cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4861406.v1
title: What would disprove interdependence? (data and code)

description: These are the datasets and R code accompanying the article "What would disprove interdependence? Lessons learned from a study on biliteracy in Portuguese heritage language speakers in Switzerland" by Raphael Berthele and Jan Vanhove. All analyses reported in this paper can be reproduced using the datasets and code provided here.<br>
DOI: 10.6084/m9.figshare.4865333.v3
title: ASPECT: Advanced Solver for Problems in Earth's ConvecTion, User Manual

description: This is the manual of the ASPECT mantle convection code
DOI: 10.6084/m9.figshare.4859606.v1
title: Supplementary Material for: Autologous Stem Cell Transplantation in Multiple Myeloma in the Era of Novel Drug Induction: A Retrospective Single-Center Analysis

description: Within this retrospective single-center study, we analyzed the survival of 320 multiple myeloma (MM) patients receiving melphalan high-dose chemotherapy (HDCT) and either single (<i>n</i> = 286) or tandem (<i>n</i> = 34) autologous stem cell transplantation (ASCT) from 1996 to 2012. Additionally, the impact of novel induction regimens was assessed. Median follow-up was 67 months, median overall survival (OS) 62 months, median progression-free survival (PFS) 33 months (95% CI 27-39), and treatment-related death (TRD) 3%. Multivariate analysis revealed age ≥60 years (<i>p = </i>0.03) and stage 3 according to the International Staging System (<i>p = </i>0.006) as adverse risk factors regarding PFS. Median OS was significantly better in newly diagnosed MM patients receiving induction therapy with novel agents, e.g., bortezomib, thalidomide, or lenalidomide, compared with a traditional regimen (69 vs. 58 months; <i>p = </i>0.01). More patients achieved at least a very good partial remission in the period from 2005 to 2012 than from 1996 to 2004 (65 vs. 30%; <i>p</i> &lt; 0.001), with a longer median OS in the later period (71 vs. 52 months, <i>p</i> = 0.027). In conclusion, our analysis confirms HDCT-ASCT as an effective therapeutic strategy in an unselected large myeloma patient cohort with a low TRD rate and improved prognosis due to novel induction strategies.
DOI: 10.6084/m9.figshare.4858385
title: paRNA in CDH1 promoter

description: paRNA with high and low confidence predicted in CDH1 promoter<br>
DOI: 10.6084/m9.figshare.4861406.v2
title: What would disprove interdependence? (data and code)

description: These are the datasets and R code accompanying the article "What would disprove interdependence? Lessons learned from a study on biliteracy in Portuguese heritage language speakers in Switzerland" by Raphael Berthele and Jan Vanhove. All analyses reported in this paper can be reproduced using the datasets and code provided here.<br><br>The HTML file contains the output of all computations, including tables with all estimated model coefficients.<br>
DOI: 10.6084/m9.figshare.4857887
title: Supplementary Material for: Expression of the ERBB Family of Ligands and Receptors in Gastric Cancer

description: <b><i>Objective:</i></b> Gastric cancer (GC) is the second most common cancer and the third leading cause of cancer-related death in Korea. Alterations in the ERBB (homology to the erythroblastoma viral gene product, v-erbB) receptor family and ERBB-related signaling pathways are frequently observed in GC. However, the roles of the ERBB receptors and their ligands in GC are not well established. <b><i>Methods:</i></b> We evaluated the expression levels of various ERBB receptor ligands (i.e., heparin-binding epidermal growth factor-like growth factor [HBEGF], transforming growth factor-α [TGFA], amphiregulin [AREG], epiregulin [EREG], epidermal growth factor [EGF], and betacellulin [BTC]) and 3 ERBB family receptors (i.e., epidermal growth factor receptor [EGFR], human EGFR2 [HER2], and ERBB3) in 313 cases of GC using immunohistochemistry, fluorescence in situ hybridization, and mRNA in situ hybridization. <b><i>Results:</i></b> A high expression of EGFR, HER2, and ERBB3 was observed in 30, 32, and 27 cases, respectively. A high expression of HBEGF, TGFA, AREG, EREG, EGF, and BTC was observed in 91, 97, 151, 74, 26, and 37 cases, respectively. A high expression of TGFA was associated with better survival, while a high expression of BTC was associated with worse survival. These results were confirmed using Cox proportional hazards analysis. HBEGF, TGFA, AREG, tumor-node-metastasis classification, Lauren's classification, and ERBB3 were significant survival parameters in multivariate analysis. <b><i>Conclusion:</i></b> Among the ERBB family receptors and ligands examined, 3 ligands (i.e., TGFA, HBEGF, and AREG) and ERBB3 had a prognostic impact.
DOI: 10.6084/m9.figshare.4857887.v1
title: Supplementary Material for: Expression of the ERBB Family of Ligands and Receptors in Gastric Cancer

