistance determinants in LCT-EC001.
DOI: 10.6084/m9.figshare.8163680.v1
title: MOESM1 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 1. Gene annotation of LCT-EC001.
DOI: 10.6084/m9.figshare.6590906
title: Exploration of DNA methylation markers for diagnosis and prognosis of patients with endometrial cancer

description: The accurate diagnosis of endometrial cancer (EC) holds great promise for improving its treatment choice and prognosis prediction. This work aimed to identify diagnostic biomarkers for differentiating EC tumors from tumors in other tissues, as well as prognostic signatures for predicting survival in EC patients. We identified 48 tissue-specific markers using a cohort of genome-wide methylation data from three common gynecological tumors and their corresponding normal tissues. A diagnostic classifier was constructed based on these 48 CpG markers that could predict cancerous versus normal tissue with an overall correct rate of 98.3% in the entire repository. Fifteen CpG markers associated with the overall survival (OS) and development of EC were also identified based on the methylation patterns of the EC samples. A prognostic model that aggregated these prognostic CpG markers was established and shown to have a higher discriminative ability to distinguish EC patients with an elevated risk of mortality than the FIGO staging system and several other clinical prognostic variables. This study presents the utility of DNA methylation in identifying biomarkers for the diagnosis and prognosis of EC and will help improve our understanding of the underlying mechanisms involved in the development of EC.
DOI: 10.6084/m9.figshare.8163563
title: Additional file 2: of Endometrioid endometrial cancer â recurringâ as high-grade serous adenocarcinoma in the inguinal lymph nodes in a patient with germline MLH1 mutated Lynch syndrome: consequence or coincidence?

description: The raw data of sequencing results of metastatic tumors. (XLSX 1156 kb)
DOI: 10.6084/m9.figshare.6590906.v1
title: Exploration of DNA methylation markers for diagnosis and prognosis of patients with endometrial cancer

description: The accurate diagnosis of endometrial cancer (EC) holds great promise for improving its treatment choice and prognosis prediction. This work aimed to identify diagnostic biomarkers for differentiating EC tumors from tumors in other tissues, as well as prognostic signatures for predicting survival in EC patients. We identified 48 tissue-specific markers using a cohort of genome-wide methylation data from three common gynecological tumors and their corresponding normal tissues. A diagnostic classifier was constructed based on these 48 CpG markers that could predict cancerous versus normal tissue with an overall correct rate of 98.3% in the entire repository. Fifteen CpG markers associated with the overall survival (OS) and development of EC were also identified based on the methylation patterns of the EC samples. A prognostic model that aggregated these prognostic CpG markers was established and shown to have a higher discriminative ability to distinguish EC patients with an elevated risk of mortality than the FIGO staging system and several other clinical prognostic variables. This study presents the utility of DNA methylation in identifying biomarkers for the diagnosis and prognosis of EC and will help improve our understanding of the underlying mechanisms involved in the development of EC.
DOI: 10.6084/m9.figshare.8163554
title: Additional file 1: of Endometrioid endometrial cancer â recurringâ as high-grade serous adenocarcinoma in the inguinal lymph nodes in a patient with germline MLH1 mutated Lynch syndrome: consequence or coincidence?

description: The raw data of sequencing results of primary tumors. (XLSX 1198 kb)
DOI: 10.6084/m9.figshare.8163692.v1
title: MOESM3 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 3. Gene distribution of LCT-EC001 in the GO database.
DOI: 10.6084/m9.figshare.8163698
title: MOESM4 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 4. Gene distribution of LCT-EC001 in the COG database.
DOI: 10.6084/m9.figshare.25231676.v1
title: Supplementary Material for: Maxillary Ameloblastoma with Local Recurrence, Orbital Invasion, and Systemic Metastases: A case report and review of the literature.

