bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of Pore‐Scale Mixing and Mechanical Dispersion to Reaction During Active Spreading by Radial Groundwater Flow
Authors: Neupauer Roseanna M. , Sather Lauren J. , Mays David C. , Crimaldi John P. , Roth Eric J. 
Published: May 2020

AbstractSpreading and mixing are complementary processes that promote reaction of two reactive aqueous solutes present in contiguous plumes in groundwater. Spreading reconfigures the plume geometry, elongating the interface between the plumes, while mixing increases the volume of aquifer occupied by each plume, bringing the solute molecules together to react. Since reaction only occurs where the two solute plumes are in contact with each other, local mechanisms that drive flow and transport near the interface between the plumes control the amount of reaction. This work uses local characteristics of the plumes and the flow field near the plume interface to analyze the relative contributions of pore‐scale mixing and mechanical dispersion to instantaneous, irreversible, bimolecular reaction in a homogeneous aquifer with active spreading caused by radial flow from a well. Two solutes are introduced in sequence at the well, creating concentric circular plumes. We allow for incomplete mixing of the solutes in the pore space, by modeling the pore space as a segregated compartment and a mixed compartment with first‐order mass transfer between the two compartments. We develop semi‐analytical expressions for concentrations of the solutes in both compartments. We found that the relative contribution of mechanical dispersion to reaction increases over time and also increases due to increases in the Peclet number, in the relative source concentration of the chasing solute, and in the mass transfer rate from the segregated compartment to the mixed compartment of the pore space.
Using the Budyko Framework for Calibrating a Global Hydrological Model
Authors: Greve P. , Burek P. , Wada Y. 
Published: May 2020

AbstractGlobal hydrological models (GHMs) have become an established tool to simulate water resources worldwide. Most of the GHMs are however uncalibrated and typically use a set of basic hydrological parameters, that could potentially lead to unrealistic projections of the terrestrial water cycle. The calibration of hydrological models is usually performed by using and comparing modeled to observed discharge. Accurate station data and reliable time series data of discharge are, however, often not available for many parts of the world and classic calibration approaches are therefore not feasible. In this paper, we aim to develop a new calibration approach that requires no additional data, is easy to implement, and substantially improves model performance, especially in regions where uncalibrated model performance is rather poor. This is achieved by using the Budyko framework, which provides a conceptual representation of the long‐term water and energy balance. We use a state‐of‐the‐art GHM and calibrate the model within nine river catchments of different sizes and characteristics. Since observed river discharge is available for these catchments, we are able to compare the Budyko‐based calibration approach to a classic discharge‐based calibration scheme and the uncalibrated model version. In all catchments, the Budyko‐based calibration approach decreases biases and increases model performance compared to the uncalibrated model version although performance improvements obtained through a classic calibration approach are greater. Nonetheless, a Budyko‐based calibration is a valuable, intermediate approach between use of a basic set of a priori hydrological parameters and classical calibration against discharge data.
River Dunes and Tidal Sand Waves: Are They Generated by the Same Physical Mechanism?
Authors: Vittori G. , Blondeaux P. 
Published: May 2020

AbstractMany subaerial and subaqueous morphological patterns are repetitive both in space and time, and a characteristic wavelength L and a characteristic period T can be associated with the bottom forms, along with a migration speed cr=L/T. In this contribution we focus our attention on river dunes, which form under steady flows, and on tidal sand waves, which form under oscillatory flows. Now, it is widely accepted that these bedforms arise because of the instability of the plane interface between the riverbed/seabed, made up of cohesionless sand, and the water flowing over it. However, the physical mechanisms commonly suggested to explain the growth of these two bottom forms differ. In the present contribution, the theories of formation of river dunes and sand waves, based on modal stability analysis, are revisited, and it is shown that the different physical mechanisms proposed to explain the formation of river dunes and sand waves exhibit more similarity than was believed until today.
RETRACTED ARTICLE: Optimization of oncolytic effect of Newcastle disease virus Clone30 by selecting sensitive tumor host and constructing more oncolytic viruses
Authors: Liu Tianyan , Zhang Yu , Cao Yukai , Jiang Shan , Sun Rui , Yin Jiechao , Gao Zhenqiu , Ren Guiping , Wang Zhenzhong , Yu Qingzhong , Sui Guangchao , Sun Xu , Sun Wenying , Xiao Wei , Li Deshan 
Published: May 2020

