cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25402/bmm.14785212.v1
title: Supplementary Table 2 Differentially expressed lncRNAs identified by RNA-seq

description: Aim: To explore the
 expression profiles of lncRNAs and identify novel lncRNAs as biomarkers for
 early diagnosis and therapy of hepatocellular carcinoma (HCC). Materials
 & methods: Expression profiles of lncRNAs and mRNAs in five paired HCC
 and adjacent normal tissues were obtained by RNA-seq. Eight lncRNAs,
 including two novel liver-specific lncRNAs (NONHSAT059247.2 and
 NONHSAT013897.2), were validated in another 74 pairs of HCC and adjacent
 normal tissues by qRT-PCR. Results: The results of qRT-PCR showed that
 NONHSAT252133.1, NONHSAT112116.2, and NONHSAT242657.1 were significantly
 upregulated in HCC tissues, whereas NONHSAT169790.1, NONHSAT059247.2, and
 NONHSAT013897.2 were significantly downregulated. Two liver-specific lncRNAs
 demonstrated excellent diagnostic performance: NONHSAT059247.2 (AUC=0.941,
 95% CI: 0.902-0.979, P&lt;0.0001), NONHSAT013897.2 (AUC=0.944, 95% CI:
 0.906-0.983, P&lt;0.0001).
 
 




Conclusion: The liver-specific lncRNAs
NONHSAT059247.2 and NONHSAT013897.2, may provide new biomarkers for the future
study on diagnosis, therapy, and mechanisms of HCC.
DOI: 10.6084/m9.figshare.6396644.v1
title: Global expression profiling and pathway analysis of mouse mammary tumor reveals strain and stage specific dysregulated pathways in breast cancer progression

description: It is believed that the alteration of tissue microenvironment would affect cancer initiation and progression. However, little is known in terms of the underlying molecular mechanisms that would affect the initiation and progression of breast cancer. In the present study, we use two murine mammary tumor models with different speeds of tumor initiation and progression for whole genome expression profiling to reveal the involved genes and signaling pathways. The pathways regulating PI3K-Akt signaling and Ras signaling were activated in Fvb mice and promoted tumor progression. Contrastingly, the pathways regulating apoptosis and cellular senescence were activated in Fvb.B6 mice and suppressed tumor progression. We identified distinct patterns of oncogenic pathways activation at different stages of breast cancer, and uncovered five oncogenic pathways that were activated in both human and mouse breast cancers. The genes and pathways discovered in our study would be useful information for other researchers and drug development.
DOI: 10.25549/usctheses-c3-599972
title: etd-RuizSusana-3651~129
DOI: 10.25402/bmm.14785215.v1
title: Supplementary Table 4 The candidate differentially expressed lncRNAs for qRT-PCR

description: Aim: To explore the
 expression profiles of lncRNAs and identify novel lncRNAs as biomarkers for
 early diagnosis and therapy of hepatocellular carcinoma (HCC). Materials
 & methods: Expression profiles of lncRNAs and mRNAs in five paired HCC
 and adjacent normal tissues were obtained by RNA-seq. Eight lncRNAs,
 including two novel liver-specific lncRNAs (NONHSAT059247.2 and
 NONHSAT013897.2), were validated in another 74 pairs of HCC and adjacent
 normal tissues by qRT-PCR. Results: The results of qRT-PCR showed that
 NONHSAT252133.1, NONHSAT112116.2, and NONHSAT242657.1 were significantly
 upregulated in HCC tissues, whereas NONHSAT169790.1, NONHSAT059247.2, and
 NONHSAT013897.2 were significantly downregulated. Two liver-specific lncRNAs
 demonstrated excellent diagnostic performance: NONHSAT059247.2 (AUC=0.941,
 95% CI: 0.902-0.979, P&lt;0.0001), NONHSAT013897.2 (AUC=0.944, 95% CI:
 0.906-0.983, P&lt;0.0001).
 
