bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective Chemical Delivery Through Multi‐Screen Wells to Enhance Mixing and Reaction of Solute Plumes in Porous Media
Authors: Ye Yu , Zhang Yu , Lu Chunhui , Xie Yifan , Luo Jian 
Published: February 2021

AbstractIn‐situ groundwater remediation is usually limited by the incomplete mixing of reactive species due to creeping flow characteristics and limited dispersion in porous media. In this study, we propose a novel approach to deliver chemicals through a multi‐screen well (MSW) to enhance the in‐situ remediation efficiency without extra energy or labor costs. The basic idea is to separate the injected solution into several plumes to enlarge the contact area between injected chemical compounds and ambient contaminants and enhance the mass exchange flux and reactive mixing. We perform laboratory experiments and numerical simulations of steady‐state instantaneous reactive transport in two‐dimensional porous media. We consider three separate screens in an MSW for the injection of treatment solutions and compare its plume distributions with a classical single‐screen well system. The experimental results confirm our conjecture and demonstrate the reliability of the numerical model. Furthermore, we derive an optimal injection interval of the MSW system by comparing analytical and numerical methods and demonstrate its capability to achieve effective transverse mixing and reaction enhancement. An interval that is smaller than the optimal injection interval leads to the exhaustion of contaminants between the injected plumes and the coalescence of the separate injected plumes at the downgradient portion along the travel distance, which reduces the effectiveness of the MSW system. We also investigate the sensitivity of the injected concentration, individual screen length, transverse dispersivity, and seepage rate on the determination of the optimal injection interval and provide suggestions about the design of an MSW system.
Morphodynamics of Boulder‐Bed Semi‐Alluvial Streams in Northern Fennoscandia: A Flume Experiment to Determine Sediment Self‐Organization
Authors: Polvi L. E. 
Published: February 2021

AbstractIn northern Fennoscandia, semi‐alluvial boulder‐bed channels with coarse glacial legacy sediment are abundant, and due to widespread anthropogenic manipulation during timber‐floating, unimpacted reference reaches are rare. The landscape context of these semi‐alluvial rapids—with numerous mainstem lakes that buffer high flows and sediment connectivity in addition to a regional low sediment yield—contribute to low amounts of fine sediment and incompetent flows to transport boulders. To determine the morphodynamics of semi‐alluvial rapids and potential self‐organization of sediment with multiple high flows, a flume experiment was designed and carried out to mimic conditions in semi‐alluvial rapids in northern Fennoscandia. Two slope setups (2% and 5%) were used to model a range of flows (Q1 (summer high flow), Q2, Q10, and Q50) in a 8 × 1.1 m flume with a sediment distribution analogous to field conditions; bed topography was measured using structure‐from‐motion photogrammetry after each flow to obtain DEMs. No classic steep coarse‐bed channel bedforms (e.g., step‐pools) developed. However, similarly to boulder‐bed channels with low relative submergence, at Q10 and Q50 flows, sediment deposited upstream of boulders and scoured downstream. Because the Q50 flow was not able to rework the channel by disrupting grain‐interlocking from preceding lower flows, transporting boulders, or forming channel‐spanning boulders, the channel‐forming discharge is larger than the Q50. These results have implications for restoration of gravel spawning beds in northern Fennoscandia and highlight the importance of large grains in understanding channel morphodynamics.
Viral vector platforms within the gene therapy landscape
Authors: Bulcha Jote T. , Wang Yi , Ma Hong , Tai Phillip W. L. , Gao Guangping 
Published: February 2021