AbstractThe direct oncolytic effect of Newcastle disease virus (NDV) depends on the following two aspects: the susceptibility of cancer cells to virus infection and the ability of virus itself to lyse cancer cells. First, we investigate the susceptibility of cancer cells to NDV infection, HepG2, MDA-MB-231, and SH-SY5Y cells were susceptible, A549, MCF7, and LoVo cells were less susceptible. To investigate the molecular mechanism responsible for cancer cell susceptibility, transcriptome sequencing was carried out. We found that the levels of alpha-sialic acid acyltransferase were upregulated in MDA-MB-231 cells compared with MCF7 cells, and the interferon was downregulated. Second, to optimize the oncolytic capacity of the wild-type rClone30, a series of chimeric viruses rClone30-Anh(HN), rClone30-Anh(F), and rClone30-Anh(HN-F) were constructed by exchanging the HN gene, F gene or both of non-lytic rClone30 strain with lytic strain Anhinga. rClone30-Anh(F) and rClone30-Anh(HN-F) enhanced the oncolytic effect of the rClone30, and this enhancement is more obvious in the susceptible cells. The oncolytic mechanism of rClone30-Anh(F) was analyzed by transcriptome analyses, in comparison with rClone30, rClone30-Anh(F) upregulated the expression of ATG5, Beclin 1, and MAP1LC3B, thus activating autophagy and promoting the production of syncytia. In conclusion, our study provides a strategy to enhance the oncolytic effect of rClone30.
The glassy solid as a statistical ensemble of crystalline microstates
Authors: Jones Eric B. , Stevanović Vladan 
Published: May 2020

AbstractWe present an alternative and, for the purpose of non-crystalline materials design, a more suitable description of covalent and ionic glassy solids as statistical ensembles of crystalline local minima on the potential energy surface. Motivated by the concept of partially broken ergodicity, we analytically formulate the set of approximations under which the structural features of ergodic systems such as the radial distribution function (RDF) and powder X-ray diffraction (XRD) intensity can be rigorously expressed as statistical ensemble averages over different local minima. Validation is carried out by evaluating these ensemble averages for elemental Si and SiO2 over the local minima obtained through the first-principles random structure sampling that we performed using relatively small simulation cells, thereby restricting the sampling to a set of predominantly crystalline structures. The comparison with XRD and RDF from experiments (amorphous silicon) and molecular dynamics simulations (glassy SiO2) shows excellent agreement, thus supporting the ensemble picture of glasses and opening the door to fully predictive description without the need for experimental inputs.
Robust entanglement preparation against noise by controlling spatial indistinguishability
Authors: Nosrati Farzam , Castellini Alessia , Compagno Giuseppe , Lo Franco Rosario 
Published: May 2020

AbstractInitialization of composite quantum systems into highly entangled states is usually a must to enable their use for quantum technologies. However, unavoidable noise in the preparation stage makes the system state mixed, hindering this goal. Here, we address this problem in the context of identical particle systems within the operational framework of spatially localized operations and classical communication (sLOCC). We define the entanglement of formation for an arbitrary state of two identical qubits. We then introduce an entropic measure of spatial indistinguishability as an information resource. Thanks to these tools we find that spatial indistinguishability, even partial, can be a property shielding nonlocal entanglement from preparation noise, independently of the exact shape of spatial wave functions. These results prove quantum indistinguishability is an inherent control for noise-free entanglement generation.
Giant magnetoresistive biosensors for real-time quantitative detection of protease activity
Authors: Adem Sandeep , Jain Sonal , Sveiven Michael , Zhou Xiahan , O’Donoghue Anthony J. , Hall Drew A. 
Published: May 2020

