bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term Pseudogymnoascus destructans surveillance data reveal factors contributing to pathogen presence
Authors: Grider John F. , Russell Robin E. , Ballmann Anne E. , Hefley Trevor J. 
Published: November 2021

AbstractThe disease white‐nose syndrome (WNS) was first recognized in upstate New York in 2006 and has since spread across much of the United States (U.S.), causing severe mortality in several North American bat species. To aid in the identification and monitoring of at‐risk bat populations, we evaluate factors associated with the presence of the causative fungal agent of WNS, Pseudogymnoascus destructans (Pd), in the continental United States. We obtained Pd samples through hibernaculum surveys conducted from 2013 to 2020, with all samples analyzed at the U.S. Geological Survey National Wildlife Health Center. Using generalized additive models, we estimated the likelihood of Pd presence under three different hypotheses: human‐mediated, species‐mediated, and hibernaculum type. In addition to hypothesis‐related predictor variables, a subset of models included a smoothed nonseparable effect of longitude and latitude and a smoothed effect of time since study onset to account for spatial and temporal autocorrelation. Under all hypotheses, models indicated probability of Pd detection is best described by the smoothed nonseparable effect of longitude and latitude and a smoothed effect of time since onset of this study. After accounting for spatial and temporal autocorrelations, only hibernaculum type significantly affected Pd presence, with mines and culverts/tunnels less likely to contain Pd compared with caves. Reduced likelihood of Pd presence in mines and culverts/tunnels bodes well for bats of the western and southern United States, where use of these hibernaculum types is more common. While our findings can help guide monitoring and management efforts, the potential for long‐distance dispersal combined with variation in community composition and hibernation ecology between the western and eastern United States necessitates the continued monitoring of Pd presence.
Targeted next‐generation sequencing of environmental DNA improves detection of invasive European green crab (Carcinus maenas)
Authors: Westfall Kristen Marie , Therriault Thomas W. , Abbott Cathryn L. 
Published: November 2021

AbstractIn the northeast Pacific Ocean, there is high interest in developing eDNA‐based survey methods to aid management of invasive populations of European green crab (Carcinus maenas). Expected benefits are improved sensitivity for early detection of secondary spread and to assess the outcome of eradication efforts. A new eDNA‐based approach we term “targeted next‐generation sequencing (tNGS)” is introduced here and shown to improve detection relative to qPCR at sites with lower green crab CPUE values measured by trapping. DNA standards (gBlock) with starting molecule copies that were 10 to 100 times lower than the qPCR limit of detection returned significant numbers of sequencing reads, which in our field assessments translated to a 7%–10% increase in detection probability from tNGS relative to qPCR at sites with lower CPUE. We also found the number of sequencing reads from tNGS was significantly correlated with green crab CPUE whereas Ct values from qPCR were not. When sources of variation were partitioned for each assay, we found the difference between mean within‐site and mean between‐site variation was much larger and had non‐overlapping confidence intervals for tNGS relative to qPCR, suggesting the former may offer more power for detecting spatial variation in eDNA availability. Results presented here indicate this approach is suitable for species of known low abundances where a positive detection has high economic or environmental consequences, or for labs doing eDNA surveys for whom NGS‐based workflows are operationally more efficient than qPCR given its upward scalability. Any species with an existing qPCR assay can be easily tested with a tNGS assay using the approach presented here. We conclude with a discussion on the fitness for purpose of tNGS vs. qPCR for various applications and on how to best apply molecular surveys in management programs.
A Simple Synthetic Route to Well‐Defined [Pd(NHC)Cl(1‐tBu‐indenyl)] Pre‐catalysts for Cross‐Coupling Reactions
Authors: Liu Yaxu , Scattolin Thomas , Gobbo Alberto , Beliš Marek , Van Hecke Kristof , Nolan Steven P. , Cazin Catherine S. J. 
Published: November 2021

