bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Turbulence‐Resolving Numerical Investigation of Wave‐Supported Gravity Flows
Authors: Yue Liangyi , Cheng Zhen , Hsu Tian‐Jian 
Published: February 2020

AbstractWave‐supported gravity flows (WSGFs) have been identified as a key process driving the offshore delivery of fine sediment across continental shelves. However, our understanding on the various factors controlling the maximum sediment load and the resulting gravity current speed remains incomplete. We adopt a new turbulence‐resolving numerical model for fine sediment transport to investigate the formation, evolution, and termination of WSGFs. We consider the simplest scenario in which fine sediments are supported by the wave‐induced fluid turbulence at a low critical shear stress of erosion over a flat sloping bed. Under the energetic wave condition reported on the Northern California Coast with a shelf slope of 0.005, simulation results show that WSGFs are transitionally turbulent and that the sediment concentration cannot exceed 30 kg/m
(g/L) due to the attenuation of turbulence by the sediment‐induced stable density stratification. Wave direction is found to be important in the resulting gravity current intensity. When waves are in cross‐shelf direction, the downslope current has a maximum velocity of 1.2 cm/s, which increases to 2.1 cm/s when waves propagate in the along‐shelf direction. Further analysis on the wave‐averaged momentum balance confirms that when waves are parallel to the slope (cross‐shelf) direction, the more intense wave‐current interaction results in larger wave‐averaged Reynolds shear stress and thus in a smaller current speed. Findings from this study suggest that the more intense cross‐shelf gravity current observed in the field may be caused by additional processes, which may enhance the sediment‐carrying capacity of flow, such as the ambient current or bedforms.
The megabiota are disproportionately important for biosphere functioning
Authors: Enquist Brian J. , Abraham Andrew J. , Harfoot Michael B. J. , Malhi Yadvinder , Doughty Christopher E. 
Published: February 2020

AbstractA prominent signal of the Anthropocene is the extinction and population reduction of the megabiota—the largest animals and plants on the planet. However, we lack a predictive framework for the sensitivity of megabiota during times of rapid global change and how they impact the functioning of ecosystems and the biosphere. Here, we extend metabolic scaling theory and use global simulation models to demonstrate that (i) megabiota are more prone to extinction due to human land use, hunting, and climate change; (ii) loss of megabiota has a negative impact on ecosystem metabolism and functioning; and (iii) their reduction has and will continue to significantly decrease biosphere functioning. Global simulations show that continued loss of large animals alone could lead to a 44%, 18% and 92% reduction in terrestrial heterotrophic biomass, metabolism, and fertility respectively. Our findings suggest that policies that emphasize the promotion of large trees and animals will have disproportionate impact on biodiversity, ecosystem processes, and climate mitigation.
Compartmentalized microbes and co-cultures in hydrogels for on-demand bioproduction and preservation
Authors: Johnston Trevor G. , Yuan Shuo-Fu , Wagner James M. , Yi Xiunan , Saha Abhijit , Smith Patrick , Nelson Alshakim , Alper Hal S. 
Published: February 2020

AbstractMost mono- and co-culture bioprocess applications rely on large-scale suspension fermentation technologies that are not easily portable, reusable, or suitable for on-demand production. Here, we describe a hydrogel system for harnessing the bioactivity of embedded microbes for on-demand small molecule and peptide production in microbial mono-culture and consortia. This platform bypasses the challenges of engineering a multi-organism consortia by utilizing a temperature-responsive, shear-thinning hydrogel to compartmentalize organisms into polymeric hydrogels that control the final consortium composition and dynamics without the need for synthetic control of mutualism. We demonstrate that these hydrogels provide protection from preservation techniques (including lyophilization) and can sustain metabolic function for over 1 year of repeated use. This approach was utilized for the production of four chemical compounds, a peptide antibiotic, and carbohydrate catabolism by using either mono-cultures or co-cultures. The printed microbe-laden hydrogel constructs’ efficiency in repeated production phases, both pre- and post-preservation, outperforms liquid culture.
Multicomponent molecular memory
Authors: Arcadia Christopher E. , Kennedy Eamonn , Geiser Joseph , Dombroski Amanda , Oakley Kady , Chen Shui-Ling , Sprague Leonard , Ozmen Mustafa , Sello Jason , Weber Peter M. , Reda Sherief , Rose Christopher , Kim Eunsuk , Rubenstein Brenda M. , Rosenstein Jacob K. 
Published: February 2020