AbstractProteases are enzymes that cleave proteins and are crucial to physiological processes such as digestion, blood clotting, and wound healing. Unregulated protease activity is a biomarker of several human diseases. Synthetic peptides that are selectively hydrolyzed by a protease of interest can be used as reporter substrates of unregulated protease activity. We developed an activity-based protease sensor by immobilizing magnetic nanoparticles (MNPs) to the surface of a giant magnetoresistive spin-valve (GMR SV) sensor using peptides. Cleavage of these peptides by a protease releases the magnetic nanoparticles resulting in a time-dependent change in the local magnetic field. Using this approach, we detected a significant release of MNPs after 3.5 minutes incubation using just 4 nM of the cysteine protease, papain. In addition, we show that proteases in healthy human urine do not release the MNPs, however addition of 20 nM of papain to the urine samples resulted in a time-dependent change in magnetoresistance. This study lays the foundation for using GMR SV sensors as a platform for real-time, quantitative detection of protease activity in biological fluids.
Transfrontier Conservation Areas and Human-Wildlife Conflict: The Case of the Namibian Component of the Kavango-Zambezi (KAZA) TFCA
Authors: Stoldt Mirja , Göttert Thomas , Mann Carsten , Zeller Ulrich 
Published: May 2020

AbstractOur study deals with human-wildlife conflicts in the Namibian component of the Kavango-Zambezi Transfrontier Conservation Area (KAZA TFCA). The study reconstructs the historical occurrence of selected mammal species and adopts a socio-ecological approach to assess the impact of human dimensions in the KAZA TFCA. Our results reveal pronounced human–wildlife conflicts with considerable impacts on the livelihoods of communities. Human–wildlife conflict has the potential to become a significant contributor to the failure of the TFCA concept. Conflicts are influenced by a growing human population and large mammal species re-colonising formerly abandoned areas. Mapping the occurrence of selected mammal species over time reveals an interesting picture: although conservation initiatives have led to an increase in the population size of selected species, their occurrence is more restricted than in times of heavily decimated wildlife populations. The increasing restriction of wildlife to protected areas reduces the resilience of the ecosystem. To sustainably manage and conserve wildlife populations, a bigger picture including areas outside of the current borders of KAZA TFCA should be considered. This could support re-connecting ecologically important areas for congested populations to move to and reduces the concentration of wildlife and pressure on the land and people of the region.
The brain tracks auditory rhythm predictability independent of selective attention
Authors: Foldal Maja D. , Blenkmann Alejandro O. , Llorens Anaïs , Knight Robert T. , Solbakk Anne-Kristin , Endestad Tor 
Published: May 2020

AbstractThe brain responds to violations of expected rhythms, due to extraction- and prediction of the temporal structure in auditory input. Yet, it is unknown how probability of rhythm violations affects the overall rhythm predictability. Another unresolved question is whether predictive processes are independent of attention processes. In this study, EEG was recorded while subjects listened to rhythmic sequences. Predictability was manipulated by changing the stimulus-onset-asynchrony (SOA deviants) for given tones in the rhythm. When SOA deviants were inserted rarely, predictability remained high, whereas predictability was lower with more frequent SOA deviants. Dichotic tone-presentation allowed for independent manipulation of attention, as specific tones of the rhythm were presented to separate ears. Attention was manipulated by instructing subjects to attend to tones in one ear only, while keeping the rhythmic structure of tones constant. The analyses of event-related potentials revealed an attenuated N1 for tones when rhythm predictability was high, while the N1 was enhanced by attention to tones. Bayesian statistics revealed no interaction between predictability and attention. A right-lateralization of attention effects, but not predictability effects, suggested potentially different cortical processes. This is the first study to show that probability of rhythm violation influences rhythm predictability, independent of attention.
Superparamagnetic iron oxide as a tracer for sentinel lymph node detection in uterine cancer: a pilot study
Authors: Murakami Kosuke , Kotani Yasushi , Suzuki Ayako , Takaya Hisamitsu , Nakai Hidekatsu , Matsuki Mitsuru , Sato Takao , Mandai Masaki , Matsumura Noriomi 
Published: May 2020