AbstractThe development of robust, more efficient, general, easily accessible Pd(II)–NHC pre‐catalysts remains a key issue in cross‐coupling applications. A selection of well‐defined, air and moisture stable [Pd(NHC)Cl(1‐tBu‐indenyl)] (NHC=IPr, IPrCl, IMes, SIMes, IPr*) pre‐catalysts have been synthesized in good to excellent yields by reacting [Pd(1‐tBu‐indenyl)(μ‐Cl)]2 and various NHC⋅HCl precursors in the presence of the weak base K2CO3 in green acetone. The synthesized Pd(II)‐NHC derivatives displayed excellent catalytic activity in classical Suzuki‐Miyaura and Buchwald–Hartwig reactions, especially when IPrCl is employed as ancillary ligand. Additionally, in the challenging Suzuki‐Miyaura reaction between esters and arylboronic acids, the [Pd(IPr*)Cl(1‐tBu‐indenyl)] complex exhibited the optimum catalytic activity under very mild reaction conditions.
Ionic‐Liquid‐Catalyzed Synthesis of Imines, Benzimidazoles, Benzothiazoles, Quinoxalines and Quinolines through C−N, C−S, and C−C Bond Formation
Authors: Badhani Gaurav , Joshi Abhisek , Adimurthy Subbarayappa 
Published: November 2021

AbstractWe report the tetramethyl ammonium hydroxide catalyzed oxidative coupling of amines and alcohols for the synthesis of imines under metal‐free conditions by utilizing oxygen from air as the terminal oxidant. Under the same conditions, with ortho‐phenylene diamines and 2‐aminobenzenethiols the corresponding benzimidazoles and benzothiazoles were obtained. Quinoxalines were obtained from ortho‐phenylene diamines and 1‐phenylethane‐1,2‐diol, the conditions were then extended to the synthesis of quinoline building blocks by reaction of 2‐amino benzyl alcohols either with 1‐phenylethan‐1‐ol or acetophenone derivatives. The formation of C−N, C−S and C−C bonds was achieved under metal‐free conditions. A broad range of amines (aromatic, aliphatic, cyclic and heteroaromatic) as well as benzylic alcohols including heteroaryl alcohols reacted smoothly and provided the desired products. The mild reaction conditions, commercially available catalyst, metal‐free, good functional‐group tolerance, broad range of products (imines, benzimidazoles, benzothiazoles, quinoxalines and quinolines) and applicability at gram scale reactions are the advantages of the present strategy.
Scalable multiple changepoint detection for functional data sequences
Authors: Harris Trevor , Li Bo , Tucker J. Derek 
Published: November 2021

AbstractWe propose the multiple changepoint isolation (MCI) method for detecting multiple changes in the mean and covariance of a functional process. We first introduce a pair of projections to represent the variability “between” and “within” the functional observations. We then present an augmented fused lasso procedure to split the projections into multiple regions robustly. These regions act to isolate each changepoint away from the others so that the powerful univariate CUSUM statistic can be applied region‐wise to identify the changepoints. Simulations show that our method accurately detects the number and locations of changepoints under many different scenarios. These include light and heavy tailed data, data with symmetric and skewed distributions, sparsely and densely sampled changepoints, and mean and covariance changes. We show that our method outperforms a recent multiple functional changepoint detector and several univariate changepoint detectors applied to our proposed projections. We also show that MCI is more robust than existing approaches and scales linearly with sample size. Finally, we demonstrate our method on a large time series of water vapor mixing ratio profiles from atmospheric emitted radiance interferometer measurements.
Astrocyte reactivity in a mouse model of SCN8A epileptic encephalopathy
Authors: Thompson Jeremy A. , Miralles Raquel M. , Wengert Eric R. , Wagley Pravin K. , Yu Wenxi , Wenker Ian C. , Patel Manoj K. 
Published: November 2021

