cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1625564
title: Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women

description: Breast cancer is more common in European Americans (EAs) than in African Americans (AAs) but mortality from breast cancer is higher among AAs. While there are racial differences in DNA methylation and gene expression in breast tumors, little is known whether such racial differences exist in breast tissues of healthy women. Genome-wide DNA methylation and gene expression profiling was performed in histologically normal breast tissues of healthy women. Linear regression models were used to identify differentially-methylated CpG sites (CpGs) between EAs (n = 61) and AAs (n = 22). Correlations for methylation and expression were assessed. Biological functions of the differentially-methylated genes were assigned using the Ingenuity Pathway Analysis. Among 485 differentially-methylated CpGs by race, 203 were hypermethylated in EAs, and 282 were hypermethylated in AAs. Promoter-related differentially-methylated CpGs were more frequently hypermethylated in EAs (52%) than AAs (27%) while gene body and intergenic CpGs were more frequently hypermethylated in AAs. The differentially-methylated CpGs were enriched for cancer-associated genes with roles in cell death and survival, cellular development, and cell-to-cell signaling. In a separate analysis for correlation in EAs and AAs, different patterns of correlation were found between EAs and AAs. The correlated genes showed different biological networks between EAs and AAs; networks were connected by Ubiquitin C. To our knowledge, this is the first comprehensive genome-wide study to identify differences in methylation and gene expression between EAs and AAs in breast tissues from healthy women. These findings may provide further insights regarding the contribution of epigenetic differences to racial disparities in breast cancer.
DOI: 10.6084/m9.figshare.1625564.v1
title: Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women

description: Breast cancer is more common in European Americans (EAs) than in African Americans (AAs) but mortality from breast cancer is higher among AAs. While there are racial differences in DNA methylation and gene expression in breast tumors, little is known whether such racial differences exist in breast tissues of healthy women. Genome-wide DNA methylation and gene expression profiling was performed in histologically normal breast tissues of healthy women. Linear regression models were used to identify differentially-methylated CpG sites (CpGs) between EAs (n = 61) and AAs (n = 22). Correlations for methylation and expression were assessed. Biological functions of the differentially-methylated genes were assigned using the Ingenuity Pathway Analysis. Among 485 differentially-methylated CpGs by race, 203 were hypermethylated in EAs, and 282 were hypermethylated in AAs. Promoter-related differentially-methylated CpGs were more frequently hypermethylated in EAs (52%) than AAs (27%) while gene body and intergenic CpGs were more frequently hypermethylated in AAs. The differentially-methylated CpGs were enriched for cancer-associated genes with roles in cell death and survival, cellular development, and cell-to-cell signaling. In a separate analysis for correlation in EAs and AAs, different patterns of correlation were found between EAs and AAs. The correlated genes showed different biological networks between EAs and AAs; networks were connected by Ubiquitin C. To our knowledge, this is the first comprehensive genome-wide study to identify differences in methylation and gene expression between EAs and AAs in breast tissues from healthy women. These findings may provide further insights regarding the contribution of epigenetic differences to racial disparities in breast cancer.
DOI: 10.6084/m9.figshare.1625566.v2
title: Characterizing patients with psoriasis on injectable biologics adalimumab, etanercept, and ustekinumab: A chart review study