AbstractThroughout its 40-year history, the field of gene therapy has been marked by many transitions. It has seen great strides in combating human disease, has given hope to patients and families with limited treatment options, but has also been subject to many setbacks. Treatment of patients with this class of investigational drugs has resulted in severe adverse effects and, even in rare cases, death. At the heart of this dichotomous field are the viral-based vectors, the delivery vehicles that have allowed researchers and clinicians to develop powerful drug platforms, and have radically changed the face of medicine. Within the past 5 years, the gene therapy field has seen a wave of drugs based on viral vectors that have gained regulatory approval that come in a variety of designs and purposes. These modalities range from vector-based cancer therapies, to treating monogenic diseases with life-altering outcomes. At present, the three key vector strategies are based on adenoviruses, adeno-associated viruses, and lentiviruses. They have led the way in preclinical and clinical successes in the past two decades. However, despite these successes, many challenges still limit these approaches from attaining their full potential. To review the viral vector-based gene therapy landscape, we focus on these three highly regarded vector platforms and describe mechanisms of action and their roles in treating human disease.
Berberine alleviates visceral hypersensitivity in rats by altering gut microbiome and suppressing spinal microglial activation
Authors: Zhang Jin-dong , Liu Jiao , Zhu Shi-wei , Fang Yuan , Wang Ben , Jia Qiong , Hao Hui-feng , Kao John Y. , He Qi-hua , Song Li-jin , Liu Fei , Zhu Bao-li , Owyang Chung , Duan Li-ping 
Published: February 2021

AbstractAccumulating evidence shows that agents targeting gut dysbiosis are effective for improving symptoms of irritable bowel syndrome (IBS). However, the potential mechanisms remain unclear. In this study we investigated the effects of berberine on the microbiota-gut-brain axis in two rat models of visceral hypersensitivity, i.e., specific pathogen-free SD rats subjected to chronic water avoidance stress (WAS) and treated with berberine (200 mg· kg−1 ·d−1, ig, for 10 days) as well as germ-free (GF) rats subjected to fecal microbiota transplantation (FMT) from a patient with IBS (designated IBS-FMT) and treated with berberine (200 mg· kg−1 ·d−1, ig, for 2 weeks). Before the rats were sacrificed, visceral sensation and depressive behaviors were evaluated. Then colonic tryptase was measured and microglial activation in the dorsal lumbar spinal cord was assessed. The fecal microbiota was profiled using 16S rRNA sequencing, and short chain fatty acids (SCFAs) were measured. We showed that berberine treatment significantly alleviated chronic WAS-induced visceral hypersensitivity and activation of colonic mast cells and microglia in the dorsal lumbar spinal cord. Transfer of fecal samples from berberine-treated stressed donors to GF rats protected against acute WAS. FMT from a patient with IBS induced visceral hypersensitivity and pro-inflammatory phenotype in microglia, while berberine treatment reversed the microglial activation and altered microbial composition and function and SCFA profiles in stools of IBS-FMT rats. We demonstrated that berberine did not directly influence LPS-induced microglial activation in vitro. In both models, several SCFA-producing genera were enriched by berberine treatment, and positively correlated to the morphological parameters of microglia. In conclusion, activation of microglia in the dorsal lumbar spinal cord was involved in the pathogenesis of IBS caused by dysregulation of the microbiota–gut–brain axis, and the berberine-altered gut microbiome mediated the modulatory effects of the agent on microglial activation and visceral hypersensitivity, providing a potential option for the treatment of IBS.
Tetraarsenic hexoxide enhances generation of mitochondrial ROS to promote pyroptosis by inducing the activation of caspase-3/GSDME in triple-negative breast cancer cells
Authors: An Haein , Heo Jin Sun , Kim Pyunggang , Lian Zenglin , Lee Siyoung , Park Jinah , Hong Eunji , Pang Kyoungwha , Park Yuna , Ooshima Akira , Lee Jihee , Son Minjung , Park Hyeyeon , Wu Zhaoyan , Park Kyung-Soon , Kim Seong-Jin , Bae Illju , Yang Kyung-Min 
Published: February 2021

