cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3439058
title: Camera detections of seed station visitors

description: This data set is a result of an observational study conducted in a southern California, semi-arid shrubland (Rancho Jamul Ecological Reserve, Jamul, CA). As a master's student in Biology/Ecology, I was interested in whether seed predators preferentially removed non-native over native seeds. Additionally (and most importantly), I evaluated whether field equipment intended to parse out relative patterns of seed removal between different taxa (birds, rodents, ants) were inhibiting the taxon of interest. More specifically, does the exclusion cage/PVC tube intended to permit access to rodents, but not rabbits and birds, inhibit visitation by rodents?<br><br>I deployed field cameras at every seed station to directly observe seed removal by visitors. In this data set, we collected: the genus of visitor; whether they visited a seed dish (Y/N); if so, if they removed from the open dish (open to all visitors) or the "tube" dish (open only to rodents/insects); if they removed native or non-native seed from the dish; how long they remained at the dish. This study was conducted three times (spring, fall, and winter) across 28 seed stations. <br><br>A separate data set contains the measured seed removal from each side (native vs. non-native) of each dish (open vs. "tube"). <br>
DOI: 10.6084/m9.figshare.3439058.v1
title: Camera detections of seed station visitors

description: This data set is a result of an observational study conducted in a southern California, semi-arid shrubland (Rancho Jamul Ecological Reserve, Jamul, CA). As a master's student in Biology/Ecology, I was interested in whether seed predators preferentially removed non-native over native seeds. Additionally (and most importantly), I evaluated whether field equipment intended to parse out relative patterns of seed removal between different taxa (birds, rodents, ants) were inhibiting the taxon of interest. More specifically, does the exclusion cage/PVC tube intended to permit access to rodents, but not rabbits and birds, inhibit visitation by rodents?<br><br>I deployed field cameras at every seed station to directly observe seed removal by visitors. In this data set, we collected: the genus of visitor; whether they visited a seed dish (Y/N); if so, if they removed from the open dish (open to all visitors) or the "tube" dish (open only to rodents/insects); if they removed native or non-native seed from the dish; how long they remained at the dish. This study was conducted three times (spring, fall, and winter) across 28 seed stations. <br><br>A separate data set contains the measured seed removal from each side (native vs. non-native) of each dish (open vs. "tube"). <br>
DOI: 10.6084/m9.figshare.3439049
title: Supplementary Material for: The Relative Functionality of Freshly Isolated and Cryopreserved Human Adipose-Derived Stromal/Stem Cells

description: The capability of multipotent mesenchymal stem cells to maintain cell viability, phenotype and differentiation ability upon thawing is critical if they are to be banked and used for future therapeutic purposes. In the present study, we examined the effect of 9-10 months of cryostorage on the morphology, immunophenotype, colony-forming unit (CFU) and differentiation capacity of fresh and cryopreserved human adipose-derived stromal/stem cells (ASCs) from the same donors. Cryopreservation did not reduce the CFU frequency and the expression levels of CD29, CD73, CD90 and CD105 remained unchanged with the exception of CD34 and CD45; however, the differentiation capacity of cryopreserved ASCs relative to fresh cells was significantly reduced. While our findings suggest that future studies are warranted to improve cryopreservation methods and agents, cryopreserved ASCs retain sufficient features to ensure their practical utility for both research and clinical applications.
DOI: 10.6084/m9.figshare.3438959
title: Supplementary Material for: A Prospective Study of the Use of Fetal Intelligent Navigation Echocardiography (FINE) to Obtain Standard Fetal Echocardiography Views