description: <i>Objective</i>: This study examined plaque psoriasis (PsO) patient characteristics across injectable biologics. <i>Methods</i>: Data were collected from 400 US dermatologists randomly selecting five charts each for patients with PsO (patient <i>n</i> = 2000): adalimumab (ADA; <i>n</i> = 447), etanercept (ETA; 539), ustekinumab (UST) 45 mg (511) and UST 90 mg (503). Physicians had to have been in practice 2–30 years, managing 10+ patients (5 + with biologics for PsO). Generalized estimating equation models, weighted according to inverse probability of patient selection and accounting for patient correlation within physicians, examined patient measures as a function of treatment (UST 90 mg = reference). <i>Results</i>: Patients on UST 90 mg had higher odds of weighing &gt;100 kg (adjusted mean = 34.4%) vs. ADA (10.9%), ETA (5.5%) or UST 45 mg (6.8%), greater body surface affected and higher odds of severe PsO prior to treatment and higher odds of prior biologics use. Mean prior biologics used was higher with UST 90 mg versus ADA or ETA. Number of comorbidities was higher with UST 90 mg versus ETA or UST 45 mg. <i>Conclusions</i>: Among biologics-treated patients with PsO, UST 90 mg appears to be used in patients with greater weight, baseline severity and prior biologics experience than ADA, ETA or UST 45 mg. UST 90 mg is used in patients with more comorbidities than other treatments except ADA.
DOI: 10.6084/m9.figshare.1625559
title: The rock art of Kondoa District, Tanzania

description: We review the history of rock art research in Kondoa District, Tanzania, specifically the area covered by the ‘Kondoa Rock Art Sites UNESCO World Heritage Site’. We examine why, after nearly a century of research, there is neither a broadly agreed upon stylistic sequence for the rock art of the area nor a clear ascription of authorship. We seek to provide a solution to this impasse by introducing a rigorous and systematised analytical approach that considers both the content of the art and the location in which it was situated. The findings of our analysis, as presented here, demonstrate three clearly identifiable traditions of art, each with elements of overlap and borrowing. We provide an evidence-based ascription of authorship to each tradition that confirms the ethnic complexity of the settlement of this area and lays the foundation for future studies of rock art interpretation and cultural interaction.
DOI: 10.6084/m9.figshare.1625559.v1
title: The rock art of Kondoa District, Tanzania

description: We review the history of rock art research in Kondoa District, Tanzania, specifically the area covered by the ‘Kondoa Rock Art Sites UNESCO World Heritage Site’. We examine why, after nearly a century of research, there is neither a broadly agreed upon stylistic sequence for the rock art of the area nor a clear ascription of authorship. We seek to provide a solution to this impasse by introducing a rigorous and systematised analytical approach that considers both the content of the art and the location in which it was situated. The findings of our analysis, as presented here, demonstrate three clearly identifiable traditions of art, each with elements of overlap and borrowing. We provide an evidence-based ascription of authorship to each tradition that confirms the ethnic complexity of the settlement of this area and lays the foundation for future studies of rock art interpretation and cultural interaction.
DOI: 10.6084/m9.figshare.1625355.v1
title: A coupled analytical model for salt intrusion and tides in convergent estuaries

description: In this paper we develop a coupled analytical model for salinity and tidal propagation in estuaries where the cross-sectional area varies exponentially. A simple analytical model for tidal dynamics has been used to estimate the tidal excursion, which has an important influence on the salt intrusion process since it determines the extreme salinities (i.e. salinity distribution for high water slack and low water slack). The objective of the coupling is to reduce the number of calibration parameters, which subsequently strengthens the reliability of the salt intrusion model. Moreover, the coupling enables us to assess the potential impacts of external changes, both human-induced interventions (e.g. dredging) and natural changes (e.g. global sea level rise), on the salt intrusion process. In addition, the fully analytical solution for hydrodynamics allows immediate estimation of the tidally averaged depth and friction coefficient for given water level recordings and salinity measurements. This is particularly useful when a geometric survey is not available. The coupled model has been applied to six previously unsurveyed estuaries in Malaysia and the results show that the correspondence between analytical estimations and observations is very good. Thus, the coupled model proves to be a useful tool to obtain estimates of salt intrusion in estuaries based on a minimum amount of information required and for assessing the effect of human-induced or natural changes. <b>EDITOR</b> D. Koutsoyiannis <b>ASSOCIATE EDITOR</b> B. Dewals <b>EDITOR</b> D. Koutsoyiannis <b>ASSOCIATE EDITOR</b> B. Dewals
DOI: 10.6084/m9.figshare.1625344
title: Macrofungal diversity in community-managed sal (<i>Shorea robusta</i>) forests in central Nepal

