bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the propensity for thermally activated β events in metallic glasses via interpretable machine learning
Authors: Wang Qi , Ding Jun , Zhang Longfei , Podryabinkin Evgeny , Shapeev Alexander , Ma Evan 
Published: December 2020

AbstractThe elementary excitations in metallic glasses (MGs), i.e., β processes that involve hopping between nearby sub-basins, underlie many unusual properties of the amorphous alloys. A high-efficacy prediction of the propensity for those activated processes from solely the atomic positions, however, has remained a daunting challenge. Recently, employing well-designed site environment descriptors and machine learning (ML), notable progress has been made in predicting the propensity for stress-activated β processes (i.e., shear transformations) from the static structure. However, the complex tensorial stress field and direction-dependent activation could induce non-trivial noises in the data, limiting the accuracy of the structure-property mapping learned. Here, we focus on the thermally activated elementary excitations and generate high-quality data in several Cu-Zr MGs, allowing quantitative mapping of the potential energy landscape. After fingerprinting the atomic environment with short- and medium-range interstice distribution, ML can identify the atoms with strong resistance or high compliance to thermal activation, at a high accuracy over ML models for stress-driven activation events. Interestingly, a quantitative “between-task” transferring test reveals that our learnt model can also generalize to predict the propensity of shear transformation. Our dataset is potentially useful for benchmarking future ML models on structure-property relationships in MGs.
Clinical utility of genomic sequencing: a measurement toolkit
Authors: Hayeems Robin Z. , Dimmock David , Bick David , Belmont John W. , Green Robert C. , Lanpher Brendan , Jobanputra Vaidehi , Mendoza Roberto , Kulkarni Shashi , Grove Megan E. , Taylor Stacie L. , Ashley Euan ,   Medical Genome Initiative
Published: December 2020

AbstractWhole-genome sequencing (WGS) is positioned to become one of the most robust strategies for achieving timely diagnosis of rare genomic diseases. Despite its favorable diagnostic performance compared to conventional testing strategies, routine use and reimbursement of WGS are hampered by inconsistencies in the definition and measurement of clinical utility. For example, what constitutes clinical utility for WGS varies by stakeholder’s perspective (physicians, patients, families, insurance companies, health-care organizations, and society), clinical context (prenatal, pediatric, critical care, adult medicine), and test purpose (diagnosis, screening, treatment selection). A rapidly evolving technology landscape and challenges associated with robust comparative study design in the context of rare disease further impede progress in this area of empiric research. To address this challenge, an expert working group of the Medical Genome Initiative was formed. Following a consensus-based process, we align with a broad definition of clinical utility and propose a conceptually-grounded and empirically-guided measurement toolkit focused on four domains of utility: diagnostic thinking efficacy, therapeutic efficacy, patient outcome efficacy, and societal efficacy. For each domain of utility, we offer specific indicators and measurement strategies. While we focus on diagnostic applications of WGS for rare germline diseases, this toolkit offers a flexible framework for best practices around measuring clinical utility for a range of WGS applications. While we expect this toolkit to evolve over time, it provides a resource for laboratories, clinicians, and researchers looking to characterize the value of WGS beyond the laboratory.
A randomized controlled double-blind study of rotigotine on neuropsychiatric symptoms in de novo PD
Authors: Castrioto A. , Thobois S. , Anheim M. , Quesada J. L. , Lhommée E. , Klinger H. , Bichon A. , Schmitt E. , Durif F. , Azulay J. P. , Houeto J. L. , Longato N. , Philipps C. , Pelissier P. , Broussolle E. , Moro E. , Tranchant C. , Fraix V. , Krack P. ,   for the Honeymoon study group
Published: December 2020

AbstractManagement of apathy, depression and anxiety in Parkinson’s disease (PD) represents a challenge. Dopamine agonists have been suggested to be effective. This multicenter, randomized (1:1), double-blind study assessed the 6-month effect of rotigotine versus placebo on apathy, depression and anxiety in de novo PD. The primary outcome was the change of apathy, measured with the LARS. The secondary outcomes were the change in depression and anxiety, measured with BDI-2 and STAI-trait and state. Forty-eight drug-naive PD patients were included. The primary outcome was not reached, with a surprisingly high placebo effect on apathy (60%). There was no significant difference in the change of depression at 6 months between rotigotine and placebo. Trait-anxiety was significantly improved by rotigotine compared to placebo (p = 0.04). Compared to placebo, low dose rotigotine significantly improved trait anxiety, but not apathy and depression. The major placebo effect on apathy points towards the importance of a multidisciplinary and tight follow-up in the management of neuropsychiatric symptoms.
Dataset on the 6-year radiocesium transport in rivers near Fukushima Daiichi nuclear power plant
Authors: Taniguchi Keisuke , Onda Yuichi , Smith Hugh G. , Blake William , Yoshimura Kazuya , Yamashiki Yosuke , Kuramoto Takayuki 
Published: December 2020