AbstractObjectiveSCN8A epileptic encephalopathy is caused predominantly by de novo gain‐of‐function mutations in the voltage‐gated sodium channel Nav1.6. The disorder is characterized by early onset of seizures and developmental delay. Most patients with SCN8A epileptic encephalopathy are refractory to current anti‐seizure medications. Previous studies determining the mechanisms of this disease have focused on neuronal dysfunction as Nav1.6 is expressed by neurons and plays a critical role in controlling neuronal excitability. However, glial dysfunction has been implicated in epilepsy and alterations in glial physiology could contribute to the pathology of SCN8A encephalopathy. In the current study, we examined alterations in astrocyte and microglia physiology in the development of seizures in a mouse model of SCN8A epileptic encephalopathy.MethodsUsing immunohistochemistry, we assessed microglia and astrocyte reactivity before and after the onset of spontaneous seizures. Expression of glutamine synthetase and Nav1.6, and Kir4.1 channel currents were assessed in astrocytes in wild‐type (WT) mice and mice carrying the N1768D SCN8A mutation (D/+).ResultsAstrocytes in spontaneously seizing D/+ mice become reactive and increase expression of glial fibrillary acidic protein (GFAP), a marker of astrocyte reactivity. These same astrocytes exhibited reduced barium‐sensitive Kir4.1 currents compared to age‐matched WT mice and decreased expression of glutamine synthetase. These alterations were only observed in spontaneously seizing mice and not before the onset of seizures. In contrast, microglial morphology remained unchanged before and after the onset of seizures.SignificanceAstrocytes, but not microglia, become reactive only after the onset of spontaneous seizures in a mouse model of SCN8A encephalopathy. Reactive astrocytes have reduced Kir4.1‐mediated currents, which would impair their ability to buffer potassium. Reduced expression of glutamine synthetase would modulate the availability of neurotransmitters to excitatory and inhibitory neurons. These deficits in potassium and glutamate handling by astrocytes could exacerbate seizures in SCN8A epileptic encephalopathy. Targeting astrocytes may provide a new therapeutic approach to seizure suppression.
Surrogate probabilistic seismic demand modelling of inelastic single‐degree‐of‐freedom systems for efficient earthquake risk applications
Authors: Gentile Roberto , Galasso Carmine 
Published: November 2021

AbstractThis paper proposes surrogate models (or metamodels) mapping the parameters controlling the dynamic behaviour of inelastic single‐degree‐of‐freedom (SDoF) systems (i.e., force‐displacement capacity curve, hysteretic behaviour) and the parameters of their probabilistic seismic demand model (PSDM, i.e., conditional distribution of an engineering demand parameter [EDP] given a ground‐motion intensity measure [IM]). These metamodels allow the rapid derivation of fragility curves of SDoF representation of structures. Gaussian Process (GP) regression is selected as the metamodelling approach because of their flexibility in implementation, the resulting accuracy and computational efficiency. The metamodel training dataset includes 10,000 SDoF systems analysed via cloud‐based non‐linear time‐history analysis (NLTHA) using recorded ground motions. The proposed GP regressions are tested in predicting the PSDM of both the SDoF database (through ten‐fold cross validation) and eight realistic reinforced concrete (RC) frames, benchmarking the results against NLTHA. An application is conducted to propagate such modelling uncertainty to both fragility and vulnerability/loss estimations. Error levels are deemed satisfactory for practical applications, especially considering the low required modelling effort and analysis time. Regarding single‐building applications enabled by the proposed metamodel, this paper presents a first attempt at a direct loss‐based design procedure, which allows setting a target loss level for the designed structure (shown for a realistic RC frame). An earthquake risk model involving dynamic exposure and vulnerability modules is illustrated as an example of building portfolio applications. Specifically, the proposed application considers a retrofit‐based seismic risk‐reduction policy for a synthetic building portfolio, for which it is possible estimating the loss evolution over time.
Risk Assessment of Gypsum Amendment on Agricultural Fields: Effects of Sulfate on Riverine Biota
Authors: Rantamo Krista , Arola Hanna , Aroviita Jukka , Hämälainen Heikki , Hannula Maija , Laaksonen Rami , Laamanen Tiina , Leppänen Matti T. , Salmelin Johanna , Syrjänen Jukka T. , Taskinen Antti , Turunen Jarno , Ekholm Petri 
Published: November 2021