AbstractMulticomponent reactions enable the synthesis of large molecular libraries from relatively few inputs. This scalability has led to the broad adoption of these reactions by the pharmaceutical industry. Here, we employ the four-component Ugi reaction to demonstrate that multicomponent reactions can provide a basis for large-scale molecular data storage. Using this combinatorial chemistry we encode more than 1.8 million bits of art historical images, including a Cubist drawing by Picasso. Digital data is written using robotically synthesized libraries of Ugi products, and the files are read back using mass spectrometry. We combine sparse mixture mapping with supervised learning to achieve bit error rates as low as 0.11% for single reads, without library purification. In addition to improved scaling of non-biological molecular data storage, these demonstrations offer an information-centric perspective on the high-throughput synthesis and screening of small-molecule libraries.
TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages
Authors: Bottai Daria , Frigui Wafa , Sayes Fadel , Di Luca Mariagrazia , Spadoni Dalila , Pawlik Alexandre , Zoppo Marina , Orgeur Mickael , Khanna Varun , Hardy David , Mangenot Sophie , Barbe Valerie , Medigue Claudine , Ma Laurence , Bouchier Christiane , Tavanti Arianna , Larrouy-Maumus Gerald , Brosch Roland 
Published: February 2020

AbstractMycobacterium tuberculosis (Mtb) strains are classified into different phylogenetic lineages (L), three of which (L2/L3/L4) emerged from a common progenitor after the loss of the MmpS6/MmpL6-encoding Mtb-specific deletion 1 region (TbD1). These TbD1-deleted “modern” lineages are responsible for globally-spread tuberculosis epidemics, whereas TbD1-intact “ancestral” lineages tend to be restricted to specific geographical areas, such as South India and South East Asia (L1) or East Africa (L7). By constructing and characterizing a panel of recombinant TbD1-knock-in and knock-out strains and comparison with clinical isolates, here we show that deletion of TbD1 confers to Mtb a significant increase in resistance to oxidative stress and hypoxia, which correlates with enhanced virulence in selected cellular, guinea pig and C3HeB/FeJ mouse infection models, the latter two mirroring in part the development of hypoxic granulomas in human disease progression. Our results suggest that loss of TbD1 at the origin of the L2/L3/L4 Mtb lineages was a key driver for their global epidemic spread and outstanding evolutionary success.
Direct electrical stimulation of the premotor cortex shuts down awareness of voluntary actions
Authors: Fornia Luca , Puglisi Guglielmo , Leonetti Antonella , Bello Lorenzo , Berti Anna , Cerri Gabriella , Garbarini Francesca 
Published: February 2020

AbstractA challenge for neuroscience is to understand the conscious and unconscious processes underlying construction of willed actions. We investigated the neural substrate of human motor awareness during awake brain surgery. In a first experiment, awake patients performed a voluntary hand motor task and verbally monitored their real-time performance, while different brain areas were transiently impaired by direct electrical stimulation (DES). In a second experiment, awake patients retrospectively reported their motor performance after DES. Based on anatomo-clinical evidence from motor awareness disorders following brain damage, the premotor cortex (PMC) was selected as a target area and the primary somatosensory cortex (S1) as a control area. In both experiments, DES on both PMC and S1 interrupted movement execution, but only DES on PMC dramatically altered the patients’ motor awareness, making them unconscious of the motor arrest. These findings endorse PMC as a crucial hub in the anatomo-functional network of human motor awareness.
Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model
Authors: Gilbert Rachel , Torres Medaya , Clemens Rachel , Hateley Shannon , Hosamani Ravikumar , Wade William , Bhattacharya Sharmila 
Published: February 2020