description: <b><i>Objective:</i></b> To evaluate the performance of Fetal Intelligent Navigation Echocardiography (FINE) applied to spatiotemporal image correlation (STIC) volume datasets of the normal fetal heart in generating standard fetal echocardiography views. <b><i>Methods:</i></b> In this prospective cohort study of patients with normal fetal hearts (19-30 gestational weeks), one or more STIC volume datasets were obtained of the apical four-chamber view. Each STIC volume successfully obtained was evaluated by STICLoop™ to determine its appropriateness before applying the FINE method. Visualization rates for standard fetal echocardiography views using diagnostic planes and/or Virtual Intelligent Sonographer Assistance (VIS-Assistance®) were calculated. <b><i>Results:</i></b> One or more STIC volumes (total n = 463) were obtained from 246 patients. A single STIC volume per patient was analyzed using the FINE method. In normal cases, FINE was able to generate nine fetal echocardiography views using: (1) diagnostic planes in 76-100% of the cases, (2) VIS-Assistance® in 96-100% of the cases, and (3) a combination of diagnostic planes and/or VIS-Assistance® in 96-100% of the cases. <b><i>Conclusion:</i></b> FINE applied to STIC volumes can successfully generate nine standard fetal echocardiography views in 96-100% of cases in the 2nd and 3rd trimesters. This suggests that the technology can be used as a method of screening for congenital heart disease.
DOI: 10.6084/m9.figshare.3438959.v1
title: Supplementary Material for: A Prospective Study of the Use of Fetal Intelligent Navigation Echocardiography (FINE) to Obtain Standard Fetal Echocardiography Views

description: <b><i>Objective:</i></b> To evaluate the performance of Fetal Intelligent Navigation Echocardiography (FINE) applied to spatiotemporal image correlation (STIC) volume datasets of the normal fetal heart in generating standard fetal echocardiography views. <b><i>Methods:</i></b> In this prospective cohort study of patients with normal fetal hearts (19-30 gestational weeks), one or more STIC volume datasets were obtained of the apical four-chamber view. Each STIC volume successfully obtained was evaluated by STICLoop™ to determine its appropriateness before applying the FINE method. Visualization rates for standard fetal echocardiography views using diagnostic planes and/or Virtual Intelligent Sonographer Assistance (VIS-Assistance®) were calculated. <b><i>Results:</i></b> One or more STIC volumes (total n = 463) were obtained from 246 patients. A single STIC volume per patient was analyzed using the FINE method. In normal cases, FINE was able to generate nine fetal echocardiography views using: (1) diagnostic planes in 76-100% of the cases, (2) VIS-Assistance® in 96-100% of the cases, and (3) a combination of diagnostic planes and/or VIS-Assistance® in 96-100% of the cases. <b><i>Conclusion:</i></b> FINE applied to STIC volumes can successfully generate nine standard fetal echocardiography views in 96-100% of cases in the 2nd and 3rd trimesters. This suggests that the technology can be used as a method of screening for congenital heart disease.
DOI: 10.6084/m9.figshare.3438956
title: Formation of Additive-Containing Nanothermites and Modifications to their Friction Sensitivity

description: Nanothermites can provide high energy densities and reaction rates but can also display extreme friction sensitivities. Additives that provide friction modification offer the potential to reduce the friction sensitivity of nanothermites. In the present work, MoS<sub>2</sub>, graphene, and hexadecane additives were dispersed in MoO<sub>3</sub> prior to nanothermite formation with the aim of reducing friction sensitivity. Nanothermites were subsequently prepared using a palmitic acid–passivated nano-aluminum (L-Al) and additive-containing nano-MoO<sub>3</sub> by the resonant acoustic mixing of dry powders. In general, the incorporation of additives results in a reduction in friction sensitivity with the baseline minimum ignition friction rising from 10 to 120 N using 0.5% wt/wt micrometer-sized MoS<sub>2</sub> or 5% wt/wt hexadecane. However, the relationships between loading and performance are complex and vary by additive; for example, the friction sensitivity dependence using micrometer-diameter MoS<sub>2</sub> displays a maximum at 0.5% wt/wt and declines to 7 N using 5% MoS<sub>2</sub>.
DOI: 10.6084/m9.figshare.3438956.v1
title: Formation of Additive-Containing Nanothermites and Modifications to their Friction Sensitivity

