bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of Canopy Morphology on Flow Over a Two‐Dimensional Isolated Ridge
Authors: Ma Yulong , Liu Heping , Banerjee Tirtha , Katul Gabriel G. , Yi Chuixiang , Pardyjak Eric R. 
Published: September 2020

AbstractMomentum and mass exchanges between the atmosphere and forests situated on complex terrain continue to draw significant research attention primarily because of their significance to a plethora of applications. In this paper, we investigated flows behavior on the leeward side of a two‐dimensional forested ridge under neutrally stratified conditions using large‐eddy simulations (LESs). The goal is to understand how variations in leaf area index (LAI), vertical canopy foliage distributions, and forest edge positions affect mean/turbulent flow statistics, momentum fluxes, and onset of recirculation patterns. Although pressure perturbations are dominated by the hill shape, it is demonstrated here that changes in canopy foliage distribution modulate intensities and patterns of the leeward adverse pressure gradients. Such changes in the adverse pressure gradients alter the mean velocity streamlines including the patterns and magnitudes of the leeward downward mean vertical velocity and the velocity variances and momentum flux in the wake region. While a downwind recirculation zone develops in all cases, the details regarding the incipient location and recirculation zone size vary including positions of the separation and reattachment points. Furthermore, changes in the strength and depth of the zone occur due to canopy‐induced changes in adverse pressure gradients, advection, and canopy drag. Because the recirculation zone impacts the local mean advective terms in momentum and scalar exchanges, the simulations here indicate that canopy morphology‐induced changes in the leeward flows have significant implications to both measurements and models of biosphere‐atmosphere exchange over complex terrain.
Salt Marsh Pond Biogeochemistry Changes Hourly‐to‐Yearly but Does Not Scale With Dimensions or Geospatial Position
Authors: Spivak Amanda C. , Denmark Alexander , Gosselin Kelsey M. , Sylva Sean P. 
Published: September 2020

AbstractShallow ponds are expanding in many salt marshes with potential impacts on ecosystem functioning. Determining how pond characteristics change over time and scale with physical dimensions and other spatial predictors could facilitate incorporation of ponds into projections of ecosystem change. We evaluated scaling relationships across six differently sized ponds in three regions of the high marshes within the Plum Island Ecosystems‐Long Term Ecological Research site (MA, USA). We further characterized diel fluctuations in surface water chemistry in two ponds to understand short‐term processes that affect emergent properties (e.g., habitat suitability). Primary producers drove oxygen levels to supersaturation during the day, while nighttime respiration resulted in hypoxic to anoxic conditions. Diel swings in oxygen were mirrored by pH and resulted in successive shifts in redox‐sensitive metabolisms, as indicated by nitrate consumption at dusk followed by peaks in ammonium and then sulfide overnight. Abundances of macroalgae and Ruppia maritima correlated with whole‐pond oxygen metabolism rates, but not with surface area (SA), volume (V), or SA:V. Moreover, there were no clear patterns in primary producer abundances, surface water chemistry, or pond metabolism rates across marsh regions supplied by different tidal creeks or that differed in distance to upland borders or creekbanks. Comparisons with data from 2 years prior demonstrate that plant communities and biogeochemical processes are not in steady state. Factors contributing to variability between ponds and years are unclear but likely include infrequent tidal exchange. Temporal and spatial variability and the absence of scaling relationships complicate the integration of high marsh ponds into ecosystem biogeochemical models.
Conductance Model for Extreme Events: Impact of Auroral Conductance on Space Weather Forecasts
Authors: Mukhopadhyay Agnit , Welling Daniel T. , Liemohn Michael W. , Ridley Aaron J. , Chakraborty Shibaji , Anderson Brian J. 
Published: September 2020