description: Introduction: Maxillary ameloblastoma is a rare, slow growing odontogenic tumor that can recur after surgical excision, be locally aggressive and rarely develop systemic metastases. We describe the course and management of a patient with recurrent maxillary ameloblastoma with orbital invasion and systemic metastases, the fourth case of its kind to be described in the literature. 
Case presentation: A 50-year-old female presented with left hyperglobus. A diagnosis of maxillary ameloblastoma was made based on biopsy and neuroimaging with MRI and CT. Surgical management included partial maxillectomy with orbital floor reconstruction given orbital invasion. Three years later, left hyperglobus recurred and the patient was found to have orbital recurrence and lung metastases on PET imaging. The lung and orbital lesions have responded well to chemoradiation therapy without surgical intervention.
Conclusion: Maxillary ameloblastoma is a rare tumor that typically arises from odontogenic tissues. Though considered benign, they can recur and in the case of our patient, metastasize. Complete surgical excision with wide surgical margins is associated with a shorter average time to recurrence and lower incidence of metastasis. Cases of metastasis are managed with chemotherapy with or without adjuvant radiotherapy. Precision medicine may play a role in managing this entity in the future given the discovery of differing profiles of maxillary ameloblastoma compared to mandibular. Ophthalmologists should be aware of this tumor, as it can invade the orbit, resulting in significant ocular morbidity and mortality.
DOI: 10.6084/m9.figshare.8163710
title: MOESM6 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 6. Gene length of 68 antibiotic resistance determinants in LCT-EC001.
DOI: 10.6084/m9.figshare.8163686.v1
title: MOESM2 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 2. Repeat sequences of LCT-EC001.
DOI: 10.6084/m9.figshare.8163836
title: Additional file 3: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S2. Information of peptides identified from the leaves and roots of stylo. (XLSX 1836â kb)
DOI: 10.6084/m9.figshare.8163836.v1
title: Additional file 3: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S2. Information of peptides identified from the leaves and roots of stylo. (XLSX 1836â kb)
DOI: 10.6084/m9.figshare.8163842
title: Additional file 4: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S3. Information of proteins identified from the leaves and roots of stylo. (XLSX 789â kb)
DOI: 10.6084/m9.figshare.8163698.v1
title: MOESM4 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 4. Gene distribution of LCT-EC001 in the COG database.
DOI: 10.6084/m9.figshare.8163845
title: Additional file 5: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S4. Differentially expressed proteins identified from the leaves and roots of stylo. (XLSX 1133â kb)
DOI: 10.6084/m9.figshare.6590954.v1
title: Linc-smad7 promotes myoblast differentiation and muscle regeneration via sponging miR-125b

description: Long noncoding RNAs (lncRNAs) are involved in the regulation of skeletal muscle development. In the present study, differentially expressed lncRNAs were identified from RNA-seq data derived from myoblasts and myotubes. We conducted studies to elucidate the function and molecular mechanism of action of Linc-smad7 during skeletal muscle development. Our findings show that Linc-smad7 is upregulated during the early phase of myoblasts differentiation. In <i>in vitro</i> studies, we showed that overexpression of Linc-smad7 promoted the arrest of myoblasts in G1 phase, inhibited DNA replication, and induced myoblast differentiation. Our <i>in vivo</i> studies suggest that Linc-smad7 stimulates skeletal muscle regeneration in cardiotoxin-induced muscle injury. Mechanistically, Linc-smad7 overexpression increased smad7 and IGF2 protein levels. On the contrary, overexpression of miR-125b reduced smad7 and IGF2 protein levels. Results of RNA immunoprecipitation analysis and biotin-labeled miR-125b capture suggest that Linc-smad7 could act as a competing endogenous RNA (ceRNA) for miRNA-125b. Taken together, our findings suggest that the novel noncoding regulator Linc-smad7 regulates skeletal muscle development.
DOI: 10.6084/m9.figshare.8163704.v1
title: MOESM5 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 5. Gene distribution of LCT-EC001 in the KEGG database.
DOI: 10.6084/m9.figshare.8163842.v1
title: Additional file 4: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S3. Information of proteins identified from the leaves and roots of stylo. (XLSX 789â kb)
DOI: 10.6084/m9.figshare.8163716
title: MOESM7 of Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes

description: Additional file 7. Location and database source of 68 antibiotic resistance determinants in LCT-EC001.
DOI: 10.6084/m9.figshare.20221934.v1
title: Additional file 1 of Refractive error characteristics and influence on ocular parameters in patients with unilateral congenital ptosis

description: Additional file 1.
DOI: 10.6084/m9.figshare.6590954
title: Linc-smad7 promotes myoblast differentiation and muscle regeneration via sponging miR-125b

description: Long noncoding RNAs (lncRNAs) are involved in the regulation of skeletal muscle development. In the present study, differentially expressed lncRNAs were identified from RNA-seq data derived from myoblasts and myotubes. We conducted studies to elucidate the function and molecular mechanism of action of Linc-smad7 during skeletal muscle development. Our findings show that Linc-smad7 is upregulated during the early phase of myoblasts differentiation. In <i>in vitro</i> studies, we showed that overexpression of Linc-smad7 promoted the arrest of myoblasts in G1 phase, inhibited DNA replication, and induced myoblast differentiation. Our <i>in vivo</i> studies suggest that Linc-smad7 stimulates skeletal muscle regeneration in cardiotoxin-induced muscle injury. Mechanistically, Linc-smad7 overexpression increased smad7 and IGF2 protein levels. On the contrary, overexpression of miR-125b reduced smad7 and IGF2 protein levels. Results of RNA immunoprecipitation analysis and biotin-labeled miR-125b capture suggest that Linc-smad7 could act as a competing endogenous RNA (ceRNA) for miRNA-125b. Taken together, our findings suggest that the novel noncoding regulator Linc-smad7 regulates skeletal muscle development.
DOI: 10.6084/m9.figshare.8163830.v1
title: Additional file 2: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S1. Number of peptides, proteins and DEPs identified from the samples. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8163830
title: Additional file 2: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S1. Number of peptides, proteins and DEPs identified from the samples. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8163851
title: Additional file 6: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S5. List of primers used in the study for gene expression analysis. (XLSX 9â kb)
DOI: 10.6084/m9.figshare.8163866
title: Additional file 3: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Table S1. Statistics and designation of L1 subfamilies and families. “Ory” stands for O. palustris and “Sig” stands for S. hispidus. “Peak” indicates the peak of the L1 divergence distribution of the subfamily or family identified by kernel smoothing. Copy numbers are normalized as copies per three Gbp of MiSeq sequence used for the search, which approximates the copy number per haploid genome. Designation of families is only shown after the first subfamily that belongs to it; all subsequent subfamilies belong to this family until the demarcation of the next family. Characters in family names: “S” represents S. hispidus-specific, “OS” for shared by O. palustris and S. hispidus and “OSP” for shared by O. palustris, S. hispidus and P. maniculatus. Numbers in the family names reflect their divergence among the family group with “1” being the youngest. Copy numbers of families are rounded sums of subfamily copy numbers per three Gbp of sequences and, thus, are occasionally off by one. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8163872.v1
title: Additional file 4: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Table S2. Statistics and designation of B1 subfamilies and families. “Ory” stands for O. palustris and “Sig” stands for S. hispidus. “Peak” indicates the peak of the B1 divergence distribution of the subfamily or family identified by kernel smoothing. Copy numbers are normalized as copies per three Gbp of MiSeq sequence used for the search. Designation of families is only shown after the first subfamily that belongs to it; all subsequent subfamilies belong to this family until the demarcation of the next family. Characters in family names: “OS” represents families shared by O. palustris and S. hispidus and “OSP” for families shared by O. palustris, S. hispidus and P. maniculatus. Numbers in the family names reflect their divergence within the family group with “1” being the youngest. Copy numbers of families are rounded sums of subfamily copy numbers per three Gbp of sequences.and S. hispidus genome. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8163878.v1
title: Additional file 5: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Alignment of L1 subfamily sequences used in the tables and figures. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (FA 15 kb)
DOI: 10.6084/m9.figshare.8163845.v1
title: Additional file 5: of Physiological responses and proteomic changes reveal insights into Stylosanthes response to manganese toxicity