AbstractAlthough tetraarsenic hexoxide is known to exert an anti-tumor effect by inducing apoptosis in various cancer cells, its effect on other forms of regulated cell death remains unclear. Here, we show that tetraarsenic hexoxide induces the pyroptotic cell death through activation of mitochondrial reactive oxygen species (ROS)-mediated caspase-3/gasdermin E (GSDME) pathway, thereby suppressing tumor growth and metastasis of triple-negative breast cancer (TNBC) cells. Interestingly, tetraarsenic hexoxide-treated TNBC cells exhibited specific pyroptotic characteristics, including cell swelling, balloon-like bubbling, and LDH releases through pore formation in the plasma membrane, eventually suppressing tumor formation and lung metastasis of TNBC cells. Mechanistically, tetraarsenic hexoxide markedly enhanced the production of mitochondrial ROS by inhibiting phosphorylation of mitochondrial STAT3, subsequently inducing caspase-3-dependent cleavage of GSDME, which consequently promoted pyroptotic cell death in TNBC cells. Collectively, our findings highlight tetraarsenic hexoxide-induced pyroptosis as a new therapeutic strategy that may inhibit cancer progression of TNBC cells.
Darwinian properties and their trade-offs in autocatalytic RNA reaction networks
Authors: Ameta Sandeep , Arsène Simon , Foulon Sophie , Saudemont Baptiste , Clifton Bryce E. , Griffiths Andrew D. , Nghe Philippe 
Published: February 2021

AbstractDiscovering autocatalytic chemistries that can evolve is a major goal in systems chemistry and a critical step towards understanding the origin of life. Autocatalytic networks have been discovered in various chemistries, but we lack a general understanding of how network topology controls the Darwinian properties of variation, differential reproduction, and heredity, which are mediated by the chemical composition. Using barcoded sequencing and droplet microfluidics, we establish a landscape of thousands of networks of RNAs that catalyze their own formation from fragments, and derive relationships between network topology and chemical composition. We find that strong variations arise from catalytic innovations perturbing weakly connected networks, and that growth increases with global connectivity. These rules imply trade-offs between reproduction and variation, and between compositional persistence and variation along trajectories of network complexification. Overall, connectivity in reaction networks provides a lever to balance variation (to explore chemical states) with reproduction and heredity (persistence being necessary for selection to act), as required for chemical evolution.
Alloying–realloying enabled high durability for Pt–Pd-3d-transition metal nanoparticle fuel cell catalysts
Authors: Wu Zhi-Peng , Caracciolo Dominic T. , Maswadeh Yazan , Wen Jianguo , Kong Zhijie , Shan Shiyao , Vargas Jorge A. , Yan Shan , Hopkins Emma , Park Keonwoo , Sharma Anju , Ren Yang , Petkov Valeri , Wang Lichang , Zhong Chuan-Jian 
Published: February 2021

AbstractAlloying noble metals with non-noble metals enables high activity while reducing the cost of electrocatalysts in fuel cells. However, under fuel cell operating conditions, state-of-the-art oxygen reduction reaction alloy catalysts either feature high atomic percentages of noble metals (>70%) with limited durability or show poor durability when lower percentages of noble metals (<50%) are used. Here, we demonstrate a highly-durable alloy catalyst derived by alloying PtPd (<50%) with 3d-transition metals (Cu, Ni or Co) in ternary compositions. The origin of the high durability is probed by in-situ/operando high-energy synchrotron X-ray diffraction coupled with pair distribution function analysis of atomic phase structures and strains, revealing an important role of realloying in the compressively-strained single-phase alloy state despite the occurrence of dealloying. The implication of the finding, a striking departure from previous perceptions of phase-segregated noble metal skin or complete dealloying of non-noble metals, is the fulfilling of the promise of alloy catalysts for mass commercialization of fuel cells.
Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes
Authors: Wittig Sabine , Ganzella Marcelo , Barth Marie , Kostmann Susann , Riedel Dietmar , Pérez-Lara Ángel , Jahn Reinhard , Schmidt Carla 
Published: February 2021