 




Conclusion: The liver-specific lncRNAs
NONHSAT059247.2 and NONHSAT013897.2, may provide new biomarkers for the future
study on diagnosis, therapy, and mechanisms of HCC.
DOI: 10.25549/usctheses-c3-599952
title: etd-RuizSusana-3651~109
DOI: 10.25549/usctheses-c3-577217
title: etd-CardenasMi-3510_109
DOI: 10.25549/usctheses-c3-600014
title: etd-RuizSusana-3651~171
DOI: 10.25549/usctheses-c3-599848
title: etd-RuizSusana-3651~005
DOI: 10.25549/usctheses-c3-599892
title: etd-RuizSusana-3651~049
DOI: 10.25549/usctheses-c3-599959
title: etd-RuizSusana-3651~116
DOI: 10.25549/usctheses-c3-589761
title: etd-ChiuCathle-3452~093
DOI: 10.25549/usctheses-c3-601301
title: etd-GaddisMala-3657~82
DOI: 10.6084/m9.figshare.12689270
title: The genome sequences of Cerasus humilis polished with Illumina short reads

description: This genome was assembled using Falcon and then chromosome-level assembled with Hi-C data. After assembly, NextPolish was used to polish the genome.<br>
DOI: 10.25549/usctheses-c3-599905
title: etd-RuizSusana-3651~062
DOI: 10.25549/usctheses-c3-589734
title: etd-ChiuCathle-3452~066
DOI: 10.25549/usctheses-c3-577155
title: etd-CardenasMi-3510_047
DOI: 10.25549/usctheses-c3-599903
title: etd-RuizSusana-3651~060
DOI: 10.25549/usctheses-c3-599995
title: etd-RuizSusana-3651~152
DOI: 10.25549/usctheses-c3-589672
title: etd-ChiuCathle-3452~004
DOI: 10.25549/usctheses-c3-599849
title: etd-RuizSusana-3651~006
DOI: 10.25549/usctheses-c3-589701
title: etd-ChiuCathle-3452~033
DOI: 10.25549/usctheses-c3-599920
title: etd-RuizSusana-3651~077
DOI: 10.25549/usctheses-c3-577139
title: etd-CardenasMi-3510_031
DOI: 10.25549/usctheses-c3-599933
title: etd-RuizSusana-3651~090
DOI: 10.25549/usctheses-c3-577115
title: etd-CardenasMi-3510_007
DOI: 10.25549/usctheses-c3-577224
title: etd-CardenasMi-3510_116
DOI: 10.25549/usctheses-c3-589730
title: etd-ChiuCathle-3452~062
DOI: 10.25549/usctheses-c3-601276
title: etd-GaddisMala-3657~57
DOI: 10.25549/usctheses-c3-601245
title: etd-GaddisMala-3657~26
DOI: 10.25549/usctheses-c3-589728
title: etd-ChiuCathle-3452~060
DOI: 10.25549/usctheses-c3-599968
title: etd-RuizSusana-3651~125
DOI: 10.25549/usctheses-c3-589766
title: etd-ChiuCathle-3452~098
DOI: 10.25549/usctheses-c3-577202
title: etd-CardenasMi-3510_094
DOI: 10.25549/usctheses-c3-599964
title: etd-RuizSusana-3651~121
DOI: 10.25549/usctheses-c3-589674
title: etd-ChiuCathle-3452~006
DOI: 10.25549/usctheses-c3-589711
title: etd-ChiuCathle-3452~043
DOI: 10.25549/usctheses-c3-577210
title: etd-CardenasMi-3510_102
DOI: 10.25549/usctheses-c3-577132
title: etd-CardenasMi-3510_024
DOI: 10.25549/usctheses-c3-601234
title: etd-GaddisMala-3657~15
DOI: 10.25549/usctheses-c3-577121
title: etd-CardenasMi-3510_013
DOI: 10.25549/usctheses-c3-577131
title: etd-CardenasMi-3510_023
DOI: 10.25549/usctheses-c3-589682
title: etd-ChiuCathle-3452~014
DOI: 10.25549/usctheses-c3-577118
title: etd-CardenasMi-3510_010
DOI: 10.25549/usctheses-c3-577145
title: etd-CardenasMi-3510_037
DOI: 10.25549/usctheses-c3-577143
title: etd-CardenasMi-3510_035
DOI: 10.6084/m9.figshare.23699404
title: Integrative analysis of Mendelian randomization and gene expression profiles reveals a null causal relationship between adiponectin and diabetic retinopathy