AbstractSentinel lymph node (SLN) mapping using dye or radioisotopes has been performed in patients with uterine cancer. Superparamagnetic iron oxide (SPIO) can be handled safely and is taken up by lymph nodes (LNs); however, its efficacy in detecting SLNs in uterine cancer remains unknown. This pilot study evaluated the use of SPIO as a tracer for SLN detection in patients with uterine cancer. SPIO was injected into the uterine cervixes of 15 patients with uterine cancer scheduled for pelvic LN dissection. Magnetic resonance imaging (MRI) was performed preoperatively. Five patients also underwent radioisotope injection and single-photon emission computed tomography/computed tomography. Dissected LNs were stained with iron and examined pathologically. Of the radioisotope-positive LNs, 92% were also SPIO/MRI-positive. SPIO/MRI and iron staining were positively correlated. SLNs were identified by iron staining in 93% of cases. Iron staining was strongly positive in two of the five areas of LN metastasis; these were considered SLNs. Staining was negative or very weak in the other three areas and lymph flow disturbance was considered. SPIO and radioisotopes are taken up similarly by SLNs. SPIO/MRI and iron staining may thus be useful for detection of SLNs and diagnosis of LN metastasis in patients with uterine cancer.
Generation and evaluation of artificial mental health records for Natural Language Processing
Authors: Ive Julia , Viani Natalia , Kam Joyce , Yin Lucia , Verma Somain , Puntis Stephen , Cardinal Rudolf N. , Roberts Angus , Stewart Robert , Velupillai Sumithra 
Published: May 2020

AbstractA serious obstacle to the development of Natural Language Processing (NLP) methods in the clinical domain is the accessibility of textual data. The mental health domain is particularly challenging, partly because clinical documentation relies heavily on free text that is difficult to de-identify completely. This problem could be tackled by using artificial medical data. In this work, we present an approach to generate artificial clinical documents. We apply this approach to discharge summaries from a large mental healthcare provider and discharge summaries from an intensive care unit. We perform an extensive intrinsic evaluation where we (1) apply several measures of text preservation; (2) measure how much the model memorises training data; and (3) estimate clinical validity of the generated text based on a human evaluation task. Furthermore, we perform an extrinsic evaluation by studying the impact of using artificial text in a downstream NLP text classification task. We found that using this artificial data as training data can lead to classification results that are comparable to the original results. Additionally, using only a small amount of information from the original data to condition the generation of the artificial data is successful, which holds promise for reducing the risk of these artificial data retaining rare information from the original data. This is an important finding for our long-term goal of being able to generate artificial clinical data that can be released to the wider research community and accelerate advances in developing computational methods that use healthcare data.
Real-time monitoring of live mycobacteria with a microfluidic acoustic-Raman platform
Authors: Baron Vincent O. , Chen Mingzhou , Hammarstrom Björn , Hammond Robert J. H. , Glynne-Jones Peter , Gillespie Stephen H. , Dholakia Kishan 
Published: May 2020

AbstractTuberculosis (TB) remains a leading cause of death worldwide. Lipid rich, phenotypically antibiotic tolerant, bacteria are more resistant to antibiotics and may be responsible for relapse and the need for long-term TB treatment. We present a microfluidic system that acoustically traps live mycobacteria, M. smegmatis, a model organism for M. tuberculosis. We then perform optical analysis in the form of wavelength modulated Raman spectroscopy (WMRS) on the trapped M. smegmatis for up to eight hours, and also in the presence of isoniazid (INH). The Raman fingerprints of M. smegmatis exposed to INH change substantially in comparison to the unstressed condition. Our work provides a real-time assessment of the impact of INH on the increase of lipids in these mycobacteria, which could render the cells more tolerant to antibiotics. This microfluidic platform may be used to study any microorganism and to dynamically monitor its response to different conditions and stimuli.
Weighted gene correlation network analysis reveals novel regulatory modules associated with recurrent early pregnancy loss
Authors: Li Xiaoxiao , He Yuanqi , Hao Cuifang , Li Xiaona , Li Xue 
Published: May 2020