AbstractRadiocesium released from the Fukushima Daiichi nuclear power plant (FDNPP) and deposited in the terrestrial environment has been transported to the sea through rivers. To study the long-term effect of riverine transport on the remediation process near the FDNPP, a monitoring project was initiated by the University of Tsukuba. It was commissioned by the Ministry of Education, Culture, Sports, Science, and Technology, and the Nuclear Regulatory Commission in June 2011, and was taken over by the Fukushima Prefectural Centre for Environmental Creation from April 2015. The activity concentration and monthly flux of radiocesium in a suspended form were measured in the project. This provides valuable measurement data to evaluate the impact of the accidentally released radiocesium on residents and the marine environment. It can also be used as verification data in the development and testing of numerical models to predict future impacts.
Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes
Authors: Lee Yongjae , Lee Namil , Hwang Soonkyu , Kim Woori , Jeong Yujin , Cho Suhyung , Palsson Bernhard O. , Cho Byung-Kwan 
Published: December 2020

AbstractStreptomyces species are gram-positive bacteria with GC-rich linear genomes and they serve as dominant reservoirs for producing clinically and industrially important secondary metabolites. Genome mining of Streptomyces revealed that each Streptomyces species typically encodes 20–50 secondary metabolite biosynthetic gene clusters (smBGCs), emphasizing their potential for novel compound discovery. Unfortunately, most of smBGCs are uncharacterized in terms of their products and regulation since they are silent under laboratory culture conditions. To translate the genomic potential of Streptomyces to practical applications, it is essential to understand the complex regulation of smBGC expression and to identify the underlying regulatory elements. To progress towards these goals, we applied two Next-Generation Sequencing methods, dRNA-Seq and Term-Seq, to industrially relevant Streptomyces species to reveal the 5´ and 3´ boundaries of RNA transcripts on a genome scale. This data provides a fundamental resource to aid our understanding of Streptomyces’ regulation of smBGC expression and to enhance their potential for secondary metabolite synthesis.
The MoCA dataset, kinematic and multi-view visual streams of fine-grained cooking actions
Authors: Nicora Elena , Goyal Gaurvi , Noceti Nicoletta , Vignolo Alessia , Sciutti Alessandra , Odone Francesca 
Published: December 2020

AbstractMoCA is a bi-modal dataset in which we collect Motion Capture data and video sequences acquired from multiple views, including an ego-like viewpoint, of upper body actions in a cooking scenario. It has been collected with the specific purpose of investigating view-invariant action properties in both biological and artificial systems. Besides that, it represents an ideal test bed for research in a number of fields – including cognitive science and artificial vision – and application domains – as motor control and robotics. Compared to other benchmarks available, MoCA provides a unique compromise for research communities leveraging very different approaches to data gathering: from one extreme of action recognition in the wild – the standard practice nowadays in the fields of Computer Vision and Machine Learning – to motion analysis in very controlled scenarios – as for motor control in biomedical applications. In this work we introduce the dataset and its peculiarities, and discuss a baseline analysis as well as examples of applications for which the dataset is well suited.
Oxidative stress as a hidden cost of attractiveness in postmenopausal women
Authors: Marcinkowska Urszula M. , Ziomkiewicz Anna , Kleisner Karel , Galbarczyk Andrzej , Klimek Magdalena , Sancilio Amelia , Jasienska Grazyna , Bribiescas Richard G. 
Published: December 2020