description: Observational studies have been conducted to investigate the correlation between adiponectin and diabetic retinopathy (DR), but no consistent relationship has been established. In this study, we employed an integrative analysis that combined Mendelian randomization (MR) and bioinformatics analyses to comprehensively explore the association between DR and adiponectin, aiming to provide a unified answer of their relationship. Using the inverse-variance weighted (IVW) method, the odd ratio (OR) of developing DR per 1 mg/dL increment in genetically predicted log-transformed adiponectin concentration was estimated to be 0.949 (<i>P</i> = 0.557). Other robust MR methods produced consistent results, confirming the absence of a causal effect of adiponectin on DR. Additionally, the expression levels of the six adiponectin-related genes showed no significant differences among normal controls, individuals with diabetes but without DR, and those with DR Furthermore, the biological pathways enriched by these genes were not strongly relevant to DR. At both the individual gene and pathway levels, there were no overlaps between the adiponectin-related genes and the differentially expressed genes, indicating a lack of association between adiponectin and DR based on gene expression profiles. In summary, the integrative analysis, which combined MR and bioinformatics data mining, yielded compelling evidence supporting the notion that adiponectin is not a risk factor for DR.
DOI: 10.6084/m9.figshare.23699404.v1
title: Integrative analysis of Mendelian randomization and gene expression profiles reveals a null causal relationship between adiponectin and diabetic retinopathy

description: Observational studies have been conducted to investigate the correlation between adiponectin and diabetic retinopathy (DR), but no consistent relationship has been established. In this study, we employed an integrative analysis that combined Mendelian randomization (MR) and bioinformatics analyses to comprehensively explore the association between DR and adiponectin, aiming to provide a unified answer of their relationship. Using the inverse-variance weighted (IVW) method, the odd ratio (OR) of developing DR per 1 mg/dL increment in genetically predicted log-transformed adiponectin concentration was estimated to be 0.949 (<i>P</i> = 0.557). Other robust MR methods produced consistent results, confirming the absence of a causal effect of adiponectin on DR. Additionally, the expression levels of the six adiponectin-related genes showed no significant differences among normal controls, individuals with diabetes but without DR, and those with DR Furthermore, the biological pathways enriched by these genes were not strongly relevant to DR. At both the individual gene and pathway levels, there were no overlaps between the adiponectin-related genes and the differentially expressed genes, indicating a lack of association between adiponectin and DR based on gene expression profiles. In summary, the integrative analysis, which combined MR and bioinformatics data mining, yielded compelling evidence supporting the notion that adiponectin is not a risk factor for DR.
DOI: 10.25549/usctheses-c3-589689
title: etd-ChiuCathle-3452~021
DOI: 10.25549/usctheses-c3-577195
title: etd-CardenasMi-3510_087
DOI: 10.25549/usctheses-c3-577152
title: etd-CardenasMi-3510_044
DOI: 10.25549/usctheses-c3-577146
title: etd-CardenasMi-3510_038
DOI: 10.25549/usctheses-c3-601305
title: etd-GaddisMala-3657~86
DOI: 10.25549/usctheses-c3-601313
title: etd-GaddisMala-3657~94
DOI: 10.25549/usctheses-c3-589726
title: etd-ChiuCathle-3452~058
DOI: 10.25549/usctheses-c3-577151
title: etd-CardenasMi-3510_043
DOI: 10.25549/usctheses-c3-599969
title: etd-RuizSusana-3651~126
DOI: 10.25549/usctheses-c3-624516
title: etd-DeeSylviaG-3790~022
DOI: 10.25549/usctheses-c3-621843
title: etd-PrasadAdit-3772~38
DOI: 10.25549/usctheses-c3-624639
title: etd-DeeSylviaG-3790~145
DOI: 10.25549/usctheses-c3-624569
title: etd-DeeSylviaG-3790~075
DOI: 10.6084/m9.figshare.23699498
title: The prevalence of burnout among pulmonologists or respiratory therapists pre- and post-COVID-19: a systematic review and meta-analysis