AbstractWhile it has been shown that astronauts suffer immune disorders after spaceflight, the underlying causes are still poorly understood and there are many variables to consider when investigating the immune system in a complex environment. Additionally, there is growing evidence that suggests that not only is the immune system being altered, but the pathogens that infect the host are significantly influenced by spaceflight and ground-based spaceflight conditions. In this study, we demonstrate that Serratia marcescens (strain Db11) was significantly more lethal to Drosophila melanogaster after growth on the International Space Station than ground-based controls, but the increased virulence phenotype of S. marcescens did not persist after the bacterial cultures were passaged on the ground. Increased virulence was also observed in bacteria that were grown in simulated microgravity conditions on the ground using the rotating wall vessel. Increased virulence of the space-flown bacteria was similar in magnitude between wild-type flies and those that were mutants for the well-characterized immune pathways Imd and Toll, suggesting that changes to the host immune system after infection are likely not a major factor contributing towards increased susceptibility of ground-reared flies infected with space-flown bacteria. Characterization of the bacteria shows that at later timepoints spaceflight bacteria grew at a greater rate than ground controls in vitro, and in the host. These results suggest complex physiological changes occurring in pathogenic bacteria in space environments, and there may be novel mechanisms mediating these physiological effects that need to be characterized.
Projecting an ultra-strongly-coupled system in a non-energy-eigenbasis with a driven nonlinear resonator
Authors: Endo Suguru , Matsuzaki Yuichiro , Kakuyanagi Kosuke , Saito Shiro , Lambert Neill , Nori Franco 
Published: February 2020

AbstractWe explore the problem of projecting the ground-state of an ultra-strong-coupled circuit-QED system into a non-energy-eigenstate. As a measurement apparatus we consider a nonlinear driven resonator. We find that the post-measurement state of the nonlinear resonator exhibits a large correlation with the post-measurement state of the ultra-strongly coupled system even when the coupling between measurement device and system is much smaller than the energy scales of the system itself. While the projection is imperfect, we argue that because of the strong nonlinear response of the resonator it works in a practical regime where a linear measurement apparatus would fail.
Temporal variation in nutrient requirements of tea (Camellia sinensis) in China based on QUEFTS analysis
Authors: Tang Sheng , Liu Yanling , Zheng Nan , Li Yu , Ma Qingxu , Xiao Han , Zhou Xuan , Xu Xinpeng , Jiang Taiming , He Ping , Wu Lianghuan 
Published: February 2020

AbstractFertilisation datasets collected from field experiments (n = 21) in tea-producing areas from 2016 to 2018 were used to build a quantitative evaluation of the fertility of tropical soils (QUEFTS) model to estimate nutrient uptake of tea plants, and to investigate relationships between tea yield and nutrient accumulation. The production of 1000 kg spring tea (based on one bud with two young expanding leaves) required 12.2 kg nitrogen (N), 1.2 kg phosphorus (P), and 3.9 kg potassium (K), and the corresponding internal efficiencies (IEs) for N, P, and K were 82.0, 833.3, and 256.4 kg kg−1. To produce 1000 kg summer tea, 9.1 kg N, 0.8 kg P, and 3.1 kg K were required, and the corresponding IEs for N, P, and K were 109.9, 1250.0, and 322.6 kg kg−1. For autumn tea, 8.8 kg N, 1.0 kg P, and 3.2 kg K were required to produce 1000 kg tea, and the corresponding IEs for N, P, and K were 113.6, 1000.0, and 312.5 kg kg−1. Field validation experiments performed in 2019 suggested that the QUEFTS model can appropriately estimate nutrient uptake of tea plants at a certain yield and contribute to developing a fertiliser recommendation strategy for tea production.
A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response
Authors: Xu Dongyang , Cai Ye , Tang Lu , Han Xueer , Gao Fan , Cao Huifen , Qi Fei , Kapranov Philipp 
Published: February 2020

