bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intake of food rich in saturated fat in relation to subclinical atherosclerosis and potential modulating effects from single genetic variants
Authors: Laguzzi Federica , Maitusong Buamina , Strawbridge Rona J. , Baldassarre Damiano , Veglia Fabrizio , Humphries Steve E. , Rauramaa Rainer , Kurl Sudhir , Smit Andries J. , Giral Philippe , Silveira Angela , Tremoli Elena , Hamsten Anders , de Faire Ulf , Gigante Bruna , Leander Karin ,   IMPROVE Study group, Sirtori C. R. , Calabresi L. , Amato M. , Frigerio B. , Ravani A. , Sansaro D. , Tedesco C. , Coggi D. , Capra N. , Bonomi A. , Eriksson P. , Cooper J. , Acharya J. , Savonen K. , Huttunen K. , Rauramaa E. , Penttila I. M. , Törrönen J. , van Gessel A. I. , van Roon A. M. , Nicolai A. , Mulder D. J. , Kontush A. , Carrié A. , Gallo A. , Karppi J. , Nurmi T. , Nyyssönen K. , Tuomainen T. P. , Tuomainen J. , Kauhanen J. , Sennblad B. , Pirro M. , Vaudo G. , Siepi D. , Lupattelli G. , Mannarino M. R. , Bianconi V. 
Published: April 2021

AbstractThe relationship between intake of saturated fats and subclinical atherosclerosis, as well as the possible influence of genetic variants, is poorly understood and investigated. We aimed to investigate this relationship, with a hypothesis that it would be positive, and to explore whether genetics may modulate it, using data from a European cohort including 3,407 participants aged 54–79 at high risk of cardiovascular disease. Subclinical atherosclerosis was assessed by carotid intima-media thickness (C-IMT), measured at baseline and after 30 months. Logistic regression (OR; 95% CI) was employed to assess the association between high intake of food rich in saturated fat (vs. low) and: (1) the mean and the maximum values of C-IMT in the whole carotid artery (C-IMTmean, C-IMTmax), in the bifurcation (Bif-), the common (CC-) and internal (ICA-) carotid arteries at baseline (binary, cut-point ≥ 75th), and (2) C-IMT progression (binary, cut-point > zero). For the genetic-diet interaction analyses, we considered 100,350 genetic variants. We defined interaction as departure from additivity of effects. After age- and sex-adjustment, high intake of saturated fat was associated with increased C-IMTmean (OR:1.27;1.06–1.47), CC-IMTmean (OR:1.22;1.04–1.44) and ICA-IMTmean (OR:1.26;1.07–1.48). However, in multivariate analysis results were no longer significant. No clear associations were observed between high intake of saturated fat and risk of atherosclerotic progression. There was no evidence of interactions between high intake of saturated fat and any of the genetic variants considered, after multiple testing corrections. High intake of saturated fats was not independently associated with subclinical atherosclerosis. Moreover, we did not identify any significant genetic-dietary fat interactions in relation to risk of subclinical atherosclerosis.
Predicting women with depressive symptoms postpartum with machine learning methods
Authors: Andersson Sam , Bathula Deepti R. , Iliadis Stavros I. , Walter Martin , Skalkidou Alkistis 
Published: April 2021

AbstractPostpartum depression (PPD) is a detrimental health condition that affects 12% of new mothers. Despite negative effects on mothers’ and children’s health, many women do not receive adequate care. Preventive interventions are cost-efficient among high-risk women, but our ability to identify these is poor. We leveraged the power of clinical, demographic, and psychometric data to assess if machine learning methods can make accurate predictions of postpartum depression. Data were obtained from a population-based prospective cohort study in Uppsala, Sweden, collected between 2009 and 2018 (BASIC study, n = 4313). Sub-analyses among women without previous depression were performed. The extremely randomized trees method provided robust performance with highest accuracy and well-balanced sensitivity and specificity (accuracy 73%, sensitivity 72%, specificity 75%, positive predictive value 33%, negative predictive value 94%, area under the curve 81%). Among women without earlier mental health issues, the accuracy was 64%. The variables setting women at most risk for PPD were depression and anxiety during pregnancy, as well as variables related to resilience and personality. Future clinical models that could be implemented directly after delivery might consider including these variables in order to identify women at high risk for postpartum depression to facilitate individualized follow-up and cost-effectiveness.
Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Authors: Brandt Miriam I. , Pradillon Florence , Trouche Blandine , Henry Nicolas , Liautard-Haag Cathy , Cambon-Bonavita Marie-Anne , Cueff-Gauchard Valérie , Wincker Patrick , Belser Caroline , Poulain Julie , Arnaud-Haond Sophie , Zeppilli Daniela 
Published: April 2021