AbstractIonospheric conductance is a crucial factor in regulating the closure of magnetospheric field‐aligned currents through the ionosphere as Hall and Pedersen currents. Despite its importance in predictive investigations of the magnetosphere‐ionosphere coupling, the estimation of ionospheric conductance in the auroral region is precarious in most global first‐principles‐based models. This impreciseness in estimating the auroral conductance impedes both our understanding and predictive capabilities of the magnetosphere‐ionosphere system during extreme space weather events. In this article, we address this concern, with the development of an advanced Conductance Model for Extreme Events (CMEE) that estimates the auroral conductance from field‐aligned current values. CMEE has been developed using nonlinear regression over a year's worth of 1‐min resolution output from assimilative maps, specifically including times of extreme driving of the solar wind‐magnetosphere‐ionosphere system. The model also includes provisions to enhance the conductance in the aurora using additional adjustments to refine the auroral oval. CMEE has been incorporated within the Ridley Ionosphere Model (RIM) of the Space Weather Modeling Framework (SWMF) for usage in space weather simulations. This paper compares performance of CMEE against the existing conductance model in RIM, through a validation process for six space weather events. The performance analysis indicates overall improvement in the ionospheric feedback to ground‐based space weather forecasts. Specifically, the model is able to improve the prediction of ionospheric currents, which impact the simulated dB/dt and ΔB, resulting in substantial improvements in dB/dt predictive skill.
N,N-dimethyltryptamine compound found in the hallucinogenic tea ayahuasca, regulates adult neurogenesis in vitro and in vivo
Authors: Morales-Garcia Jose A. , Calleja-Conde Javier , Lopez-Moreno Jose A. , Alonso-Gil Sandra , Sanz-SanCristobal Marina , Riba Jordi , Perez-Castillo Ana 
Published: September 2020

AbstractN,N-dimethyltryptamine (DMT) is a component of the ayahuasca brew traditionally used for ritual and therapeutic purposes across several South American countries. Here, we have examined, in vitro and vivo, the potential neurogenic effect of DMT. Our results demonstrate that DMT administration activates the main adult neurogenic niche, the subgranular zone of the dentate gyrus of the hippocampus, promoting newly generated neurons in the granular zone. Moreover, these mice performed better, compared to control non-treated animals, in memory tests, which suggest a functional relevance for the DMT-induced new production of neurons in the hippocampus. Interestingly, the neurogenic effect of DMT appears to involve signaling via sigma-1 receptor (S1R) activation since S1R antagonist blocked the neurogenic effect. Taken together, our results demonstrate that DMT treatment activates the subgranular neurogenic niche regulating the proliferation of neural stem cells, the migration of neuroblasts, and promoting the generation of new neurons in the hippocampus, therefore enhancing adult neurogenesis and improving spatial learning and memory tasks.
Efficacy of probiotics on digestive disorders and acute respiratory infections: a controlled clinical trial in young Vietnamese children
Authors: Mai Truong Tuyet , Thi Thu Pham , Thi Hang Hoang , Trang Tran Thi Thu , Yui Shintaro , Shigehisa Akira , Tien Vu Thuy , Dung Truong Viet , Nga Phan Bich , Hung Nguyen Trong , Tuyen Le Danh 
Published: September 2020

Abstract
Objectives
To evaluate the efficacy of fermented milk containing Lactobacillus casei strain Shirota (LcS) on the incidence of constipation, diarrhea, acute respiratory infections (ARI), and nutritional status of young Vietnamese children.

Methods
A controlled field trial was conducted with 1003 children (3–5 years old) in Thanh Hoa province in Vietnam. The probiotic group (n = 510) consumed fermented milk 65 mL/day containing 108 CFU/mL of LcS for the 12-week intervention period, whereas the control group (n = 493) was not given any. The incidence of constipation, diarrhea, ARI, and anthropometry in children was determined at baseline, after 4, 8, and 12-week intervention, and after the 4-week follow-up period.