AbstractLong non-coding (lnc) RNAs represent a fascinating class of transcripts that remains highly controversial mainly due to ambiguity surrounding overall biological relevance of these RNAs. Multitude of reverse genetics studies showing functionality of lncRNAs are unfortunately based on assays that are either plagued by non-specific effects and/or cannot unambiguously assign observed phenotypes to the transcript per se. Here, we show application of the novel CRISPR/Cas13 RNA knockdown system that has superior specificity compared to other transcript-targeting knockdown methods like RNAi. We applied this method to a novel widespread subclass of nuclear lncRNAs — very long intergenic non-coding (vlinc) RNAs — in a high-throughput phenotypic assay based on survival challenge in response to anticancer drug treatments. We used multiple layers of controls including mismatch control for each targeting gRNA to ensure uncovering true phenotype-transcript relationships. We found evidence supporting importance for cellular survival for up to 60% of the tested protein-coding mRNAs and, importantly, 64% of vlincRNAs. Overall, this study demonstrates utility of CRISPR/Cas13 as a highly sensitive and specific tool for reverse genetics study of both protein-coding genes and lncRNAs. Furthermore, importantly, this approach provides evidence supporting biological significance of the latter transcripts in anticancer drug response.
The condensed tannins of Okoume (Aucoumea klaineana Pierre): A molecular structure and thermal stability study
Authors: Engozogho Anris Starlin Péguy , Bi Athomo Arsène Bikoro , Safou Tchiama Rodrigue , Santiago-Medina Francisco José , Cabaret Thomas , Pizzi Antonio , Charrier Bertrand 
Published: February 2020

AbstractIn order to promote convenient strategies for the valorization ofAucoumea klaineanaPierre (Okoume) plywood and sawmill wastes industry in the fields of adhesives and composites, the total phenolic content of Okoume bark, sapwood and heartwood was measured. The molecular structure of tannins extracted from the bark was determined by Matrix Assisted Laser Desorption/Ionization Time-Of-Flight (Maldi-ToF) mass spectrometry and Fourier transform infrared spectroscopy (FTIR). The total phenolic content displayed significant difference (p = 0.001) between the bark, sapwood and heartwood which decreased as follows: 6 ± 0.4, 2 ± 0.8 and 0.7 ± 0.1% respectively. The pro-anthocyanidins content was also significantly different (p = 0.01) among the three wood wastes, and the bark was the richest in condensed tannins (4.2 ± 0.4%) compared to the sapwood (0.5 ± 0.1%) and heartwood (0.2 ± 0.2%). Liquid chromatography coupled mass spectroscopy (LC-MS) and Maldi-ToF analysis of the bark showed for the first time that Okoume condensed tannins are fisetinidin, gallocatechin and trihydroxyflavan based monomers and complex polymers obtained with glycosylated units. No free catechin or robitinidin units were detected, whereas distinctive dihydroxy or trihydroxyflavan-3-benzoate dimers were observed in the investigated condensed tannin extracts. FTIR analysis showed the occurrence of glucan- and mannan-like sugars in the condensed tannins, and Maldi-ToF highlighted that these sugars should account for ten glycosylated units chemically bonded with two fisetinidins and one gallocatechin trimer. The condensation of these polyphenols with formaldehyde led to Stiasny numbers of 83.3, 73.3 and 53.3% for the bark, sapwood and heartwood, respectively.
Development of Magnetic Probe for Sentinel Lymph Node Detection in Laparoscopic Navigation for Gastric Cancer Patients
Authors: Kuwahata Akihiro , Tanaka Ryo , Matsuda Sachiko , Amada En , Irino Tomoyuki , Mayanagi Shuhei , Chikaki Shinichi , Saito Itsuro , Tanabe Norio , Kawakubo Hirofumi , Takeuchi Hiroya , Kitagawa Yuko , Kusakabe Moriaki , Sekino Masaki 
Published: February 2020

AbstractNew laparoscopic sentinel lymph node navigation using a dedicated magnetic probe and magnetic nanoparticle tracer for gastric cancer patients allows minimally invasive surgeries. By identifying the sentinel lymph nodes containing magnetic nanoparticles, patients can avoid excessive lymph node extraction without nuclear facilities and radiation exposure. This paper describes the development of the laparoscopic magnetic probe, ACDC-probe, for laparoscopic sentinel lymph node identification utilizing the nonlinear response of the magnetic nanoparticles magnetized by an alternating magnetic field with a static magnetic field. For highly sensitive detection, the ratio of static to alternating magnetic fields was optimized to approximately 5. The longitudinal detection length was approximately 10 mm for 140 μg of iron, and the detectable amount of iron was approximately 280 ng at a distance of 1 mm. To demonstrate the feasibility of laparoscopic detection using the ACDC-probe and magnetic tracers, an experiment was performed on a wild swine. The gastric sentinel lymph node was clearly identified during laparoscopic navigation. These results suggest that the newly developed ACDC-probe is useful for laparoscopic sentinel lymph node detection and this magnetic technique appears to be a promising method for future sentinel lymph node navigation of gastric cancer patients.
In vitro examination of starch digestibility of Saba banana [Musa ‘saba’(Musa acuminata × Musa balbisiana)]: impact of maturity and physical properties of digesta
Authors: Reginio Florencio Collado , Ketnawa Sunantha , Ogawa Yukiharu 
Published: February 2020