AbstractDespite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.
Hypersonic impact properties of pristine and hybrid single and multi-layer C3N and BC3 nanosheets
Authors: Molaei Fatemeh , Eshkalak Kasra Einalipour , Sadeghzadeh Sadegh , Siavoshi Hossein 
Published: April 2021

AbstractCarbon, nitrogen, and boron nanostructures are promising ballistic protection materials due to their low density and excellent mechanical properties. In this study, the ballistic properties of C3N and BC3 nanosheets against hypersonic bullets with Mach numbers greater than 6 were studied. The critical perforation conditions, and thus, the intrinsic impact strength of these 2D materials were determined by simulating ballistic curves of C3N and BC3 monolayers. Furthermore, the energy absorption scaling law with different numbers of layers and interlayer spacing was investigated, for homogeneous or hybrid configurations (alternated stacking of C3N and the BC3). Besides, we created a hybrid sheet using van der Waals bonds between two adjacent sheets based on the hypervelocity impacts of fullerene (C60) molecules utilizing molecular dynamics simulation. As a result, since the higher bond energy between N–C compared to B-C, it was shown that C3N nanosheets have higher absorption energy than BC3. In contrast, in lower impact speeds and before penetration, single-layer sheets exhibited almost similar behavior. Our findings also reveal that in hybrid structures, the C3N layers will improve the ballistic properties of BC3. The energy absorption values with a variable number of layers and variable interlayer distance (X = 3.4 Å and 4X = 13.6 Å) are investigated, for homogeneous or hybrid configurations. These results provide a fundamental understanding of ultra-light multilayered armors' design using nanocomposites based on advanced 2D materials. The results can also be used to select and make 2D membranes and allotropes for DNA sequencing and filtration.
Impact of image compression on deep learning-based mammogram classification
Authors: Jo Yong-Yeon , Choi Young Sang , Park Hyun Woo , Lee Jae Hyeok , Jung Hyojung , Kim Hyo-Eun , Ko Kyounglan , Lee Chan Wha , Cha Hyo Soung , Hwangbo Yul 
Published: April 2021

AbstractImage compression is used in several clinical organizations to help address the overhead associated with medical imaging. These methods reduce file size by using a compact representation of the original image. This study aimed to analyze the impact of image compression on the performance of deep learning-based models in classifying mammograms as “malignant”—cases that lead to a cancer diagnosis and treatment—or “normal” and “benign,” non-malignant cases that do not require immediate medical intervention. In this retrospective study, 9111 unique mammograms–5672 normal, 1686 benign, and 1754 malignant cases were collected from the National Cancer Center in the Republic of Korea. Image compression was applied to mammograms with compression ratios (CRs) ranging from 15 to 11 K. Convolutional neural networks (CNNs) with three convolutional layers and three fully-connected layers were trained using these images to classify a mammogram as malignant or not malignant across a range of CRs using five-fold cross-validation. Models trained on images with maximum CRs of 5 K had an average area under the receiver operating characteristic curve (AUROC) of 0.87 and area under the precision-recall curve (AUPRC) of 0.75 across the five folds and compression ratios. For images compressed with CRs of 10 K and 11 K, model performance decreased (average 0.79 in AUROC and 0.49 in AUPRC). Upon generating saliency maps that visualize the areas each model views as significant for prediction, models trained on less compressed (CR <  = 5 K) images had maps encapsulating a radiologist’s label, while models trained on images with higher amounts of compression had maps that missed the ground truth completely. In addition, base ResNet18 models pre-trained on ImageNet and trained using compressed mammograms did not show performance improvements over our CNN model, with AUROC and AUPRC values ranging from 0.77 to 0.87 and 0.52 to 0.71 respectively when trained and tested on images with maximum CRs of 5 K. This paper finds that while training models on images with increased the robustness of the models when tested on compressed data, moderate image compression did not substantially impact the classification performance of DL-based models.
Short-range UV-LED irradiation in postmenopausal osteoporosis using ovariectomized mice
Authors: Ochiai Satoshi , Nishida Yoshihiro , Higuchi Yoshitoshi , Morita Daigo , Makida Kazuya , Seki Taisuke , Ikuta Kunihiro , Imagama Shiro 
Published: April 2021