Abstract
At present, the etiology and pathogenesis of recurrent early pregnancy loss (REPL) are not completely clear. Therefore, identifying the underlying diagnostic and prognostic biomarkers of REPL can provide new ideas for the diagnosis and treatment of REPL. The chip data of REPL (GSE63901) were downloaded from the NCBI Gene Expression Omnibus (GEO) database. Weighted Gene Co-Expression Network Analysis (WGCNA) was used to construct a co-expression module for studying the relationship between gene modules and clinical features. In addition, functional analysis of hub genes in modules of interest was performed. A total of 23 co-expression modules were identified, two of which were most significantly associated with three clinical features. The MEbrown module was positively correlated with cyclin E level and the out-of-phase trait while the MEred module was positively correlated with the effect of progesterone. We identified 17 hub genes in the MEred module. The functional enrichment analysis indicated that such hub genes were mainly involved in pathways related to cellular defense response and natural killer (NK) cell-mediated cytotoxicity. In the MEbrown module, we identified 19 hub genes, which were mainly enriched in cell adhesion molecule production, regulation of cellular response to growth factor stimulus, epithelial cell proliferation, and transforming growth factor-β (TGF-β) signaling pathway. In addition, the hub genes were validated by using other datasets and three true hub genes were finally obtained, namely DOCK2 for the MEred module, and TRMT44 and ERVMER34-1 for the MEbrown module. In conclusion, our results screened potential biomarkers that might contribute to the diagnosis and treatment of REPL.
Adaptations for centromere function in meiosis
Authors: Prosée Reinier F. , Wenda Joanna M. , Steiner Florian A. 
Published: May 2020

Abstract
The aim of mitosis is to segregate duplicated chromosomes equally into daughter cells during cell division. Meiosis serves a similar purpose, but additionally separates homologous chromosomes to produce haploid gametes for sexual reproduction. Both mitosis and meiosis rely on centromeres for the segregation of chromosomes. Centromeres are the specialized regions of the chromosomes that are attached to microtubules during their segregation. In this review, we describe the adaptations and layers of regulation that are required for centromere function during meiosis, and their role in meiosis-specific processes such as homolog-pairing and recombination. Since female meiotic divisions are asymmetric, meiotic centromeres are hypothesized to evolve quickly in order to favor their own transmission to the offspring, resulting in the rapid evolution of many centromeric proteins. We discuss this observation using the example of the histone variant CENP-A, which marks the centromere and is essential for centromere function. Changes in both the size and the sequence of the CENP-A N-terminal tail have led to additional functions of the protein, which are likely related to its roles during meiosis. We highlight the importance of CENP-A in the inheritance of centromere identity, which is dependent on the stabilization, recycling, or re-establishment of CENP-A-containing chromatin during meiosis.
Auditory Processing Differences in Toddlers With Autism Spectrum Disorder
Authors: Jones Maranda K. , Kraus Nina , Bonacina Silvia , Nicol Trent , Otto-Meyer Sebastian , Roberts Megan Y. 
Published: May 2020

Purpose
Auditory processing measures have been used in an attempt to understand the relationship between neurological mechanisms and autism spectrum disorder (ASD) symptomatology in school-age children. The focus of the current study was to understand neural auditory processing in 2- to 3-year-olds with ASD.

Method

Auditory processing measures (click auditory brainstem responses and speech-evoked frequency-following responses) were hypothesized to differ between typically developing children (
n
= 18) and children with ASD (
n
= 18). Auditory processing measures were hypothesized to relate to language development in children with ASD.

Results
The current study found limited differences in auditory processing measures between the two groups. No relationships were found between auditory processing measures and language development measures.

Conclusions
Future research is necessary to characterize auditory processing in toddlers with ASD. Longitudinal approaches should be considered when studying auditory processing in children with ASD in order to explore its developmental relationship with ASD symptomatology.