description: Macrofungi constitute a group of the high-value forest resources worldwide. In this paper, we report species richness and composition of the macrofungi in sal (<i>Shorea robusta</i>) forests of mid-hill central Nepal, which were managed for 4–29 years by the local communities. The sal forests were rich in macrofungi (115 species) with Polyporaceae being the largest family followed by Clavariaceae. Saprotrophic fungi were more common than mycorrhizal species. The proportion of mycorrhiza was &lt;40% of the total macrofungi species which might have indicated the deteriorated condition of the forests before the initiation of conservation management. However, the proportion of mycorrhizal species was slightly higher in the forests managed for &gt;10 years than in the forests managed for short period. The species richness increased with increasing canopy and litter cover. Since silvicultural activities and resource utilization often have negative impacts to macrofungal diversity, these activities need to be optimized to keep balance between forest management and biodiversity conservation.
DOI: 10.6084/m9.figshare.1625344.v1
title: Macrofungal diversity in community-managed sal (<i>Shorea robusta</i>) forests in central Nepal

description: Macrofungi constitute a group of the high-value forest resources worldwide. In this paper, we report species richness and composition of the macrofungi in sal (<i>Shorea robusta</i>) forests of mid-hill central Nepal, which were managed for 4–29 years by the local communities. The sal forests were rich in macrofungi (115 species) with Polyporaceae being the largest family followed by Clavariaceae. Saprotrophic fungi were more common than mycorrhizal species. The proportion of mycorrhiza was &lt;40% of the total macrofungi species which might have indicated the deteriorated condition of the forests before the initiation of conservation management. However, the proportion of mycorrhizal species was slightly higher in the forests managed for &gt;10 years than in the forests managed for short period. The species richness increased with increasing canopy and litter cover. Since silvicultural activities and resource utilization often have negative impacts to macrofungal diversity, these activities need to be optimized to keep balance between forest management and biodiversity conservation.
DOI: 10.6084/m9.figshare.1625320
title: Myxofibrosarcoma directly invading superior vena cava causing obstruction successfully relieved by endovascular stent

description: Myxofibrosarcoma directly invading superior vena cava causing obstruction successfully relieved by endovascular stent
DOI: 10.6084/m9.figshare.1625321
title: Early preventive exercises versus usual care does not seem to reduce trismus in patients treated with radiotherapy for cancer in the oral cavity or oropharynx: A randomised clinical trial

description: <b>Purpose.</b> In head and neck cancer patients undergoing curative radiotherapy, we investigated the benefits and harms of an early exercise regime on trismus.<b>Material and methods.</b> Patients with head and neck cancer undergoing radiotherapy were centrally randomised to exercises 5–6 times for 45 minutes during and after radiotherapy supervised by a physiotherapist in addition to usual care versus usual care alone. The primary outcome was change in maximal interincisor distance (MID) measured at 5 and 12 months. Secondary outcomes were change in cervical ranges of motion, tissue tightness, and health-related quality of life. Mixed model analysis of repeated measures adjusted for tumour size and operation was conducted to assess the effect of early preventive exercises across time periods.<b>Results.</b> Of the 100 patients included, two patients withdrew and one died before the onset of radiotherapy. The unadjusted mean difference in MID at 12 months after having completed radiotherapy was 0.83 mm (95% confidence interval (CI) –3.64–5.29, p = 0.71) in the exercise intervention group compared with the control group. When adjusted for operation and tumour size, the effect of the exercise intervention on mean MID from baseline to 12-month follow-up was 5.92 mm (95% CI –0.48–12.33, p = 0.07). Of the secondary outcomes, cervical rotation showed a statistically significant deterioration in the exercise group compared with the control group (p = 0.01). No significant effects were observed on the other secondary outcomes.<b>Conclusions.</b> In patients with cancer in the oral cavity or oropharynx, early supervised exercises combined with self-care treatment focusing on mobility exercises to reduce trismus do not seem to provide additional beneficial effects compared with usual care during curative radiotherapy.
DOI: 10.6084/m9.figshare.1625320.v1
title: Myxofibrosarcoma directly invading superior vena cava causing obstruction successfully relieved by endovascular stent