AbstractPostmenopausal osteoporosis is crucial condition that reduces the QOL of affected patients just like aged type osteoporosis. The aim of this study was to evaluate the effectiveness of short-range UV-LED irradiation in postmenopausal osteoporosis using ovariectomized mice. Preliminary experiments identified the time of onset of osteoporosis after ovariectomy (8 weeks) in our model. We have set up a total of 4 groups (n = 8/group); vitamin D-repletion with UV irradiation (Vit.D+UV+), vitamin D-repletion without UV irradiation (Vit.D+UV−), vitamin D-deficiency with UV irradiation (Vit.D-UV+), vitamin D-deficiency without UV irradiation (Vit.D-UV−), and. From 8 weeks after ovariectomy, UV was irradiated for 24 weeks. At the time of 16 and 24 weeks’ irradiation, serum Vit.D levels, various markers of bone metabolism, bone mineral density, and bone strength were evaluated, and histological analyses were performed. In addition, muscle strength was analyzed. Serum 25-hydroxyvitamin D [25 (OH) D] levels at 40 and 48 weeks of age were increased in the Vit.D-UV+ group compared to the Vit.D-UV−group. Cortical thickness evaluated with micro-CT and strength of bone were significantly higher in Vit.D-UV+ group than those in Vit.D-UV− group. There was no difference in muscle strength between Vit.D-UV+ group and Vit.D-UV− group. No obvious adverse effects were observed in UV-irradiated mice including skin findings. Short-range UV irradiation may ameliorate postmenopausal osteoporosis associated with a state of vitamin D deficiency.
Computing inelastic neutron scattering spectra from molecular dynamics trajectories
Authors: Harrelson Thomas F. , Dettmann Makena , Scherer Christoph , Andrienko Denis , Moulé Adam J. , Faller Roland 
Published: April 2021

AbstractInelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation method that is frequently used to simulate semicrystalline/amorphous materials. We illustrate the technique by analyzing spectra of a well-studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) and conclude that our technique provides improved volume and structural variety, but that the classical force field requires improvement before the morphology can be accurately interpreted.
A highly prevalent SINE mutation in the myostatin (MSTN) gene promoter is associated with low circulating myostatin concentration in Thoroughbred racehorses
Authors: O’Hara Victoria , Cowan Amélie , Riddell Dominique , Massey Claire , Martin John , Piercy Richard J. 
Published: April 2021