Results
Probiotic drink decreased the incidence of constipation after the 12-week intervention period (12.0% vs. 32.0%, OR = 0.28 (95% CI: 0.21–0.40), p < 0.001), tended to decrease the incidence of diarrhea (4.9% vs. 7.9%, OR = 0.60 (95% CI: 0.35–1.01), p = 0.068), and prevented the occurrence of ARI (15.9% vs. 24.5%, OR = 0.58 (95% CI: 0.42–0.79), p < 0.001), when compared with the control group. In contrast, no probiotic effects were observed for the duration of diarrhea or ARI. Weight gain was higher in the probiotic group than in the control group after 4, 8, and 12-week intervention and after the 4-week follow-up period (p < 0.05).

Conclusions
Daily intake of fermented milk containing LcS strongly prevented the incidence of constipation and ARI in Vietnamese children. This study also revealed the potential effects of the use of a probiotic drink on diarrhea prevention as well as nutritional status improvement.
Realizing a deterministic source of multipartite-entangled photonic qubits
Authors: Besse Jean-Claude , Reuer Kevin , Collodo Michele C. , Wulff Arne , Wernli Lucien , Copetudo Adrian , Malz Daniel , Magnard Paul , Akin Abdulkadir , Gabureac Mihai , Norris Graham J. , Cirac J. Ignacio , Wallraff Andreas , Eichler Christopher 
Published: September 2020

AbstractSources of entangled electromagnetic radiation are a cornerstone in quantum information processing and offer unique opportunities for the study of quantum many-body physics in a controlled experimental setting. Generation of multi-mode entangled states of radiation with a large entanglement length, that is neither probabilistic nor restricted to generate specific types of states, remains challenging. Here, we demonstrate the fully deterministic generation of purely photonic entangled states such as the cluster, GHZ, and W state by sequentially emitting microwave photons from a controlled auxiliary system into a waveguide. We tomographically reconstruct the entire quantum many-body state for up to N = 4 photonic modes and infer the quantum state for even larger N from process tomography. We estimate that localizable entanglement persists over a distance of approximately ten photonic qubits.
Modeling lung perfusion abnormalities to explain early COVID-19 hypoxemia
Authors: Herrmann Jacob , Mori Vitor , Bates Jason H. T. , Suki Béla 
Published: September 2020

AbstractEarly stages of the novel coronavirus disease (COVID-19) are associated with silent hypoxia and poor oxygenation despite relatively minor parenchymal involvement. Although speculated that such paradoxical findings may be explained by impaired hypoxic pulmonary vasoconstriction in infected lung regions, no studies have determined whether such extreme degrees of perfusion redistribution are physiologically plausible, and increasing attention is directed towards thrombotic microembolism as the underlying cause of hypoxemia. Herein, a mathematical model demonstrates that the large amount of pulmonary venous admixture observed in patients with early COVID-19 can be reasonably explained by a combination of pulmonary embolism, ventilation-perfusion mismatching in the noninjured lung, and normal perfusion of the relatively small fraction of injured lung. Although underlying perfusion heterogeneity exacerbates existing shunt and ventilation-perfusion mismatch in the model, the reported hypoxemia severity in early COVID-19 patients is not replicated without either extensive perfusion defects, severe ventilation-perfusion mismatch, or hyperperfusion of nonoxygenated regions.
Viral gene drive in herpesviruses
Authors: Walter Marius , Verdin Eric 
Published: September 2020

AbstractGene drives are genetic modifications designed to propagate in a population with high efficiency. Current gene drive strategies rely on sexual reproduction and are thought to be restricted to sexual organisms. Here, we report on a gene drive system that allows the spread of an engineered trait in populations of DNA viruses and, in particular, herpesviruses. We describe the successful transmission of a gene drive sequence between distinct strains of human cytomegalovirus (human herpesvirus 5) and show that gene drive viruses can efficiently target and replace wildtype populations in cell culture experiments. Moreover, by targeting sequences necessary for viral replication, our results indicate that a viral gene drive can be used as a strategy to suppress a viral infection. Taken together, this work offers a proof of principle for the design of a gene drive in viruses.
Mapping the bacterial metabolic niche space
Authors: Fahimipour Ashkaan K. , Gross Thilo 
Published: September 2020