Abstract
Gypsum (CaSO4∙2H2O) amendment is a promising way of decreasing the phosphorus loading of arable lands, and thus preventing aquatic eutrophication. However, in freshwaters with low sulfate concentrations, gypsum-released sulfate may pose a threat to the biota. To assess such risks, we performed a series of sulfate toxicity tests in the laboratory and conducted field surveys. These field surveys were associated with a large-scale pilot exercise involving spreading gypsum on agricultural fields covering 18% of the Savijoki River (Finland) catchment area. The gypsum amendment in such fields resulted in approximately a four-fold increase in the mean sulfate concentration for a 2-month period, and a transient, early peak reaching approximately 220 mg/L. The sulfate concentration gradually decreased almost to the pregypsum level after 3 years. Laboratory experiments with Unio crassus mussels and gypsum-spiked river water showed significant effects on foot movement activity, which was more intense with the highest sulfate concentration (1100 mg/L) than with the control. Survival of the glochidia after 24 and 48 h of exposure was not significantly affected by sulfate concentrations up to 1000 mg/L, nor was the length growth of the moss Fontinalis antipyretica affected. The field studies on benthic algal biomass accrual, mussel and fish density, and Salmo trutta embryo survival did not show gypsum amendment effects. Gypsum treatment did not raise the sulfate concentrations even to a level just close to critical for the biota studied. However, because the effects of sulfate are dependent on both the spatial and the temporal contexts, we advocate water quality and biota monitoring with proper temporal and spatial control in rivers within gypsum treatment areas. Environ Toxicol Chem 2022;41:108–121. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Analysis of side information impact on the physical layer security performances in wireless wiretap channel
Authors: Pakravan Saeid , Hodtani Ghosheh Abed 
Published: November 2021

AbstractInformation‐theoretic analysis of the communication systems performances is of practical and theoretical importance. In this article, we study side information impact on physical layer security in a Rayleigh fading wiretap channel by deriving closed‐form expressions for the average secrecy capacity (ASC), secrecy outage probability (SOP), secrecy coverage region (SCR), and specifically, the asymptotic behavior of SOP. The results, while including previous works as special cases, show that side information has positive effects over ASC and SOP, and also, it increases the SCR, as expected intuitively. Numerical evaluations have been done to support the claims.
An enhancedLTEhandover scheme for high‐speed railway application
Authors: Amin Sadrabadi Hossein , Ardalani Nahid , Bakhshi Hamidreza 
Published: November 2021

AbstractHigh‐speed railway (HSR) is one of the most important modes of passenger transport with many advantages, such as; safety, high capacity, short intervals, and comfort. To provide high speed mobile data to the passengers of HSR for infotainment services, the best option is LTE or LTE‐R. The LTE‐R is a railway specialized network under development. The very high speed of trains in HSR, which are far faster than conventional commuters, counteracts the seamless data service and deteriorates the QoS which is mainly due to handover (HO) failure when the user equipment (UE) is moving very fast. Conventional LTE HO schemes are not designed for very high speed of HSR. Some research studies were done to provide HO schemes with more adaptation with the HSR condition but the desired specifications are not fully satisfied. In this article, we have devised a new S3 scheme for LTE HO based on time‐to‐trigger parameter in which the required ETSI's HO success rate standard at very high speed moving UE is met with a good safety margin. In addition, the presented scheme shows better performance in terms of HO latency, reference signal received power gap and handover operation probability. To do the job, an accurate mathematical analysis was developed for the proposed S3 scheme, conventional A3 and A4 schemes and the H2 scheme that we found to be the best one out of previous research studies. The results obtained have been verified by simulations.
Ultrasonic extraction, structural characterization, and antioxidant activity of oligosaccharides from red yeast rice
Authors: Liu Kai , Xie Long , Gu Huan , Luo Jia , Li Xiaofang 
Published: November 2021

AbstractRed yeast rice is consumed as a medicinal food to lower blood lipids. Besides, it is used to color food, make wine, etc. In this study, water‐soluble oligosaccharides in red yeast rice were extracted by ultrasonic‐assisted extraction method. The parameters to extract oligosaccharides from red yeast rice were optimized by the Box‐Behnken design under the following optimal extraction conditions: extraction temperature, 60°C; extraction time, 97 min; and liquid/material ratio, 25 ml/g. The structure and the antioxidant activity of the new oligosaccharide were preliminarily investigated. Total carbohydrates extracted from red yeast rice with 80% ethanol–water solution (v/v) were first removed from pigments using D101 macroporous adsorption resin. The total sugar contents were then purified by DE52 resins and Sephadex G‐25 resins to obtain red yeast rice oligosaccharides, coded as RYRO1. Structural characterization experiments indicated that RYRO1 is an oligosaccharide with a weight average molecular weight of 874 Da and a theoretical degree of polymerization of 4.86. RYRO1 is composed of mannose, glucosamine, glucose, and galactose with a molar ratio of 0.248:0.019:1:0.026. The ABTS, DPPH, and hydroxyl free radical

scavenging assays showed antioxidant nature of RYRO1.
Connectivity‐based parcellation of normal and anatomically distorted human cerebral cortex
Authors: Doyen Stephane , Nicholas Peter , Poologaindran Anujan , Crawford Lewis , Young Isabella M. , Romero‐Garcia Rafeael , Sughrue Michael E. 
Published: November 2021