description: Nanothermites can provide high energy densities and reaction rates but can also display extreme friction sensitivities. Additives that provide friction modification offer the potential to reduce the friction sensitivity of nanothermites. In the present work, MoS<sub>2</sub>, graphene, and hexadecane additives were dispersed in MoO<sub>3</sub> prior to nanothermite formation with the aim of reducing friction sensitivity. Nanothermites were subsequently prepared using a palmitic acid–passivated nano-aluminum (L-Al) and additive-containing nano-MoO<sub>3</sub> by the resonant acoustic mixing of dry powders. In general, the incorporation of additives results in a reduction in friction sensitivity with the baseline minimum ignition friction rising from 10 to 120 N using 0.5% wt/wt micrometer-sized MoS<sub>2</sub> or 5% wt/wt hexadecane. However, the relationships between loading and performance are complex and vary by additive; for example, the friction sensitivity dependence using micrometer-diameter MoS<sub>2</sub> displays a maximum at 0.5% wt/wt and declines to 7 N using 5% MoS<sub>2</sub>.
DOI: 10.6084/m9.figshare.3438953
title: Developing immunotherapeutic strategies to target brain tumors

description: <b>Introduction</b>: Recent years have seen rapid growth in cancer treatments that enhance the anti-tumor activities of the immune system. Collectively known as immunotherapy, modulation of the immune system has shown success treating some hematological malignancies, but has yet to be successfully applied to the treatment of patients with brain tumors. <b>Areas covered</b>: This review highlights mechanistic insights from murine studies and compiled recent clinical trial data, focusing on the most aggressive brain tumor, glioblastoma (GBM). The field has recently accumulated a critical mass of data, and we discuss past treatment failures in the context of newly developed approaches now entering clinical trials. This article provides an overview of the immunotherapeutic armamentarium currently in development for the treatment of patients with GBM, who are in dire need of safe and effective therapies. <b>Expert commentary</b>: Themes that emerge include the importance of mitigating the effects of an immunosuppressive tumor microenvironment and the potential for innate immune cell activation to enhance cytotoxic anti-tumor activity. Consideration of these studies as a collective may inform the design of new immunotherapies, as well as the immune monitoring protocols for patients participating in clinical trials
DOI: 10.6084/m9.figshare.3438953.v1
title: Developing immunotherapeutic strategies to target brain tumors

description: <b>Introduction</b>: Recent years have seen rapid growth in cancer treatments that enhance the anti-tumor activities of the immune system. Collectively known as immunotherapy, modulation of the immune system has shown success treating some hematological malignancies, but has yet to be successfully applied to the treatment of patients with brain tumors. <b>Areas covered</b>: This review highlights mechanistic insights from murine studies and compiled recent clinical trial data, focusing on the most aggressive brain tumor, glioblastoma (GBM). The field has recently accumulated a critical mass of data, and we discuss past treatment failures in the context of newly developed approaches now entering clinical trials. This article provides an overview of the immunotherapeutic armamentarium currently in development for the treatment of patients with GBM, who are in dire need of safe and effective therapies. <b>Expert commentary</b>: Themes that emerge include the importance of mitigating the effects of an immunosuppressive tumor microenvironment and the potential for innate immune cell activation to enhance cytotoxic anti-tumor activity. Consideration of these studies as a collective may inform the design of new immunotherapies, as well as the immune monitoring protocols for patients participating in clinical trials
DOI: 10.6084/m9.figshare.3438941
title: Susan Southard: Unveiling the aftermath of nuclear war

description: In this interview, author and theater director Susan Southard discusses her book <i>Nagasaki: Life After Nuclear War</i>, an award-winning history of the atomic bombing of Nagasaki and its enduring impact over 70 years. Southard talks about the physical and emotional impacts of the bombing on its survivors; the differences between the Hiroshima and Nagasaki bombings; and the controversy surrounding the American narrative that the bombings were necessary to end the war and save American lives. She emphasizes the importance of survivors’ stories for putting nuclear war in historical context, and for understanding the ongoing risk of an intentional or accidental nuclear explosion.
DOI: 10.6084/m9.figshare.3438941.v1
title: Susan Southard: Unveiling the aftermath of nuclear war