AbstractSynaptic vesicles are storage organelles for neurotransmitters. They pass through a trafficking cycle and fuse with the pre-synaptic membrane when an action potential arrives at the nerve terminal. While molecular components and biophysical parameters of synaptic vesicles have been determined, our knowledge on the protein interactions in their membranes is limited. Here, we apply cross-linking mass spectrometry to study interactions of synaptic vesicle proteins in an unbiased approach without the need for specific antibodies or detergent-solubilisation. Our large-scale analysis delivers a protein network of vesicle sub-populations and functional assemblies including an active and an inactive conformation of the vesicular ATPase complex as well as non-conventional arrangements of the luminal loops of SV2A, Synaptophysin and structurally related proteins. Based on this network, we specifically target Synaptobrevin-2, which connects with many proteins, in different approaches. Our results allow distinction of interactions caused by ‘crowding’ in the vesicle membrane from stable interaction modules.
Carbon dioxide utilization in concrete curing or mixing might not produce a net climate benefit
Authors: Ravikumar Dwarakanath , Zhang Duo , Keoleian Gregory , Miller Shelie , Sick Volker , Li Victor 
Published: February 2021

AbstractCarbon capture and utilization for concrete production (CCU concrete) is estimated to sequester 0.1 to 1.4 gigatons of carbon dioxide (CO2) by 2050. However, existing estimates do not account for the CO2 impact from the capture, transport and utilization of CO2, change in compressive strength in CCU concrete and uncertainty and variability in CCU concrete production processes. By accounting for these factors, we determine the net CO2 benefit when CCU concrete produced from CO2 curing and mixing substitutes for conventional concrete. The results demonstrate a higher likelihood of the net CO2 benefit of CCU concrete being negative i.e. there is a net increase in CO2 in 56 to 68 of 99 published experimental datasets depending on the CO2 source. Ensuring an increase in compressive strength from CO2 curing and mixing and decreasing the electricity used in CO2 curing are promising strategies to increase the net CO2 benefit from CCU concrete.
The singularity response reveals entrainment properties of the plant circadian clock
Authors: Masuda Kosaku , Tokuda Isao T. , Nakamichi Norihito , Fukuda Hirokazu 
Published: February 2021

AbstractCircadian clocks allow organisms to synchronize their physiological processes to diurnal variations. A phase response curve allows researchers to understand clock entrainment by revealing how signals adjust clock genes differently according to the phase in which they are applied. Comprehensively investigating these curves is difficult, however, because of the cost of measuring them experimentally. Here we demonstrate that fundamental properties of the curve are recoverable from the singularity response, which is easily measured by applying a single stimulus to a cellular network in a desynchronized state (i.e. singularity). We show that the singularity response of Arabidopsis to light/dark and temperature stimuli depends on the properties of the phase response curve for these stimuli. The measured singularity responses not only allow the curves to be precisely reconstructed but also reveal organ-specific properties of the plant circadian clock. The method is not only simple and accurate, but also general and applicable to other coupled oscillator systems as long as the oscillators can be desynchronized. This simplified method may allow the entrainment properties of the circadian clock of both plants and other species in nature.
Monitoring the microbiome for food safety and quality using deep shotgun sequencing
Authors: Beck Kristen L. , Haiminen Niina , Chambliss David , Edlund Stefan , Kunitomi Mark , Huang B. Carol , Kong Nguyet , Ganesan Balasubramanian , Baker Robert , Markwell Peter , Kawas Ban , Davis Matthew , Prill Robert J. , Krishnareddy Harsha , Seabolt Ed , Marlowe Carl H. , Pierre Sophie , Quintanar André , Parida Laxmi , Dubois Geraud , Kaufman James , Weimer Bart C. 
Published: February 2021

AbstractIn this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species’ viability from total RNA sequencing.
Structural aspects of lesional and non-lesional skin microbiota reveal key community changes in leprosy patients from India
Authors: Bayal Nitin , Nagpal Sunil , Haque Mohammed Monzoorul , Patole Milind S. , Shouche Yogesh , Mande Shekhar C. , Mande Sharmila S. 
Published: February 2021