description: Myxofibrosarcoma directly invading superior vena cava causing obstruction successfully relieved by endovascular stent
DOI: 10.6084/m9.figshare.1625321.v1
title: Early preventive exercises versus usual care does not seem to reduce trismus in patients treated with radiotherapy for cancer in the oral cavity or oropharynx: A randomised clinical trial

description: <b>Purpose.</b> In head and neck cancer patients undergoing curative radiotherapy, we investigated the benefits and harms of an early exercise regime on trismus.<b>Material and methods.</b> Patients with head and neck cancer undergoing radiotherapy were centrally randomised to exercises 5–6 times for 45 minutes during and after radiotherapy supervised by a physiotherapist in addition to usual care versus usual care alone. The primary outcome was change in maximal interincisor distance (MID) measured at 5 and 12 months. Secondary outcomes were change in cervical ranges of motion, tissue tightness, and health-related quality of life. Mixed model analysis of repeated measures adjusted for tumour size and operation was conducted to assess the effect of early preventive exercises across time periods.<b>Results.</b> Of the 100 patients included, two patients withdrew and one died before the onset of radiotherapy. The unadjusted mean difference in MID at 12 months after having completed radiotherapy was 0.83 mm (95% confidence interval (CI) –3.64–5.29, p = 0.71) in the exercise intervention group compared with the control group. When adjusted for operation and tumour size, the effect of the exercise intervention on mean MID from baseline to 12-month follow-up was 5.92 mm (95% CI –0.48–12.33, p = 0.07). Of the secondary outcomes, cervical rotation showed a statistically significant deterioration in the exercise group compared with the control group (p = 0.01). No significant effects were observed on the other secondary outcomes.<b>Conclusions.</b> In patients with cancer in the oral cavity or oropharynx, early supervised exercises combined with self-care treatment focusing on mobility exercises to reduce trismus do not seem to provide additional beneficial effects compared with usual care during curative radiotherapy.
DOI: 10.6084/m9.figshare.1623222
title: Biogeochemical Importance of the Bacterial Community in Uranium Waste Deposited at Key Lake, Northern Saskatchewan

description: The long-term stability of immobilized elements of concern in uranium tailings deposited in the Deilmann Tailings Management Facility (DTMF), northern Saskatchewan, is dependent upon maintenance of highly oxic conditions within the tailings mass. The main objective of this study was to investigate the effect of stimulating microbial activity on the redox potential and state of ferrihydrite, which are considered to be the primary controlling condition and mineral phase, respectively, within the tailings. To determine the potential for biologically mediated decreases in redox potential and ferrihydrite reduction, a series of microcosm assays were performed. Non-sterile material from the tailings–water interface of the DTMF site was inoculated with indigenous flora previously isolated from the tailings material and enriched with a carbon source (50 ppm trypticase soy broth) and incubated under continuous-flow or intermittent-flow conditions, and compared with an uninoculated, no-carbon control that received continuous flow. Highly reducing conditions with redox potentials of less than −300 mV were detected after 2 days of incubation within the carbon-enriched tailings of microcosms receiving continuous flow, and less than −280 mV after 11 days of incubation within carbon-enriched tailings in microcosms receiving intermittent flow. The lowest recorded Eh value (−545 mV) was recorded after 14 days in a carbon-enriched microcosm receiving intermittent flow. In contrast, the redox conditions in the control microcosm never dropped below −93 mV; thus, it was clear that microbial activity and available carbon drove the Eh conditions to become highly reducing. The occurrence of low redox conditions was concomitant with the bulk chemical detection of Fe (II) in the effluent of treated microcosms. Sites of microbial ferrihydrite reduction were also detected using scanning transmission X-ray microscopy where Fe (II) species were observed in close proximity with bacterial cells. Analysis of the microbial diversity present within the microcosms confirmed that microbes indigenous to the DTMF system have the potential to generate conditions suitable for the proliferation of sulfate and iron reducing bacteria, such as <i>Desulfosporosinus</i>, which was detected by high-throughput 16S rRNA gene sequencing.
DOI: 10.6084/m9.figshare.1623221
title: Amnion Epithelial Cells of Buffalo (<i>Bubalus bubalis</i>) Term Placenta Expressed Embryonic Stem Cells Markers and Differentiated into Cells of Neurogenic Lineage <i>In Vitro</i>