AbstractHorse racing is a popular and financially important industry worldwide and researchers and horse owners are interested in genetic and training influences that maximise athletic performance. An association has been found between the presence of a short interspersed nuclear element (SINE) mutation in the myostatin (MSTN) gene promoter and optimal race distance in Thoroughbred horses. There is previous laboratory evidence that this mutation reduces MSTN expression in a cell culture model and influences skeletal muscle fibre type proportions in horses. Manipulating MSTN expression has been proposed for illicit gene doping in human and equine athletes and already, researchers have generated homozygous and heterozygous MSTN-null horse embryos following CRISPR/Cas9 editing at the equine MSTN locus and nuclear transfer, aiming artificially to enhance performance. To date however, the role of the naturally-occurring equine MSTN SINE mutation in vivo has remained unclear; here we hypothesised that it reduces, but does not ablate circulating myostatin expression. Following validation of an ELISA for detection of myostatin in equine serum and using residual whole blood and serum samples from 176 Thoroughbred racehorses under identical management, horses were genotyped for the SINE mutation by PCR and their serum myostatin concentrations measured. In our population, the proportions of SINE homozygotes, heterozygotes and normal horses were 27%, 46% and 27% respectively. Results indicated that horses that are homozygous for the SINE mutation have detectable, but significantly lower (p < 0.0001) serum myostatin concentrations (226.8 pg/ml; 69.3–895.4 pg/ml; median; minimum–maximum) than heterozygous (766 pg/ml; 64.6–1182 pg/ml) and normal horses (1099 pg/ml; 187.8–1743 pg/ml). Heterozygotes have significantly lower (p < 0.0001) myostatin concentrations than normal horses. Variation in serum myostatin concentrations across horses was not influenced by age or sex. This is the first study to reveal the direct functional effect of a highly prevalent mutation in the equine MSTN gene associated with exercise performance. Determining the reason for variation in expression of myostatin within SINE-genotyped groups might identify additional performance-associated environmental or genetic influences in Thoroughbreds. Understanding the mechanism by which altered myostatin expression influences skeletal muscle fibre type remains to be determined.
Preference of Proteomonas sulcata anion channelrhodopsin for NO3− revealed using a pH electrode method
Authors: Kikuchi Chihiro , Kurane Hina , Watanabe Takuma , Demura Makoto , Kikukawa Takashi , Tsukamoto Takashi 
Published: April 2021

AbstractIon channel proteins are physiologically important molecules in living organisms. Their molecular functions have been investigated using electrophysiological methods, which enable quantitative, precise and advanced measurements and thus require complex instruments and experienced operators. For simpler and easier measurements, we measured the anion transport activity of light-gated anion channelrhodopsins (ACRs) using a pH electrode method, which has already been established for ion pump rhodopsins. Using that method, we successfully measured the anion transport activity and its dependence on the wavelength of light, i.e. its action spectra, and on the anion species, i.e. its selectivity or preference, of several ACRs expressed in yeast cells. In addition, we identified the strong anion transport activity and the preference for NO3− of an ACR from a marine cryptophyte algae Proteomonas sulcata, named PsuACR_353. Such a preference was discovered for the first time in microbial pump- or channel-type rhodopsins. Nitrate is one of the most stable forms of nitrogen and is used as a nitrogen source by most organisms including plants. Therefore, PsuACR_353 may play a role in NO3− transport and might take part in NO3−-related cellular functions in nature. Measurements of a mutant protein revealed that a Thr residue in the 3rd transmembrane helix, which corresponds to Cys102 in GtACR1, contributed to the preference for NO3−. These findings will be helpful to understand the mechanisms of anion transport, selectivity and preference of PsuACR_353.
Prognostic value of intratumoral Fusobacterium nucleatum and association with immune-related gene expression in oral squamous cell carcinoma patients
Authors: Neuzillet Cindy , Marchais Manon , Vacher Sophie , Hilmi Marc , Schnitzler Anne , Meseure Didier , Leclere Renaud , Lecerf Charlotte , Dubot Coraline , Jeannot Emmanuelle , Klijanienko Jerzy , Mariani Odette , Calugaru Valentin , Hoffmann Caroline , Lesnik Maria , Badois Nathalie , Borcoman Edith , Piaggio Eliane , Kamal Maud , Le Tourneau Christophe , Bieche Ivan 
Published: April 2021