description: The coronavirus disease-19 (COVID-19) increased the already heavy workload in the pulmonary and respiratory departments, which therefore possibly increased the prevalence of burnout among pulmonologists or respiratory therapists. We aimed to compare the differences in burnout among pulmonologists or respiratory therapists pre- and post-COVID-19 by doing a systematic review with meta-analysis. We searched pulmonologist, or pulmonary, or respiratory, and burnout up to 29 January 2023 in six databases. We included studies investigating pulmonologists or respiratory therapists and reporting the prevalence of burnout among them. The risk of bias was assessed by a tool for prevalence studies. The overall prevalence of burnout was pooled. A total of 2859 records were identified and 16 studies were included in the final analysis. The included studies reported 3610 responding individuals and 2336 burnouts. The pooled prevalence of burnout was 61.7% (95% confidence interval (CI), 48.6–73.2%; <i>I</i><sup>2</sup> = 96.3%). The pooled prevalence of burnout during COVID-19 was significantly higher than it was prior to the outbreak (68.4% vs. 41.6%, <i>p</i> = .01). The result of the meta-regression revealed that COVID-19 coverage was significantly associated with the prevalence of burnout (<i>p</i> = .04). Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19. Therefore, interventions were needed to reduce burnout in this specialty.KEY MESSASGESThe coronavirus disease-19 increased the already heavy workload in the pulmonary and respiratory departments.Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19. The coronavirus disease-19 increased the already heavy workload in the pulmonary and respiratory departments. Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19.
DOI: 10.6084/m9.figshare.23699498.v1
title: The prevalence of burnout among pulmonologists or respiratory therapists pre- and post-COVID-19: a systematic review and meta-analysis

description: The coronavirus disease-19 (COVID-19) increased the already heavy workload in the pulmonary and respiratory departments, which therefore possibly increased the prevalence of burnout among pulmonologists or respiratory therapists. We aimed to compare the differences in burnout among pulmonologists or respiratory therapists pre- and post-COVID-19 by doing a systematic review with meta-analysis. We searched pulmonologist, or pulmonary, or respiratory, and burnout up to 29 January 2023 in six databases. We included studies investigating pulmonologists or respiratory therapists and reporting the prevalence of burnout among them. The risk of bias was assessed by a tool for prevalence studies. The overall prevalence of burnout was pooled. A total of 2859 records were identified and 16 studies were included in the final analysis. The included studies reported 3610 responding individuals and 2336 burnouts. The pooled prevalence of burnout was 61.7% (95% confidence interval (CI), 48.6–73.2%; <i>I</i><sup>2</sup> = 96.3%). The pooled prevalence of burnout during COVID-19 was significantly higher than it was prior to the outbreak (68.4% vs. 41.6%, <i>p</i> = .01). The result of the meta-regression revealed that COVID-19 coverage was significantly associated with the prevalence of burnout (<i>p</i> = .04). Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19. Therefore, interventions were needed to reduce burnout in this specialty.KEY MESSASGESThe coronavirus disease-19 increased the already heavy workload in the pulmonary and respiratory departments.Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19. The coronavirus disease-19 increased the already heavy workload in the pulmonary and respiratory departments. Burnout was widely prevalent among pulmonologists or respiratory therapists and increasingly perceived during COVID-19.
DOI: 10.25549/usctheses-c3-601254
title: etd-GaddisMala-3657~35
DOI: 10.25549/usctheses-c3-599856
title: etd-RuizSusana-3651~013
DOI: 10.25549/usctheses-c3-599862
title: etd-RuizSusana-3651~019
DOI: 10.25549/usctheses-c3-577200
title: etd-CardenasMi-3510_092
DOI: 10.25549/usctheses-c3-599975
title: etd-RuizSusana-3651~132
DOI: 10.25549/usctheses-c3-599887
title: etd-RuizSusana-3651~044
DOI: 10.25549/usctheses-c3-577220
title: etd-CardenasMi-3510_112
DOI: 10.6084/m9.figshare.24223808
title: Additional file 1 of Integrating plasma proteomes with genome-wide association data for causal protein identification in multiple myeloma