AbstractFor over a century, neuroscientists have been working toward parcellating the human cortex into distinct neurobiological regions. Modern technologies offer many parcellation methods for healthy cortices acquired through magnetic resonance imaging. However, these methods are suboptimal for personalized neurosurgical application given that pathology and resection distort the cerebrum. We sought to overcome this problem by developing a novel connectivity‐based parcellation approach that can be applied at the single‐subject level. Utilizing normative diffusion data, we first developed a machine‐learning (ML) classifier to learn the typical structural connectivity patterns of healthy subjects. Specifically, the Glasser HCP atlas was utilized as a prior to calculate the streamline connectivity between each voxel and each parcel of the atlas. Using the resultant feature vector, we determined the parcel identity of each voxel in neurosurgical patients (n = 40) and thereby iteratively adjusted the prior. This approach enabled us to create patient‐specific maps independent of brain shape and pathological distortion. The supervised ML classifier re‐parcellated an average of 2.65% of cortical voxels across a healthy dataset (n = 178) and an average of 5.5% in neurosurgical patients. Our patient dataset consisted of subjects with supratentorial infiltrating gliomas operated on by the senior author who then assessed the validity and practical utility of the re‐parcellated diffusion data. We demonstrate a rapid and effective ML parcellation approach to parcellation of the human cortex during anatomical distortion. Our approach overcomes limitations of indiscriminately applying atlas‐based registration from healthy subjects by employing a voxel‐wise connectivity approach based on individual data.
Acquired Resistance to Antiangiogenic Therapies in Hepatocellular Carcinoma Is Mediated by Yes‐Associated Protein 1 Activation and Transient Expansion of Stem‐Like Cancer Cells
Authors: Castven Darko , Czauderna Carolin , Becker Diana , Pereira Sharon , Schmitt Jennifer , Weinmann Arndt , Shah Viral , Hajduk Jovana , Keggenhoff Friederike , Binder Harald , Keck Tobias , Heilmann‐Heimbach Stefanie , Wörns Marcus A. , Thorgeirsson Snorri S. , Breuhahn Kai , Galle Peter R. , Marquardt Jens U. 
Published: November 2021

Induction of neoangiogenesis is a hallmark feature during disease progression of hepatocellular carcinoma (HCC). Antiangiogenetic compounds represent a mainstay of therapeutic approaches; however, development of chemoresistance is observed in the majority of patients. Recent findings suggest that tumor‐initiating cells (TICs) may play a key role in acquisition of resistance, but the exact relevance for HCC in this process remains to be defined. Primary and established hepatoma cell lines were exposed to long‐term sorafenib treatment to model acquisition of resistance. Treatment effects on TICs were estimated by sphere‐forming capacity in vitro, tumorigenicity in vivo, and flow cytometry. Adaptive molecular changes were assessed by whole transcriptome analyses. Compensatory mechanisms of resistance were identified and directly evaluated. Sustained antiproliferative effect following sorafenib treatment was observed in three of six HCC cell lines and was followed by rapid regrowth, thereby mimicking responses observed in patients. Resistant cells showed induction in sphere forming in vitro and tumor‐initiating capacity in vivo as well as increased number of side population and epithelial cell adhesion molecule‐positive cells. Conversely, sensitive cell lines showed consistent reduction of TIC properties. Gene sets associated with resistance and poor prognosis, including Hippo/yes‐associated protein (YAP), were identified. Western blot and immunohistochemistry confirmed increased levels of YAP. Combined treatment of sorafenib and specific YAP inhibitor consistently revealed synergistic antioncogenic effects in resistant cell lines. Conclusion: Resistance to antiangiogenic therapy might be driven by transient expansion of TICs and activation of compensatory pro‐oncogenic signaling pathways, including YAP. Specific targeting of TICs might be an effective therapeutic strategy to overcome resistance in HCC.