AbstractThe digestibility of starch in Saba banana as affected by maturity and physical properties of digesta was investigated. Five maturity stages were identified based on peel color index which also showed significant differences in physicochemical properties and starch granule morphology. The effect of physical properties of digesta was evaluated by monitoring the viscosity throughout the simulated digestion process and comparing two different physical structures of banana: (1) unhomogenized cut samples which have intact tissue structure and (2) homogenized slurry representing disrupted cellular structure. During ripening process, a decrease in starch content was noted with a concomitant formation of sugars and increasing concentration of acids. Green unripe stages showed the highest rate of starch hydrolysis in both physical structures and a decreasing trend was observed as ripening proceeded. The high digesta viscosity values of ripe stages was found to have an inhibitory effect on starch hydrolysis. Similarly, the differences in physical structure of food affected the digestive enzymes efficiency in breaking down starch. These results suggested that the physicochemical changes accompanying maturation and the physical properties (i.e. high viscosity and presence of intact cell structure) of food could significantly impact the rate of starch digestion.
Comparisons between end-effector and exoskeleton rehabilitation robots regarding upper extremity function among chronic stroke patients with moderate-to-severe upper limb impairment
Authors: Lee Stephanie Hyeyoung , Park Gyulee , Cho Duk Youn , Kim Ha Yeon , Lee Ji-Yeong , Kim Suyoung , Park Si-Bog , Shin Joon-Ho 
Published: February 2020

AbstractEnd-effector (EE) and exoskeleton (Exo) robots have not been directly compared previously. The present study aimed to directly compare EE and Exo robots in chronic stroke patients with moderate-to-severe upper limb impairment. This single-blinded, randomised controlled trial included 38 patients with stroke who were admitted to the rehabilitation hospital. The patients were equally divided into EE and Exo groups. Baseline characteristics, including sex, age, stroke type, brain lesion side (left/right), stroke duration, Fugl–Meyer Assessment (FMA)–Upper Extremity score, and Wolf Motor Function Test (WMFT) score, were assessed. Additionally, impairment level (FMA, motor status score), activity (WMFT), and participation (stroke impact scale [SIS]) were evaluated. There were no significant differences in baseline characteristics between the groups. After the intervention, improvements were significantly better in the EE group with regard to activity and participation (WMFT–Functional ability rating scale, WMFT–Time, and SIS–Participation). There was no intervention-related adverse event. The EE robot intervention is better than the Exo robot intervention with regard to activity and participation among chronic stroke patients with moderate-to-severe upper limb impairment. Further research is needed to confirm this novel finding.
TNF-α increases breast cancer stem-like cells through up-regulating TAZ expression via the non-canonical NF-κB pathway
Authors: Liu Wenjing , Lu Xiaoqing , Shi Peiguo , Yang Guangxi , Zhou Zhongmei , Li Wei , Mao Xiaoyun , Jiang Dewei , Chen Ceshi 
Published: February 2020

AbstractBreast cancer patients often suffer from disease relapse and metastasis due to the presence of breast cancer stem-like cells (BCSCs). Numerous studies have reported that high levels of inflammatory factors, including tumor necrosis factor alpha (TNF-α), promote BCSCs. However, the mechanism by which TNF-α promotes BCSCs is unclear. In this study, we demonstrate that TNF-α up-regulates TAZ, a transcriptional co-activator promoting BCSC self-renewal capacity in human breast cancer cell lines. Depletion of TAZ abrogated the increase in BCSCs mediated by TNF-α. TAZ is induced by TNF-α through the non-canonical NF-κB pathway, and our findings suggest that TAZ plays a crucial role in inflammatory factor–promoted breast cancer stemness and could serve as a promising therapeutic target.