description: <b><i>Objective:</i></b> Gastric cancer (GC) is the second most common cancer and the third leading cause of cancer-related death in Korea. Alterations in the ERBB (homology to the erythroblastoma viral gene product, v-erbB) receptor family and ERBB-related signaling pathways are frequently observed in GC. However, the roles of the ERBB receptors and their ligands in GC are not well established. <b><i>Methods:</i></b> We evaluated the expression levels of various ERBB receptor ligands (i.e., heparin-binding epidermal growth factor-like growth factor [HBEGF], transforming growth factor-α [TGFA], amphiregulin [AREG], epiregulin [EREG], epidermal growth factor [EGF], and betacellulin [BTC]) and 3 ERBB family receptors (i.e., epidermal growth factor receptor [EGFR], human EGFR2 [HER2], and ERBB3) in 313 cases of GC using immunohistochemistry, fluorescence in situ hybridization, and mRNA in situ hybridization. <b><i>Results:</i></b> A high expression of EGFR, HER2, and ERBB3 was observed in 30, 32, and 27 cases, respectively. A high expression of HBEGF, TGFA, AREG, EREG, EGF, and BTC was observed in 91, 97, 151, 74, 26, and 37 cases, respectively. A high expression of TGFA was associated with better survival, while a high expression of BTC was associated with worse survival. These results were confirmed using Cox proportional hazards analysis. HBEGF, TGFA, AREG, tumor-node-metastasis classification, Lauren's classification, and ERBB3 were significant survival parameters in multivariate analysis. <b><i>Conclusion:</i></b> Among the ERBB family receptors and ligands examined, 3 ligands (i.e., TGFA, HBEGF, and AREG) and ERBB3 had a prognostic impact.
DOI: 10.6084/m9.figshare.4858385.v2
title: paRNA in CDH1 promoter

description: paRNA with high and low confidence predicted in CDH1 promoter<br>
DOI: 10.6084/m9.figshare.4858385.v1
title: paRNA in CDH1 promoter

description: paRNA with high and low confidence predicted in CDH1 promoter<br>
DOI: 10.6084/m9.figshare.4861406.v4
title: What would disprove interdependence? (data and code)

description: These are the datasets and R code accompanying the article "What would disprove interdependence? Lessons learned from a study on biliteracy in Portuguese heritage language speakers in Switzerland" by Raphael Berthele and Jan Vanhove. All analyses reported in this paper can be reproduced using the datasets and code provided here.<br><br>The HTML file contains the output of all computations, including tables with all estimated model coefficients.<br><br>The CSV file ReadingTask_reliabilities.csv contains, for each administration and for each group of participants separately, the Cronbach's alpha reliability for the reading task alongside the lower and upper bound of its 95% confidence interval. (These reliabilities were computed for Pestana et al. [Reading comprehension in Portuguese heritage speakers in Switzerland (HELASCOT project). In R. Berthele & A.<br>Lambelet (Eds.), Heritage and school language literacy development in migrant children: Interdependence or independence?].)<br>
DOI: 10.6084/m9.figshare.4857752
title: MAPK signaling has stage-dependent osteogenic effects on human adipose-derived stem cells <i>in vitro</i>

description: <b><i>Overview</i></b>: The use of pro-osteogenic growth factors, such as BMP2, in human adipose-derived stem cell (ASC) osteogenesis is well described. Because these growth factors work via signal transduction pathways, such as the mitogen-activated protein kinase (MAPK) cascade, a study of the relationship between MAPK signaling and ASC osteogenesis was conducted. <b><i>Materials and Methods</i></b>: ERK, JNK, and p38MAPK activation were measured in ASCs osteo-induced using either dexamethasone or vitamin D3 and correlated with mineralization. Activation and mineralization were also measured without dexamethasone or using the glucocorticoid, cortisone. The expression of the MAPK phosphatase, MKP1, and its relationship to mineralization was also assessed. The effect of decreasing MAPK activation on mineralization through the use of exogenous inhibitors was examined along with siRNA-knockdown and adenoviral overexpression of ERK1/2. Finally, the effect of ERK1/2 overexpression on ASCs induced on PLGA scaffolds was assessed. <b><i>Results</i></b>: ASC mineralization in dexamethasone or vitamin D3-induced ASCs correlated with both increased ERK1/2 and JNK1/2 activation. ASCs induced without dexamethasone also mineralized, with JNK1/2 signaling possibly mediating this event. No link between cortisone induction and MAPK signaling could be ascertained. ASCs treated with ERK, JNK, or p38MAPK inhibitors showed decreased osteogenic gene expression and diminished mineralization. Mineralization levels were also affected by viruses designed to inhibit or augment ERK1/2 expression and activity. Finally, ASC mineralization appeared to be a balance between the MAPK kinase activity and MKP1. <b><i>Conclusions</i></b>: It is likely that MAPK signaling plays a significant role in ASC osteogenesis, affecting differentiation in kinase- and stage-specific manners.
DOI: 10.6084/m9.figshare.4857836
title: Interactive design of patient-oriented video-games for rehabilitation: concept and application