description: In this interview, author and theater director Susan Southard discusses her book <i>Nagasaki: Life After Nuclear War</i>, an award-winning history of the atomic bombing of Nagasaki and its enduring impact over 70 years. Southard talks about the physical and emotional impacts of the bombing on its survivors; the differences between the Hiroshima and Nagasaki bombings; and the controversy surrounding the American narrative that the bombings were necessary to end the war and save American lives. She emphasizes the importance of survivors’ stories for putting nuclear war in historical context, and for understanding the ongoing risk of an intentional or accidental nuclear explosion.
DOI: 10.6084/m9.figshare.3438938
title: Supplementary Material for: Intrahepatic Size Regulation in a Surgical Model: Liver Resection-Induced Liver Regeneration Counteracts the Local Atrophy following Simultaneous Portal Vein Ligation

description: <b><i>Background/Aim:</i></b> Liver size regulation is based on the balance between hepatic regeneration and atrophy. To achieve a better understanding of intrahepatic size regulation, we explored the size regulation of a portally deprived liver lobe on a liver subjected to concurrent portal vein ligation (PVL) and partial hepatectomy (PHx). <b><i>Materials and Methods:</i></b> Using a surgical rat model consisting of right PVL (rPVL) plus 70% PHx, we evaluated the size regulation of liver lobes 1, 2, 3, and 7 days after the operation in terms of liver weight and hepatocyte proliferation. Portal hyperperfusion was confirmed by measuring portal flow. The portal vascular tree was visualized by injection of a contrast agent followed by CT imaging of explanted livers. Control groups consisted of 70% PHx, rPVL, and sham operation. <b><i>Results:</i></b> The size of the ligated right lobe increased to 1.4-fold on postoperative day 7 when subjected to rPVL + 70% PHx. The right lobe increased to 3-fold when subjected to 70% PHx alone and decreased to 0.3-fold when subjected to rPVL only. The small but significant increase in liver weight after the combined procedure was accompanied by a low proliferative response. In contrast, hepatocyte proliferation was undetectable in the right lobe undergoing atrophy after PVL only. The caudate lobe in the rPVL + 70% PHx group increased to 4.6-fold, which is significantly more than in the other groups. This increase in liver weight was paralleled by persisting portal hyperperfusion and a prolonged proliferative phase of 3 days. <b><i>Conclusions:</i></b> A discontinued portal blood supply does not always result in atrophy of the ligated lobe. The concurrent regenerative stimulus induced by 70% PHx seemed to counteract the local atrophy after a simultaneously performed rPVL, leading to a low but prolonged regenerative response of the portally deprived liver lobe. This observation supports the conclusion that portal flow is not necessary for liver regeneration. The persisting portal hyperperfusion may be crucial for the specific kinetics of prolonged liver regeneration after rPVL + 70% PHx in the portally supplied caudate lobe. Both observations deserve more attention regarding the underlying mechanism in further studies.
DOI: 10.6084/m9.figshare.3438878
title: Smartphone-based Cardiac Rehabilitation Program

description: This data correspond to a manuscript of Plos One (ID : PONE-D-16-16329). We introduced a cardiac rehabilitation program that utilizes only a smartphone, with no external devices. As an efficient guide for cardiac rehabilitation exercise, we developed an application to automatically indicate the exercise intensity by comparing the estimated heart rate with the target heart rate zone. To evaluate HR estimation from our developed application during exercise, we used a modified version of the Bruce protocol, which consists of 5 min of walking for a warm-up, 10 min of jogging, 5 min of rest, and additional 10 min of jogging, and 5 min of waling for cool-down, all on a treadmill. The data are from 32 subjects for motion artifact analysis plus 4 subjects for maximum exercise testing.<sub> </sub><br><br>
DOI: 10.6084/m9.figshare.3438875
title: Saccade and antisaccade data from the BRINK cohort in the MRet Study

description: In the longitudinal dataset from the MRET study, all of the participants were relatively young. In order to assess saccade and antisaccade performance in this population better, we recruited a further group of 37 normally developing participants.
DOI: 10.6084/m9.figshare.3438875.v2
title: Saccade and antisaccade data from the BRINK cohort in the MRet Study

description: In the longitudinal dataset from the MRET study, all of the participants were relatively young. In order to assess saccade and antisaccade performance in this population better, we recruited a further group of 37 normally developing participants.
DOI: 10.6084/m9.figshare.3438875.v1
title: Saccade and antisaccade data from the BRINK cohort in theMRet Study