AbstractPerceived facial attractiveness, a putative marker of high biological fitness, is costly to maintain throughout a lifetime and may cause higher oxidative stress (OS). We investigated the association between the facial features of 97 postmenopausal women and their levels of OS biomarkers 8-hydroxy-2′-deoxyguanosine (8-OHdG), superoxide dismutase (Cu-Zn SOD), and thiobarbituric acid reactive substances (TBARS). In study 1, 966 judges rated the composites (facial averages) of women with higher OS as more attractive, healthier, younger, and less symmetric. In study 2, Geometric Morphometric analysis did not reveal significant differences in facial morphology depending on OS levels. In study 3, measured facial averageness and symmetry were weakly negatively related to 8-OHdG levels. Maintaining higher perceived facial attractiveness may be costly due to increased oxidative damage in the postmenopausal period. These costs may remain hidden during the reproductive period of life due to the protective mechanisms of oxidative shielding and revealed only after menopause when shielding has ceased.
Cylindrical 3D printed configurable ultrasonic lens for subwavelength focusing enhancement
Authors: Castiñeira-Ibáñez Sergio , Tarrazó-Serrano Daniel , Uris Antonio , Rubio Constanza , Minin Oleg V. , Minin Igor V. 
Published: December 2020

AbstractIn this study, we report the characteristics of acoustic jets obtained through a mesoscale (radius less than 5 wavelengths) ABS cylinder made with a 3D printer. We have analyzed the influence of cylinder size on the characteristic parameters of an acoustic jet, such as maximum acoustic intensity at focus, Full Width at Half Maximum and length of Acoustic Jet. FWHM below 0.5 wavelength in AJ was experimentally obtained. It has been observed that there are two operating regimes depending on the cylinder radius: the resonant and the non-resonant. In the resonant regime, the excitation of Whispering Gallery Modes results in optimal parameter values of the acoustic jet. However, as it is a resonant regime, any minimal variation in cylinder size, working frequency or refractive index would make resonance disappear. In non-resonant mode, a phononic crystal has been embedded inside the cylinder and the characteristic parameters of the acoustic jet have been studied. These have been observed to improve. Finally, we have shown that curved acoustic jets can be obtained with the ABS cylinder with a phononic crystal embedded inside.
Effective field theories for interacting boundaries of 3D topological crystalline insulators through bosonisation
Authors: Salgado-Rebolledo Patricio , Palumbo Giandomenico , Pachos Jiannis K. 
Published: December 2020

AbstractHere, we analyse two Dirac fermion species in two spatial dimensions in the presence of general quartic contact interactions. By employing functional bosonisation techniques, we demonstrate that depending on the couplings of the fermion interactions the system can be effectively described by a rich variety of topologically massive gauge theories. Among these effective theories, we obtain an extended Chern–Simons theory with higher order derivatives as well as two coupled Chern–Simons theories. Our formalism allows for a general description of interacting fermions emerging, for example, at the gapped boundary of three-dimensional topological crystalline insulators.
Investigation of polymer-derived Si–(B)–C–N ceramic/reduced graphene oxide composite systems as active catalysts towards the hydrogen evolution reaction
Authors: Hanniet Quentin , Boussmen Moustapha , Barés Jonathan , Huon Vincent , Iatsunskyi Igor , Coy Emerson , Bechelany Mikhael , Gervais Christel , Voiry Damien , Miele Philippe , Salameh Chrystelle 
Published: December 2020

AbstractHydrogen Evolution Reaction (HER) is an attractive technology for chemical conversion of energy. Replacement of platinum with inexpensive and stable electrocatalysts remains a major bottleneck hampering large-scale hydrogen production by using clean and renewable energy sources. Here, we report electrocatalytically active and ultra-stable Polymer-Derived Ceramics towards HER. We successfully prepared ultrathin silicon and carbon (Si–C) based ceramic systems supported on electrically conducting 2D reduced graphene oxide (rGO) nanosheets with promising HER activity by varying the nature and the composition of the ceramic with the inclusion of nitrogen, boron and oxygen. Our results suggest that oxygen-enriched Si-B-C-N/rGO composites (O-SiBCN/rGO) display the strongest catalytic activity leading to an onset potential and a Tafel slope of − 340 mV and ~ 120 mV dec−1respectively. O-SiBCN/rGO electrodes display stability over 170 h with minimal increase of 14% of the overpotential compared to ~ 1700% for commercial platinum nanoparticles. Our study provides new insights on the performance of ceramics as affordable and robust HER catalysts calling for further exploration of the electrocatalytic activity of such unconventional materials.
Quantitative ultrasound assessment of the influence of roughness and healing time on osseointegration phenomena
Authors: Fraulob M. , Vayron R. , Le Cann S. , Lecuelle B. , Hériveaux Y. , Albini Lomami H. , Flouzat Lachaniette C. H. , Haïat G. 
Published: December 2020