description: <b>Purpose:</b> Serious video-games are innovative tools used to train the motor skills of subjects affected by neurological disorders. They are often developed to train a specific type of patients and the rules of the game are standardly defined. A system that allows the therapist to design highly patient-oriented video-games, without specific informatics skills, is proposed. <b>Method:</b> The system consists of one personal computer, two screens, a Kinect™ sensor and a specific software developed here for the design of the video-games. It was tested with the collaboration of three therapists and six patients, and two questionnaires were filled in by each patient to evaluate the appreciation of the rehabilitative sessions. <b>Results:</b> The therapists learned easily how to use the system, and no serious difficulties were encountered by the patients. The questionnaires showed an overall good satisfaction by the patients and highlighted the key-role of the therapist in involving the patients during the rehabilitative session. <b>Conclusions:</b> It was found that the proposed system is effective for developing patient-oriented video-games for rehabilitation. The two main advantages are that the therapist is allowed to (i) develop personalized video-games without informatics skills and (ii) adapt the game settings to patients affected by different pathologies. Implications for rehabilitationVirtual reality and serious video games offer the opportunity to transform the traditional therapy into a more pleasant experience, allowing patients to train their motor and cognitive skills.Both the therapists and the patients should be involved in the development of rehabilitative solutions to be highly patient-oriented.A system for the design of rehabilitative games by the therapist is described and the feedback of three therapists and six patients is reported. Virtual reality and serious video games offer the opportunity to transform the traditional therapy into a more pleasant experience, allowing patients to train their motor and cognitive skills. Both the therapists and the patients should be involved in the development of rehabilitative solutions to be highly patient-oriented. A system for the design of rehabilitative games by the therapist is described and the feedback of three therapists and six patients is reported.
DOI: 10.6084/m9.figshare.4861406.v3
title: What would disprove interdependence? (data and code)

description: These are the datasets and R code accompanying the article "What would disprove interdependence? Lessons learned from a study on biliteracy in Portuguese heritage language speakers in Switzerland" by Raphael Berthele and Jan Vanhove. All analyses reported in this paper can be reproduced using the datasets and code provided here.<br><br>The HTML file contains the output of all computations, including tables with all estimated model coefficients.<br>
DOI: 10.6084/m9.figshare.4857836.v1
title: Interactive design of patient-oriented video-games for rehabilitation: concept and application

description: <b>Purpose:</b> Serious video-games are innovative tools used to train the motor skills of subjects affected by neurological disorders. They are often developed to train a specific type of patients and the rules of the game are standardly defined. A system that allows the therapist to design highly patient-oriented video-games, without specific informatics skills, is proposed. <b>Method:</b> The system consists of one personal computer, two screens, a Kinect™ sensor and a specific software developed here for the design of the video-games. It was tested with the collaboration of three therapists and six patients, and two questionnaires were filled in by each patient to evaluate the appreciation of the rehabilitative sessions. <b>Results:</b> The therapists learned easily how to use the system, and no serious difficulties were encountered by the patients. The questionnaires showed an overall good satisfaction by the patients and highlighted the key-role of the therapist in involving the patients during the rehabilitative session. <b>Conclusions:</b> It was found that the proposed system is effective for developing patient-oriented video-games for rehabilitation. The two main advantages are that the therapist is allowed to (i) develop personalized video-games without informatics skills and (ii) adapt the game settings to patients affected by different pathologies. Implications for rehabilitationVirtual reality and serious video games offer the opportunity to transform the traditional therapy into a more pleasant experience, allowing patients to train their motor and cognitive skills.Both the therapists and the patients should be involved in the development of rehabilitative solutions to be highly patient-oriented.A system for the design of rehabilitative games by the therapist is described and the feedback of three therapists and six patients is reported. Virtual reality and serious video games offer the opportunity to transform the traditional therapy into a more pleasant experience, allowing patients to train their motor and cognitive skills. Both the therapists and the patients should be involved in the development of rehabilitative solutions to be highly patient-oriented. A system for the design of rehabilitative games by the therapist is described and the feedback of three therapists and six patients is reported.
DOI: 10.6084/m9.figshare.4857137
title: Data Set for Optics Express submission: Trade-offs between structural integrity and acquisition time in stochastic super-resolution microscopy techniques