description: In the longitudinal dataset from the MRET study, all of the participants were relatively young. In order to assess saccade and antisaccade performance in this population better, we recruited a further group of 37 normally developing participants.
DOI: 10.6084/m9.figshare.3438857
title: DATABASEfinal.xlsx

description: Dataset correspondng to the research titled "Decreased kidney graft survival in low immunological risk patients showing inflammation in "normal" protocol biopsies"
DOI: 10.6084/m9.figshare.3438857.v1
title: DATABASEfinal.xlsx

description: Dataset correspondng to the research titled "Decreased kidney graft survival in low immunological risk patients showing inflammation in "normal" protocol biopsies"
DOI: 10.6084/m9.figshare.3438848
title: Rapid and specific hypomethylation of enhancers in endothelial cells during adaptation to cell culturing

description: Epigenetics, including DNA methylation, is one way for a cell to respond to the surrounding environment. Traditionally, DNA methylation has been perceived as a quite stable modification; however, lately, there have been reports of a more dynamic CpG methylation that can be affected by, for example, long-term culturing. We recently reported that methylation in the enhancer of the gene encoding the key fibrinolytic enzyme tissue-type plasminogen activator (t-PA) was rapidly erased during cell culturing. In the present study we used sub-culturing of human umbilical vein endothelial cells (HUVECs) as a model of environmental challenge to examine how fast genome-wide methylation changes can arise. To assess genome-wide DNA methylation, the Infinium HumanMethylation450 BeadChip was used on primary, passage 0, and passage 4 HUVECs. Almost 2% of the analyzed sites changed methylation status to passage 4, predominantly displaying hypomethylation. Sites annotated as enhancers were overrepresented among the differentially methylated sites (DMSs). We further showed that half of the corresponding genes concomitantly altered their expression, most of them increasing in expression. Interestingly, the stroke-related gene <i>HDAC9</i> increased its expression several hundredfold. This study reveals a rapid hypomethylation of CpG sites in enhancer elements during the early stages of cell culturing. As many methods for methylation analysis are biased toward CpG rich promoter regions, we suggest that such methods may not always be appropriate for the study of methylation dynamics. In addition, we found that significant changes in expression arose in genes with enhancer DMSs. <i>HDAC9</i> displayed the most prominent increase in expression, indicating, for the first time, that dynamic enhancer methylation may be central in regulating this important stroke-associated gene.
DOI: 10.6084/m9.figshare.3438848.v1
title: Rapid and specific hypomethylation of enhancers in endothelial cells during adaptation to cell culturing

description: Epigenetics, including DNA methylation, is one way for a cell to respond to the surrounding environment. Traditionally, DNA methylation has been perceived as a quite stable modification; however, lately, there have been reports of a more dynamic CpG methylation that can be affected by, for example, long-term culturing. We recently reported that methylation in the enhancer of the gene encoding the key fibrinolytic enzyme tissue-type plasminogen activator (t-PA) was rapidly erased during cell culturing. In the present study we used sub-culturing of human umbilical vein endothelial cells (HUVECs) as a model of environmental challenge to examine how fast genome-wide methylation changes can arise. To assess genome-wide DNA methylation, the Infinium HumanMethylation450 BeadChip was used on primary, passage 0, and passage 4 HUVECs. Almost 2% of the analyzed sites changed methylation status to passage 4, predominantly displaying hypomethylation. Sites annotated as enhancers were overrepresented among the differentially methylated sites (DMSs). We further showed that half of the corresponding genes concomitantly altered their expression, most of them increasing in expression. Interestingly, the stroke-related gene <i>HDAC9</i> increased its expression several hundredfold. This study reveals a rapid hypomethylation of CpG sites in enhancer elements during the early stages of cell culturing. As many methods for methylation analysis are biased toward CpG rich promoter regions, we suggest that such methods may not always be appropriate for the study of methylation dynamics. In addition, we found that significant changes in expression arose in genes with enhancer DMSs. <i>HDAC9</i> displayed the most prominent increase in expression, indicating, for the first time, that dynamic enhancer methylation may be central in regulating this important stroke-associated gene.