description: Table S4. Differentially expressed proteins identified from the leaves and roots of stylo. (XLSX 1133â kb)
DOI: 10.6084/m9.figshare.20221934
title: Additional file 1 of Refractive error characteristics and influence on ocular parameters in patients with unilateral congenital ptosis

description: Additional file 1.
DOI: 10.6084/m9.figshare.8164001
title: Additional file 10: of Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.)

description: The primer sequences were used in the present study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8163866.v1
title: Additional file 3: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Table S1. Statistics and designation of L1 subfamilies and families. “Ory” stands for O. palustris and “Sig” stands for S. hispidus. “Peak” indicates the peak of the L1 divergence distribution of the subfamily or family identified by kernel smoothing. Copy numbers are normalized as copies per three Gbp of MiSeq sequence used for the search, which approximates the copy number per haploid genome. Designation of families is only shown after the first subfamily that belongs to it; all subsequent subfamilies belong to this family until the demarcation of the next family. Characters in family names: “S” represents S. hispidus-specific, “OS” for shared by O. palustris and S. hispidus and “OSP” for shared by O. palustris, S. hispidus and P. maniculatus. Numbers in the family names reflect their divergence among the family group with “1” being the youngest. Copy numbers of families are rounded sums of subfamily copy numbers per three Gbp of sequences and, thus, are occasionally off by one. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8163872
title: Additional file 4: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Table S2. Statistics and designation of B1 subfamilies and families. “Ory” stands for O. palustris and “Sig” stands for S. hispidus. “Peak” indicates the peak of the B1 divergence distribution of the subfamily or family identified by kernel smoothing. Copy numbers are normalized as copies per three Gbp of MiSeq sequence used for the search. Designation of families is only shown after the first subfamily that belongs to it; all subsequent subfamilies belong to this family until the demarcation of the next family. Characters in family names: “OS” represents families shared by O. palustris and S. hispidus and “OSP” for families shared by O. palustris, S. hispidus and P. maniculatus. Numbers in the family names reflect their divergence within the family group with “1” being the youngest. Copy numbers of families are rounded sums of subfamily copy numbers per three Gbp of sequences.and S. hispidus genome. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8163890.v1
title: Additional file 7: of Tracing the history of LINE and SINE extinction in sigmodontine rodents

description: Alignment of L1 subfamily sequences based on RepeatScout-generated seeds and S. hispidus genome. CpG sites with evidence of methylation-induced mutations were removed from the alignment. (FA 21 kb)
DOI: 10.6084/m9.figshare.8163563.v1
title: Additional file 2: of Endometrioid endometrial cancer â recurringâ as high-grade serous adenocarcinoma in the inguinal lymph nodes in a patient with germline MLH1 mutated Lynch syndrome: consequence or coincidence?

description: The raw data of sequencing results of metastatic tumors. (XLSX 1156 kb)
DOI: 10.6084/m9.figshare.25202315
title: codeberta_result on character count &gt;= 26, line count &gt;= 2

description: codeberta_result on character count &gt;= 26, line count &gt;= 2
DOI: 10.6084/m9.figshare.25202315.v1
title: codeberta_result on character count &gt;= 26, line count &gt;= 2

description: codeberta_result on character count &gt;= 26, line count &gt;= 2
DOI: 10.6084/m9.figshare.8164100
title: Additional file 10: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The top 20 enriched KEGG pathways of differentially expressed mRNAs from the three comparison groups. (XLS 31 kb)
DOI: 10.6084/m9.figshare.8164139
title: Additional file 6: of lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers

description: The top 20 enriched pathways in the TC_F vs. TC_N (A), SCC_YF vs. SCC_YN (B) and SCC_OF vs. SCC_ ON (C) comparisons (cis). (XLSX 12 kb)