description: Aim of the present study was the isolation, culture, and characterization of amniotic membrane-derived epithelial cells (AE) from term placenta collected postpartum in buffalo. We found that cultured cells were of polygonal in shape, resistance to trypsin digestion and expressed cytokeratin-18 indicating that they were of epithelial origin. These cells have negative expression of mesenchymal stem cell markers (CD29, CD44, and CD105) and positive for pluripotency marker (OCT4) genes indicated that cultured cells were not contaminated with mesenchymal stem cells. Immunofluorescence staining with pluripotent stem cell surface markers, SSEA-1, SSEA-4, TRA-1-60, and TRA-1-81 indicated that these cells may retain pluripotent stem cell characteristics even after long period of differentiation. Differentiation potential of these cells was determined by their potential to differentiate into cells of neurogenic lineages using retinoic acid. In conclusion, we demonstrate that AE cells expressed pluripotent stem cell markers and have propensity to differentiate into cells of neurogenic lineage upon directed differentiation <i>in vitro</i>.
DOI: 10.6084/m9.figshare.1625303.v2
title: <i>In vitro</i> and <i>in vivo</i> genotoxic effects of straight versus tangled multi-walled carbon nanotubes

description: Some multi-walled carbon nanotubes (MWCNTs) induce mesothelioma in rodents, straight MWCNTs showing a more pronounced effect than tangled MWCNTs. As primary and secondary genotoxicity may play a role in MWCNT carcinogenesis, we used a battery of assays for DNA damage and micronuclei to compare the genotoxicity of straight (MWCNT-S) and tangled MWCNTs (MWCNT-T) <i>in vitro</i> (primary genotoxicity) and <i>in vivo</i> (primary or secondary genotoxicity). C57Bl/6 mice showed a dose-dependent increase in DNA strand breaks, as measured by the comet assay, in lung cells 24 h after a single pharyngeal aspiration of MWCNT-S (1–200 μg/mouse). An increase was also observed for DNA strand breaks in lung and bronchoalveolar lavage (BAL) cells and for micronucleated alveolar type II cells in mice exposed to aerosolized MWCNT-S (8.2–10.8 mg/m<sup>3</sup>) for 4 d, 4 h/d. No systemic genotoxic effects, assessed by the γ-H2AX assay in blood mononuclear leukocytes or by micronucleated polychromatic erythrocytes (MNPCEs) in bone marrow or blood, were observed for MWCNT-S by either exposure technique. MWCNT-T showed a dose-related <i>decrease</i> in DNA damage in BAL and lung cells of mice after a single pharyngeal aspiration (1–200 μg/mouse) and in MNPCEs after inhalation exposure (17.5 mg/m<sup>3</sup>). <i>In vitro</i> in human bronchial epithelial BEAS-2B cells, MWCNT-S induced DNA strand breaks at low doses (5 and 10 μg/cm<sup>2</sup>), while MWCNT-T increased strand breakage only at 200 μg/cm<sup>2</sup>. Neither of the MWCNTs was able to induce micronuclei <i>in vitro</i>. Our findings suggest that both primary and secondary mechanisms may be involved in the genotoxicity of straight MWCNTs.