AbstractThe evolution of bone tissue quantity and quality in contact with the surface of orthopedic and dental implants is a strong determinant of the surgical outcome but remains difficult to be assessed quantitatively. The aim of this study was to investigate the performance of a quantitative ultrasound (QUS) method to measure bone-implant interface (BII) properties. A dedicated animal model considering coin-shaped titanium implants with two levels of surface roughness (smooth, Sa = 0.49 µm and rough, Sa = 3.5 µm) allowed to work with a reproducible geometry and a planar interface. The implants were inserted in rabbit femurs and tibiae for 7 or 13 weeks. The ultrasonic response of the BII was measured ex vivo, leading to the determination of the 2-D spatial variations of bone in contact with the implant surface. Histological analysis was carried out to determine the bone-implant contact (BIC) ratio. The amplitude of the echo was significantly higher after 7 weeks of healing time compared to 13 weeks, for both smooth (p < 0.01) and rough (p < 0.05) implants. A negative correlation (R = − 0.63) was obtained between the ultrasonic response and the BIC. This QUS technique is more sensitive to changes of BII morphology compared to histological analyses.
Record electron self-cooling in cold-electron bolometers with a hybrid superconductor-ferromagnetic nanoabsorber and traps
Authors: Gordeeva A. V. , Pankratov A. L. , Pugach N. G. , Vasenko A. S. , Zbrozhek V. O. , Blagodatkin A. V. , Pimanov D. A. , Kuzmin L. S. 
Published: December 2020

AbstractThe Cosmic Microwave Background (CMB) radiation is the only observable that allows studying the earliest stage of the Universe. Radioastronomy instruments for CMB investigation require low working temperatures around 100 mK to get the necessary sensitivity. On-chip electron cooling of receivers is a pathway for future space missions due to problems of dilution fridges at low gravity. Here, we demonstrate experimentally that in a Cold-Electron Bolometer (CEB) a theoretical limit of electron cooling down to 65 mK from phonon temperature of 300 mK can be reached. It is possible due to effective withdrawing of hot electrons from the tunnel barrier by double stock, special traps and suppression of Andreev Joule heating in hybrid Al/Fe normal nanoabsorber.
Repurposing of metformin and colchicine reveals differential modulation of acute and chronic kidney injury
Authors: El-Rashid Maryam , Nguyen-Ngo Danny , Minhas Nikita , Meijles Daniel N. , Li Jennifer , Ghimire Kedar , Julovi Sohel , Rogers Natasha M. 
Published: December 2020

AbstractAcute kidney injury (AKI) is a major health problem affecting millions of patients globally. There is no effective treatment for AKI and new therapies are urgently needed. Novel drug development, testing and progression to clinical trials is overwhelmingly expensive. Drug repurposing is a more cost-effective measure. We identified 2 commonly used drugs (colchicine and metformin) that alter inflammatory cell function and signalling pathways characteristic of AKI, and tested them in models of acute and chronic kidney injury to assess therapeutic benefit. We assessed the renoprotective effects of colchicine or metformin in C57BL/6 mice challenged with renal ischemia reperfusion injury (IRI), treated before or after injury. All animals underwent analysis of renal function and biomolecular phenotyping at 24 h, 48 h and 4 weeks after injury. Murine renal tubular epithelial cells were studied in response to in vitro mimics of IRI. Pre-emptive treatment with colchicine or metformin protected against AKI, with lower serum creatinine, improved histological changes and decreased TUNEL staining. Pro-inflammatory cytokine profile and multiple markers of oxidative stress were not substantially different between groups. Metformin augmented expression of multiple autophagic proteins which was reversed by the addition of hydroxychloroquine. Colchicine led to an increase in inflammatory cells within the renal parenchyma. Chronic exposure after acute injury to either therapeutic agent in the context of reduced renal mass did not mitigate the development of fibrosis, with colchicine significantly worsening an ischemic phenotype. These data indicate that colchicine and metformin affect acute and chronic kidney injury differently. This has significant implications for potential drug repurposing, as baseline renal disease must be considered when selecting medication.
UVC light modulates vitamin C and phenolic biosynthesis in acerola fruit: role of increased mitochondria activity and ROS production
Authors: Rabelo Marcela Cristina , Bang Woo Young , Nair Vimal , Alves Ricardo Elesbao , Jacobo-Velázquez Daniel A. , Sreedharan Shareena , de Miranda Maria Raquel Alcântara , Cisneros-Zevallos Luis 
Published: December 2020