description: Additional file 1: Table S1. Detailed information for data source of confounders used in the current study. Table S2. Genetic variants for Mendelian randomization analysis of the associations between causal risk proteins and multiple myeloma. Table S3. Mendelian randomization results of causal risk proteins on multiple myeloma. Table S4. Information of genetic variants for MR-BMA analysis. Table S5. Test of influential genetic variants in MR-BMA. Table S6. Test of outlying genetic variants in MR-BMA. Table S7. Top 10 models ranked by the model posterior probability after model diagnostics. Table S8. Meta-analysis for the effect of genetically predicted causal risk proteins on the risk of MM from FinnGen and UK Biobank. Table S9. Genetic variants for Mendelian randomisation analysis of the associations between multiple myeloma and significant proteins. Table S10. Mendelian randomization results of multiple myeloma on significant proteins. Table S11. Mendelian randomization of blood proteins on multiple myeloma using only variants in the cis-region of the gene encoding the blood proteins.
DOI: 10.6084/m9.figshare.24223808.v1
title: Additional file 1 of Integrating plasma proteomes with genome-wide association data for causal protein identification in multiple myeloma

description: Additional file 1: Table S1. Detailed information for data source of confounders used in the current study. Table S2. Genetic variants for Mendelian randomization analysis of the associations between causal risk proteins and multiple myeloma. Table S3. Mendelian randomization results of causal risk proteins on multiple myeloma. Table S4. Information of genetic variants for MR-BMA analysis. Table S5. Test of influential genetic variants in MR-BMA. Table S6. Test of outlying genetic variants in MR-BMA. Table S7. Top 10 models ranked by the model posterior probability after model diagnostics. Table S8. Meta-analysis for the effect of genetically predicted causal risk proteins on the risk of MM from FinnGen and UK Biobank. Table S9. Genetic variants for Mendelian randomisation analysis of the associations between multiple myeloma and significant proteins. Table S10. Mendelian randomization results of multiple myeloma on significant proteins. Table S11. Mendelian randomization of blood proteins on multiple myeloma using only variants in the cis-region of the gene encoding the blood proteins.
DOI: 10.25549/usctheses-c3-599949
title: etd-RuizSusana-3651~106
DOI: 10.25549/usctheses-c3-599996
title: etd-RuizSusana-3651~153
DOI: 10.25549/usctheses-c3-599897
title: etd-RuizSusana-3651~054
DOI: 10.25549/usctheses-c3-600009
title: etd-RuizSusana-3651~166
DOI: 10.25549/usctheses-c3-589716
title: etd-ChiuCathle-3452~048
DOI: 10.6084/m9.figshare.20552408
title: Additional file 1 of A novel signature to predict thyroid cancer prognosis and immune landscape using immune-related LncRNA pairs

description: Additional file 1: Table S1. A total of 1148 immune-related lncRNAs were validated by co-expression analysis (submitted as a separate EXCEL file).
DOI: 10.25549/usctheses-c3-589763
title: etd-ChiuCathle-3452~095
DOI: 10.25549/usctheses-c3-599938
title: etd-RuizSusana-3651~095
DOI: 10.25549/usctheses-c3-600005
title: etd-RuizSusana-3651~162
DOI: 10.25549/usctheses-c3-599929
title: etd-RuizSusana-3651~086
DOI: 10.25549/usctheses-c3-599955
title: etd-RuizSusana-3651~112
DOI: 10.25549/usctheses-c3-599958
title: etd-RuizSusana-3651~115
DOI: 10.6084/m9.figshare.20552408.v1
title: Additional file 1 of A novel signature to predict thyroid cancer prognosis and immune landscape using immune-related LncRNA pairs

description: Additional file 1: Table S1. A total of 1148 immune-related lncRNAs were validated by co-expression analysis (submitted as a separate EXCEL file).
DOI: 10.25549/usctheses-c3-601238
title: etd-GaddisMala-3657~19
DOI: 10.25919/5faj-mh70
title: Parkes observations for project P630 semester 2010APRS_03