description: Dataset associated with the submission: Trade-offs between structural integrity and acquisition time in stochastic super-resolution microscopy techniques, by Jean-Francois Rupprecht, Ariadna Martinez-Marrades, Zhen Zhang, Rishita Changede, Pakorn Kanchanawong, and Gilles Tessier (Dated: April 11, 2017)<br><br>1) Data_File_1_STORM_Ax647 & Data_File_2_STORM_tdEos: 2 sequences of localization from labelled tubulin; with Alexa Fluor and with tEoS.<br><br>2) Data_File_3_TIRM: sequence of localization events of gold particles.<br><br>3) Data_File_4_PALM_silane_1: 2 sequences of localization from a functionalized silane coverslip events.
DOI: 10.6084/m9.figshare.4857752.v2
title: MAPK signaling has stage-dependent osteogenic effects on human adipose-derived stem cells <i>in vitro</i>

description: <b><i>Overview</i></b>: The use of pro-osteogenic growth factors, such as BMP2, in human adipose-derived stem cell (ASC) osteogenesis is well described. Because these growth factors work via signal transduction pathways, such as the mitogen-activated protein kinase (MAPK) cascade, a study of the relationship between MAPK signaling and ASC osteogenesis was conducted. <b><i>Materials and Methods</i></b>: ERK, JNK, and p38MAPK activation were measured in ASCs osteo-induced using either dexamethasone or vitamin D3 and correlated with mineralization. Activation and mineralization were also measured without dexamethasone or using the glucocorticoid, cortisone. The expression of the MAPK phosphatase, MKP1, and its relationship to mineralization was also assessed. The effect of decreasing MAPK activation on mineralization through the use of exogenous inhibitors was examined along with siRNA-knockdown and adenoviral overexpression of ERK1/2. Finally, the effect of ERK1/2 overexpression on ASCs induced on PLGA scaffolds was assessed. <b><i>Results</i></b>: ASC mineralization in dexamethasone or vitamin D3-induced ASCs correlated with both increased ERK1/2 and JNK1/2 activation. ASCs induced without dexamethasone also mineralized, with JNK1/2 signaling possibly mediating this event. No link between cortisone induction and MAPK signaling could be ascertained. ASCs treated with ERK, JNK, or p38MAPK inhibitors showed decreased osteogenic gene expression and diminished mineralization. Mineralization levels were also affected by viruses designed to inhibit or augment ERK1/2 expression and activity. Finally, ASC mineralization appeared to be a balance between the MAPK kinase activity and MKP1. <b><i>Conclusions</i></b>: It is likely that MAPK signaling plays a significant role in ASC osteogenesis, affecting differentiation in kinase- and stage-specific manners.
DOI: 10.6084/m9.figshare.4856885
title: Supplementary Material for: Neoadjuvant Chemotherapy with Gemcitabine plus Cisplatin in Patients with Locally Advanced Bladder Cancer

description: <b><i>Background:</i></b> Neoadjuvant chemotherapy with methotrexate-vinblastine-doxorubicin-cisplatin (MVAC) is the standard of care for muscle-invasive urothelial bladder cancer. Gemcitabine plus cisplatin (GC) shows similar efficacy with less toxicity in the metastatic setting and has therefore often been used interchangeably with MVAC. We report on the efficacy and safety of neoadjuvant GC in patients with locally advanced urothelial cancer. <b><i>Materials and Methods:</i></b> We prospectively evaluated 87 patients in 2 centers. Their median age was 68 years. Treatment consisted of 3× GC prior to radical cystectomy. The primary endpoint was pathologic response. The secondary endpoints were safety, progression-free survival (PFS), and overall survival (OS). <b><i>Results:</i></b> In all, 83 patients finished chemotherapy; 80 patients were evaluable for the primary endpoint. Pathologic complete response (pCR) was achieved in 22.5% and near pCR was seen in 33.7% of the patients. The 1-year PFS rate was 79.5% among those patients achieving ≤pT2 versus 100% among those patients achieving pCR or near pCR (<i>p</i> = 0.041). Five-year OS was 61.8% (95% CI 67.6 to NA). GC was well tolerated. Grade 3/4 toxicities occurred in 38% of the patients. There was no grade 3/4 renal toxicity, febrile neutropenia, or death. <b><i>Conclusion:</i></b> Neoadjuvant GC is a well-tolerated regimen. Although the pathologic response is lower than that reported with MVAC, our data support GC as a feasible option in the absence of a prospective randomized comparison, particularly for older patients, since its toxicity is lower than that of MVAC.
DOI: 10.6084/m9.figshare.4856630
title: Genome wide paRNA