AbstractChanges in the oral microbiome, particularly Fusobacterium nucleatum, are associated with oral squamous cell carcinoma (OSCC). F. nucleatum has been reported to modulate local immunity in cancers. We aimed to assess the association between intratumoral F. nucleatum and clinico-pathological features, relapse, and overall survival (OS) in two independent cohorts of patients with OSCC, and to explore the interplay with immune-related genes. We retrospectively analyzed tissue samples from a first cohort of 122 patients with head and neck squamous cell carcinoma, including 61 OSCC (cohort #1), and a second cohort of 90 additional OSCC (cohort #2). We then performed a sensitivity analysis on the merged cohort of OSCC patients (N = 151). F. nucleatum 16S rRNA gene sequences were quantified using real-time quantitative PCR. The presence of gram-negative bacteria and macrophages was confirmed by LPS and CD163 immunostainings, respectively. F. nucleatum positivity was associated with older age, less alcohol and combined alcohol plus tobacco consumption, and less frequent lymph node invasion. There was a trend for a lower recurrence rate in F. nucleatum-positive cases, with less metastatic relapses compared to F. nucleatum-negative tumors, and significantly longer OS, relapse-free and metastasis-free survival. F. nucleatum status was independently associated with OS in multivariate analysis. Immune-related gene and immunohistochemistry analyses showed that gram-negative bacteria load inversely correlated with M2 macrophages. F. nucleatum-associated OSCC has a specific immune microenvironment, is more frequent in older, non-drinking patients, and associated with a favorable prognosis.
A robust nitridation technique for fabrication of disordered superconducting TiN thin films featuring phase slip events
Authors: Yadav Sachin , Kaushik Vinay , Saravanan M. P. , Aloysius R. P. , Ganesan V. , Sahoo Sangeeta 
Published: April 2021

AbstractDisorder induced phase slip (PS) events appearing in the current voltage characteristics (IVCs) are reported for two-dimensional TiN thin films produced by a robust substrate mediated nitridation technique. Here, high temperature annealing of Ti/Si3N4 based metal/substrate assembly is the key to produce majority phase TiN accompanied by TiSi2 & elemental Si as minority phases. The method itself introduces different level of disorder intrinsically by tuning the amount of the non-superconducting minority phases that are controlled by annealing temperature (Ta) and the film thickness. The superconducting critical temperature (Tc) strongly depends on Ta and the maximum Tc obtained from the demonstrated technique is about 4.8 K for the thickness range ~ 12 nm and above. Besides, the dynamics of IVCs get modulated by the appearance of intermediated resistive steps for decreased Ta and the steps get more prominent for reduced thickness. Further, the deviation in the temperature dependent critical current (Ic) from the Ginzburg–Landau theoretical limit varies strongly with the thickness. Finally, the Tc, intermediate resistive steps in the IVCs and the depairing current are observed to alter in a similar fashion with Ta and the thickness indicating the robustness of the synthesis process to fabricate disordered nitride-based superconductor.
An anisotropic pore-network model to estimate the shale gas permeability
Authors: Zhang Di , Zhang Xinghao , Guo Haohao , Lin Dantong , Meegoda Jay N. , Hu Liming 
Published: April 2021

AbstractThe permeability of shale is a significant and important design parameter for shale gas extraction. The shale gas permeability is usually obtained based on Darcy flow using standard laboratory permeability tests done on core samples, that do not account for different transport mechanisms at high pressures and anisotropic effects in shales due to nano-scale pore structure. In this study, the permeability of shale is predicted using a pore network model. The characteristics of pore structure can be described by specific parameters, including porosity, pore body and pore throat sizes and distributions and coordination numbers. The anisotropy was incorporated into the model using a coordination number ratio, and an algorithm that was developed for connections of pores in the shale formation. By predicting hydraulic connectivity and comparing it with several high-pressure permeability tests, the proposed three-dimensional pore network model was verified. Results show that the prediction from the anisotropic pore network model is closer to the test results than that based on the isotropic pore network model. The predicted permeability values from numerical simulation using anisotropic pore network model for four shales from Qaidam Basin, China are quite similar to those measured from laboratory tests. This study confirmed that the developed anisotropic three-dimensional pore network model could reasonably represent the natural gas flow in the actual shale formation so that it can be used as a prediction tool.