AbstractThe rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population’s persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.
Ubiquitin and TFIIH-stimulated DDB2 dissociation drives DNA damage handover in nucleotide excision repair
Authors: Ribeiro-Silva Cristina , Sabatella Mariangela , Helfricht Angela , Marteijn Jurgen A. , Theil Arjan F. , Vermeulen Wim , Lans Hannes 
Published: September 2020

AbstractDNA damage sensors DDB2 and XPC initiate global genome nucleotide excision repair (NER) to protect DNA from mutagenesis caused by helix-distorting lesions. XPC recognizes helical distortions by binding to unpaired ssDNA opposite DNA lesions. DDB2 binds to UV-induced lesions directly and facilitates efficient recognition by XPC. We show that not only lesion-binding but also timely DDB2 dissociation is required for DNA damage handover to XPC and swift progression of the multistep repair reaction. DNA-binding-induced DDB2 ubiquitylation and ensuing degradation regulate its homeostasis to prevent excessive lesion (re)binding. Additionally, damage handover from DDB2 to XPC coincides with the arrival of the TFIIH complex, which further promotes DDB2 dissociation and formation of a stable XPC-TFIIH damage verification complex. Our results reveal a reciprocal coordination between DNA damage recognition and verification within NER and illustrate that timely repair factor dissociation is vital for correct spatiotemporal control of a multistep repair process.
Extradural Motor Cortex Stimulation might improve episodic and working memory in patients with Parkinson’s disease
Authors: Piano Carla , Ciavarro Marco , Bove Francesco , Di Giuda Daniela , Cocciolillo Fabrizio , Bentivoglio Anna Rita , Cioni Beatrice , Tufo Tommaso , Calabresi Paolo , Daniele Antonio 
Published: September 2020

AbstractElectric Extradural Motor Cortex Stimulation (EMCS) is a neurosurgical procedure suggested for treatment of patients with advanced Parkinson’s disease (PD). We report two PD patients treated by EMCS, who experienced worsening of motor symptoms and cognition 5 years after surgery, when EMCS batteries became discharged. One month after EMCS restoration, they experienced a subjective improvement of motor symptoms and cognition. Neuropsychological assessments were carried out before replacement of batteries (off-EMCS condition) and 6 months afterward (on-EMCS condition). As compared to off-EMCS condition, in on-EMCS condition both patients showed an improvement on tasks of verbal episodic memory and backward spatial short-term/working memory task, and a decline on tasks of selective visual attention and forward spatial short-term memory. These findings suggest that in PD patients EMCS may induce slight beneficial effects on motor symptoms and cognitive processes involved in verbal episodic memory and in active manipulation of information stored in working memory.
Polyphyletic origin, intracellular invasion, and meiotic genes in the putatively asexual agamococcidians (Apicomplexa incertae sedis)
Authors: Miroliubova Tatiana S. , Simdyanov Timur G. , Mikhailov Kirill V. , Aleoshin Vladimir V. , Janouškovec Jan , Belova Polina A. , Paskerova Gita G. 
Published: September 2020