description: Genome-wide predicted paRNAs<br>
DOI: 10.6084/m9.figshare.4857137.v1
title: Data Set for Optics Express submission: Trade-offs between structural integrity and acquisition time in stochastic super-resolution microscopy techniques

description: Dataset associated with the submission: Trade-offs between structural integrity and acquisition time in stochastic super-resolution microscopy techniques, by Jean-Francois Rupprecht, Ariadna Martinez-Marrades, Zhen Zhang, Rishita Changede, Pakorn Kanchanawong, and Gilles Tessier (Dated: April 11, 2017)<br><br>1) Data_File_1_STORM_Ax647 & Data_File_2_STORM_tdEos: 2 sequences of localization from labelled tubulin; with Alexa Fluor and with tEoS.<br><br>2) Data_File_3_TIRM: sequence of localization events of gold particles.<br><br>3) Data_File_4_PALM_silane_1: 2 sequences of localization from a functionalized silane coverslip events.
DOI: 10.6084/m9.figshare.4857752.v1
title: MAPK Signaling has Stage-dependent Osteogenic Effects on Human Adipose-derived Stem Cells in vitro

description: <b>PURPOSE</b>: The use of pro-osteogenic growth factors, such as BMP2, in human adipose-derived stem cell (ASC) osteogenesis is well described. Because these growth factors work via signal transduction pathways, such as the mitogen-activated protein kinase (MAPK) cascade, a study of the relationship between MAPK signaling and ASC osteogenesis was conducted. <b>METHODS</b>: ERK, JNK, and p38MAPK activation were measured in ASCs osteo-induced using either dexamethasone or vitamin D3 and correlated to mineralization. Activation and mineralization were also measured without dexamethasone or using the glucocorticoid, cortisone. The expression of the MAPK phosphatase, MKP1, and its relationship to mineralization was also assessed. The effect of decreasing MAPK activation on mineralization through the use of exogenous inhibitors was examined along with siRNA-knockdown and adenoviral overexpression of ERK1/2. Finally, the effect of ERK1/2 overexpression on ASCs induced on PLGA scaffolds was assessed. <b>RESULTS</b>: ASC mineralization in dexamethasone or vitamin D3-induced ASCs correlated with both increased ERK1/2 and JNK1/2 activation. ASCs induced without dexamethasone also mineralized, with JNK1/2 signaling possibly mediating this event. No link between cortisone induction and MAPK signaling could be ascertained. ASCs treated with ERK, JNK, or p38MAPK inhibitors showed decreased osteogenic gene expression and diminished mineralization. Mineralization levels were also affected by viruses designed to inhibit or augment ERK1/2 expression and activity. Finally, ASC mineralization appeared to be a balance between MAPK kinase activity and MKP1. <b>CONCLUSIONS</b>: It is likely that MAPK signaling plays a significant role in ASC osteogenesis, affecting differentiation in kinase- and stage-specific manners.
DOI: 10.6084/m9.figshare.4856081
title: Rape: is there an app for that? An empirical analysis of the features of anti-rape apps

description: This study of mobile phone apps designed to prevent sexual violence (<i>n</i> = 215) is a quantitative analysis of all their features (<i>n</i> = 807). We analyze the intended users (victims, bystanders, and perpetrators) and rape prevention strategies of each feature, finding that anti-rape app design generally reinforces and reflects pervasive rape myths, by both targeting potential victims and reinforcing stranger-danger. To demonstrate that these limitations are primarily cultural rather than technological, we conclude by imagining apps with similar technical features that resist rather than reinforce rape myths. This study offers an empirical investigation of the relationship between technical design and social norms, and a unique methodology for uncovering the ideologies that underlie design.