description: We propose to carry out the most ambitious and comprehensive all-sky survey for pulsars and transient sources to date. Using the 20cm multibeam and a new digital filterbank array this survey will create a petabyte digital record of the sky that can be data mined in the future and used to search for relativistic binary and millisecond pulsars, RRATs, and extragalactic radio bursts. The survey should discover 100s of new millisecond and normal pulsars and help define the lower limit to pulsar periods, test theories of relativistic gravity, find transients and provide pulsars for gravitational wave detection.
DOI: 10.25549/usctheses-c3-599954
title: etd-RuizSusana-3651~111
DOI: 10.25549/usctheses-c3-599931
title: etd-RuizSusana-3651~088
DOI: 10.25549/usctheses-c3-599873
title: etd-RuizSusana-3651~030
DOI: 10.25549/usctheses-c3-589725
title: etd-ChiuCathle-3452~057
DOI: 10.6084/m9.figshare.21078189
title: Ultrahigh-pressure metamorphism and P-T-t path of the Yangkou eclogites and granitic gneisses from the central Sulu orogenic belt, eastern China, based on phase equilibria modelling

description: Coesite-bearing eclogites and garnet-bearing granitic gneisses from the Yangkou area in the middle portion of Sulu ultrahigh pressure (UHP) metamorphic belt records three stages of metamorphism: I) Prograde to peak stage, II) Early retrograde stage, and III) Late retrograde stage. The prograde stage is recorded in the core to mantle in garnet and Si (3.38–3.43) in phengite in eclogite that has the assemblage of Grt-Omp-Amp-Phg-Lws (+ Qtz + Rt + H<sub>2</sub>O), and the P-T conditions are constrained at 25–27 kbar and 585–595°C. Stage II is constrained by X<sub>gr</sub> (0.48–0.55) in garnet from mantle to rim, X<sub>An</sub> (0.009–0.011) from mantle to rim in plagioclase of granitic gneiss, and the P–T conditions are estimated to be 29–35 kbar and 865–990°C with the mineral assemblage of Grt-Bt-Pl-Phg-Liq (+ Qtz/Coe). Stage III is constrained by two P-T ranges: mineral assemblage of Grt-Ep-Bt-Pl-Phg-Liq (+ Qtz) and X<sub>gr</sub> (0.45–0.72) from mantle to rim in garnet in granitic gneiss constrained an earlier P-T range of 22–23 kbar and 800–820°C, while X<sub>gr</sub> (0.34–0.39) and X<sub>py</sub> (0.16–0.18) from mantle to rim in garnet in eclogite in the assemblage of Grt-Omp-Amp-Phg-LL (+ Qtz + Rt + H<sub>2</sub>O) constrained a later P-T range of 17–18 kbar and 675–690°C. The formation and evolution of these assemblages have important implications for the generation and differentiation of continental crust through the operation of plate tectonics. The data suggest that both mafic and granitic rocks in the Yangkou area subducted to a depth of more than 115 km and underwent UHP metamorphism. The three stages of metamorphism in the study area are consistent with the regional well-established metamorphic evolution history, from UHP eclogite facies, through HP/HT eclogite facies, to amphibole eclogite facies with the timing of 230, 225, and 195 Ma, respectively.
DOI: 10.6084/m9.figshare.6396644
title: Global expression profiling and pathway analysis of mouse mammary tumor reveals strain and stage specific dysregulated pathways in breast cancer progression

description: It is believed that the alteration of tissue microenvironment would affect cancer initiation and progression. However, little is known in terms of the underlying molecular mechanisms that would affect the initiation and progression of breast cancer. In the present study, we use two murine mammary tumor models with different speeds of tumor initiation and progression for whole genome expression profiling to reveal the involved genes and signaling pathways. The pathways regulating PI3K-Akt signaling and Ras signaling were activated in Fvb mice and promoted tumor progression. Contrastingly, the pathways regulating apoptosis and cellular senescence were activated in Fvb.B6 mice and suppressed tumor progression. We identified distinct patterns of oncogenic pathways activation at different stages of breast cancer, and uncovered five oncogenic pathways that were activated in both human and mouse breast cancers. The genes and pathways discovered in our study would be useful information for other researchers and drug development.
DOI: 10.25549/usctheses-c3-577221
title: etd-CardenasMi-3510_113