AbstractAlthough skin is the primary affected organ in Leprosy, the role of the skin microbiome in its pathogenesis is not well understood. Recent reports have shown that skin of leprosy patients (LP) harbours perturbed microbiota which grants inflammation and disease progression. Herein, we present the results of nested Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) which was initially performed for investigating the diversity of bacterial communities from lesional skin (LS) and non-lesional skin (NLS) sites of LP (n = 11). Further, we performed comprehensive analysis of 16S rRNA profiles corresponding to skin samples from participants (n = 90) located in two geographical locations i.e. Hyderabad and Miraj in India. The genusStaphylococcuswas observed to be one of the representative bacteria characterizing healthy controls (HC; n = 30), which in contrast was underrepresented in skin microbiota of LP. Taxa affiliated to phyla Firmicutes and Proteobacteria were found to be signatures of HC and LS, respectively. Observed diversity level changes, shifts in core microbiota, and community network structure support the evident dysbiosis in normal skin microbiota due to leprosy. Insights obtained indicate the need for exploring skin microbiota modulation as a potential therapeutic option for leprosy.
Electro-Quasistatic Animal Body Communication for Untethered Rodent Biopotential Recording
Authors: Sriram Shreeya , Avlani Shitij , Ward Matthew P. , Sen Shreyas 
Published: February 2021

AbstractContinuous multi-channel monitoring of biopotential signals is vital in understanding the body as a whole, facilitating accurate models and predictions in neural research. The current state of the art in wireless technologies for untethered biopotential recordings rely on radiative electromagnetic (EM) fields. In such transmissions, only a small fraction of this energy is received since the EM fields are widely radiated resulting in lossy inefficient systems. Using the body as a communication medium (similar to a ’wire’) allows for the containment of the energy within the body, yielding order(s) of magnitude lower energy than radiative EM communication. In this work, we introduce Animal Body Communication (ABC), which utilizes the concept of using the body as a medium into the domain of untethered animal biopotential recording. This work, for the first time, develops the theory and models for animal body communication circuitry and channel loss. Using this theoretical model, a sub-inch$$^3$$

3

[1″ × 1″ × 0.4″], custom-designed sensor node is built using off the shelf components which is capable of sensing and transmitting biopotential signals, through the body of the rat at significantly lower powers compared to traditional wireless transmissions. In-vivo experimental analysis proves that ABC successfully transmits acquired electrocardiogram (EKG) signals through the body with correlation $$>99\%$$

>
99
%

when compared to traditional wireless communication modalities, with a 50$$\times$$
×
reduction in power consumption.
Improving prediction and assessment of global fires using multilayer neural networks
Authors: Joshi Jaideep , Sukumar Raman 
Published: February 2021

AbstractFires determine vegetation patterns, impact human societies, and are a part of complex feedbacks into the global climate system. Empirical and process-based models differ in their scale and mechanistic assumptions, giving divergent predictions of fire drivers and extent. Although humans have historically used and managed fires, the current role of anthropogenic drivers of fires remains less quantified. Whereas patterns in fire–climate interactions are consistent across the globe, fire–human–vegetation relationships vary strongly by region. Taking a data-driven approach, we use an artificial neural network to learn region-specific relationships between fire and its socio-environmental drivers across the globe. As a result, our models achieve higher predictability as compared to many state-of-the-art fire models, with global spatial correlation of 0.92, monthly temporal correlation of 0.76, interannual correlation of 0.69, and grid-cell level correlation of 0.60, between predicted and observed burned area. Given the current socio-anthropogenic conditions, Equatorial Asia, southern Africa, and Australia show a strong sensitivity of burned area to temperature whereas northern Africa shows a strong negative sensitivity. Overall, forests and shrublands show a stronger sensitivity of burned area to temperature compared to savannas, potentially weakening their status as carbon sinks under future climate-change scenarios.