AbstractThe effects of ultraviolet-C light (UVC) on vitamin C and phenolic compounds in acerola during postharvest storage were investigated in order to elucidate the mechanism inducing the antioxidant systems. The fruits, stored at 10 °C for 7 days after a hormetic UVC irradiation (two pulses of 0.3 J/cm2), showed significantly less degradation of vitamin C and phenolic compounds than the control without the UVC challenge. UVC activated the L-galactono-1,4-lactone dehydrogenase (GalDH), a key enzyme for vitamin C biosynthesis, and altered the composition of phenolic compounds, through phenolic biosynthesis, in acerola during postharvest storage. UVC also induced reactive oxygen species (ROS) productions at immediate (day 0) and late (day 7) times during postharvest storage through the mitochondrial electron transport chain and NADPH oxidase, respectively. Results suggest that UVC helps in the retention of vitamin C and phenolic content in acerola by altering ascorbic acid and phenolic metabolism through an increase in mitochondrial activity and a ROS-mediated mechanism. Data showed the beneficial effects of UVC on maintenance of nutraceutical quality in acerola during postharvest storage and supplied new insights into understanding the mechanism by which UVC irradiation enhance the antioxidant system in fruits.
T cell signaling and Treg dysfunction correlate to disease kinetics in IL-2Rα-KO autoimmune mice
Authors: Mullins Genevieve N. , Valentine Kristen M. , Al-Kuhlani Mufadhal , Davini Dan , Jensen Kirk D. C. , Hoyer Katrina K. 
Published: December 2020

AbstractIL-2Rα, in part, comprises the high affinity receptor for IL-2, a cytokine important in immune proliferation, activation, and regulation. IL-2Rα deficient mice (IL-2Rα-KO) develop systemic autoimmune disease and die from severe anemia between 18 and 80 days of age. These mice develop kinetically distinct autoimmune progression, with approximately a quarter dying by 21 days of age and half dying after 30 days. This research aims to define immune parameters and cytokine signaling that distinguish cohorts of IL-2Rα-KO mice that develop early- versus late-stage autoimmune disease. To investigate these differences, we evaluated complete blood counts (CBC), antibody binding of RBCs, T cell numbers and activation, hematopoietic progenitor changes, and signaling kinetics, during autoimmune hemolytic anemia (AIHA) and bone marrow failure. We identified several alterations that, when combined, correlate to disease kinetics. Early onset disease correlates with anti-RBC antibodies, lower hematocrit, and reduced IL-7 signaling. CD8 regulatory T cells (Tregs) have enhanced apoptosis in early disease. Further, early and late end stage disease, while largely similar, had several differences suggesting distinct mechanisms drive autoimmune disease kinetics. Therefore, IL-2Rα-KO disease pathology rates, driven by T cell signaling, promote effector T cell activation and expansion and Treg dysfunction.
Learning fine-grained estimation of physiological states from coarse-grained labels by distribution restoration
Authors: Qin Zengyi , Chen Jiansheng , Jiang Zhenyu , Yu Xumin , Hu Chunhua , Ma Yu , Miao Suhua , Zhou Rongsong 
Published: December 2020

AbstractDue to its importance in clinical science, the estimation of physiological states (e.g., the severity of pathological tremor) has aroused growing interest in machine learning community. While the physiological state is a continuous variable, its continuity is lost when the physiological state is quantized into a few discrete classes during recording and labeling. The discreteness introduces misalignment between the true value and its label, meaning that these labels are unfortunately imprecise and coarse-grained. Most previous work did not consider the inaccuracy and directly utilized the coarse labels to train the machine learning algorithms, whose predictions are also coarse-grained. In this work, we propose to learn a precise, fine-grained estimation of physiological states using these coarse-grained ground truths. Established on mathematical rigorous proof, we utilize imprecise labels to restore the probabilistic distribution of precise labels in an approximate order-preserving fashion, then the deep neural network learns from this distribution and offers fine-grained estimation. We demonstrate the effectiveness of our approach in assessing the pathological tremor in Parkinson’s Disease and estimating the systolic blood pressure from bioelectrical signals.