AbstractAgamococcidians are enigmatic and poorly studied parasites of marine invertebrates with unexplored diversity and unclear relationships to other sporozoans such as the human pathogens Plasmodium and Toxoplasma. It is believed that agamococcidians are not capable of sexual reproduction, which is essential for life cycle completion in all well studied parasitic apicomplexans. Here, we describe three new species of agamococcidians belonging to the genus Rhytidocystis. We examined their cell morphology and ultrastructure, resolved their phylogenetic position by using near-complete rRNA operon sequences, and searched for genes associated with meiosis and oocyst wall formation in two rhytidocystid transcriptomes. Phylogenetic analyses consistently recovered rhytidocystids as basal coccidiomorphs and away from the corallicolids, demonstrating that the order Agamococcidiorida Levine, 1979 is polyphyletic. Light and transmission electron microscopy revealed that the development of rhytidocystids begins inside the gut epithelial cells, a characteristic which links them specifically with other coccidiomorphs to the exclusion of gregarines and suggests that intracellular invasion evolved early in the coccidiomorphs. We propose a new superorder Eococcidia for early coccidiomorphs. Transcriptomic analysis demonstrated that both the meiotic machinery and oocyst wall proteins are preserved in rhytidocystids. The conservation of meiotic genes and ultrastructural similarity of rhytidocystid trophozoites to macrogamonts of true coccidians point to an undescribed, cryptic sexual process in the group.
Sex differences of inflammatory and immune response in pups of Wistar rats with SIRS
Authors: Kosyreva Anna M. , Dzhalilova Dzhuliia Sh. , Makarova Olga V. , Tsvetkov Ivan S. , Zolotova Natalia A. , Diatroptova Marina A. , Ponomarenko Elena A. , Mkhitarov Vladimir A. , Khochanskiy Dmitriy N. , Mikhailova Liliya P. 
Published: September 2020

AbstractIt is a common fact, that the content of sex hormones in humans and animals varies in different age periods. The functional state of the immune system also changes with age. However, sex differences studies of inflammatory and immune responses during puberty prevail in literature. Investigation of immune responses to LPS peculiarities in prepubertal females and males may contribute to the development of more effective immunotherapy and minimize side effects of children vaccination. Therefore, the aim of this work was to investigate the LPS-induced SIRS sex differences in prepubertal Wistar rats. Despite the absence of sex differences in estradiol and testosterone levels, LPS-induced inflammatory changes in liver and lungs are more pronounced among males. Males demonstrate the increasing neopterin, corticosterone levels and alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activity. Not less important is that in females, demonstrating less morphological changes in liver and lungs, endotoxin level is tenfold higher, and corticosterone level decreases. Thus, endotoxin cannot be used as a marker of the severity of multiple organ failure in prepubertal period. The LPS-induced immune reactions in females and males are similar and are characterized by immunosuppression. Both females and males have decreased production of cytokines (IL-2, IL-4, TNF-α, TGF-β) and the absolute number of CD3 + and CD3 + CD8 + lymphocytes in blood. The acute atrophy of thymus and apoptosis of thymic cells are revealed in animals of both sexes. However, the number of CD3 + CD4 + T-helpers and CD4 + CD25 + Foxp3 + T-cells decreases only in females with SIRS, and in males there was a decrease of CD45R + B-cells. The least expressed sex differences in immune responses in the prepubertal period can be determined by the low levels of sex steroids and the absence of their immunomodulatory effect. Further studies require the identification of mechanisms, determining the sex differences in the inflammatory and immune responses in prepubertal animals.
Alcohol abrogates human norovirus infectivity in a pH-dependent manner
Authors: Sato Shintaro , Matsumoto Naomi , Hisaie Kota , Uematsu Satoshi 
Published: September 2020

AbstractAlcohol-based disinfectants are widely used for the sanitization of microorganisms, especially those that cause infectious diseases, including viruses. However, since the germicidal mechanism of alcohol is lipolysis, alcohol-based disinfectants appear to have a minimal effect on non-enveloped viruses, such as noroviruses. Because there is no cultivation method for human norovirus (HuNoV) in vitro, murine norovirus and feline calicivirus have been used as surrogates for HuNoV to analyze the efficacy of disinfectant regents. Therefore, whether these disinfectants and their conditions are effective against HuNoVs remain unknown. In this study, we report that ethanol or isopropanol alone can sufficiently suppress GII.4 genotype HuNoV replication in human iPSC-derived intestinal epithelial cells. Additionally, pH adjustments and salting-out may contribute toward the virucidal effect of alcohol against other HuNoV genotypes and cancel the impediment of organic substance contamination, respectively. Therefore, similar to sodium hypochlorite, alcohol-based disinfectants containing electrolytes can be used for HuNoV inactivation.