bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Influencing Cold Hardiness during Overwintering of Streltzoviella insularis (Lepidoptera: Cossidae)
Authors: Pei Jiahe , Li Chengcheng , Ren Lili , Zong Shixiang 
Published: February 2020

AbstractStreltzoviella insularis (Staudinger) (Lepidoptera: Cossidae) is a woodboring pest that severely damages urban and plain afforestation trees in northern China. Cold hardiness is an important strategy for the insect to survived during low winter temperatures. Understanding the strategy of S. insularis might provide insights for pest management approaches. To assess the key factors affecting cold hardiness, we measured the supercooling point, freezing point, total water content, total fat content, glycogen content, and total protein content of overwintering larvae. The relationships between supercooling points, temperature, body size, and nutrients were analyzed. The results showed that the supercooling point and freezing point of the larvae decreased first, reached the lowest point in January, and then increased during the rest of the overwintering period. The supercooling point positively correlated with the daily average temperature and the daily minimum temperature. Total lipid content negatively correlated with the supercooling point, while glycogen content had a significant positive correlation with the supercooling point. The temperature may have a major impact on cold hardiness, whereas individual body size may have no significant influence over cold tolerance. During the overwintering process, glycogen and total lipid contents may directly affect cold hardiness. Therefore, the lipid and carbohydrate metabolism may play a role in the cold tolerance of S. insularis larvae. This study provides a physiological and biochemical basis for future metabolic studies on S. insularis larva and the research of overwintering strategies.
Observational signatures of gamma-rays from bright blazars and wakefield theory
Authors: Canac N E , Abazajian K N , Tajima T , Ebisuzaki T , Horiuchi S 
Published: February 2020

ABSTRACTGamma-ray observations have revealed strong variability in blazar luminosities in the gamma-ray band over time-scales as short as minutes. We show, for the first time, that the correlation of the spectrum with intensity is consistent with the behaviour of the luminosity variation of blazar spectral energy distributions (SEDs) along a blazar sequence for low synchrotron peak blazars. We show that the observational signatures of variability with flux are consistent with wakefield acceleration of electrons initiated by instabilities in the blazar accretion disc. This mechanism reproduces the observed time variations as short as 100 s. The wakefield mechanism also predicts a reduction of the electron spectral index with increased gamma-ray luminosity, which could be detected in higher energy observations well above the inverse Compton peak.
Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Viral Meningoencephalitis in a Resource-Limited Setting
Authors: Hong Nguyen Thi Thu , Anh Nguyen To , Mai Nguyen Thi Hoang , Nghia Ho Dang Trung , Nhu Le Nguyen Truc , Thanh Tran Tan , Phu Nguyen Hoan , Deng Xutao , van Doorn H Rogier , Chau Nguyen Van Vinh , Delwart Eric , Thwaites Guy , Tan Le Van 
Published: February 2020

Abstract

Background
Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pan-pathogen assays for infectious diseases diagnosis, but few studies have been conducted in resource-limited settings.

Methods
We assessed the performance of mNGS in the cerebrospinal fluid (CSF) of 66 consecutively treated adults with meningoencephalitis in a tertiary referral hospital for infectious diseases in Vietnam, a resource-limited setting. All mNGS results were confirmed by viral-specific polymerase chain reaction (PCR). As a complementary analysis, 6 viral PCR-positive samples were analyzed using MinION-based metagenomics.

Results
Routine diagnosis could identify a virus in 15 (22.7%) patients, including herpes simplex virus (HSV; n = 7) and varicella zoster virus (VZV; n = 1) by PCR, and mumps virus (n = 4), dengue virus (DENV; n = 2), and Japanese encephalitis virus (JEV; n = 1) by serological diagnosis. mNGS detected HSV, VZV, and mumps virus in 5/7, 1/1, and 1/4 of the CSF positive by routine assays, respectively, but it detected DENV and JEV in none of the positive CSF. Additionally, mNGS detected enteroviruses in 7 patients of unknown cause. Metagenomic MinION-Nanopore sequencing could detect a virus in 5/6 PCR-positive CSF samples, including HSV in 1 CSF sample that was negative by mNGS, suggesting that the sensitivity of MinION is comparable with that of mNGS/PCR.

Conclusions
In a single assay, metagenomics could accurately detect a wide spectrum of neurotropic viruses in the CSF of meningoencephalitis patients. Further studies are needed to determine the value that real-time sequencing may contribute to the diagnosis and management of meningoencephalitis patients, especially in resource-limited settings where pathogen-specific assays are limited in number.
Carbon–Strontium Isotope Decoupling in Carbonatites from Caotan (Qinling, China): Implications for the Origin of Calcite Carbonatite in Orogenic Settings
Authors: Wei Chun-Wan , Xu Cheng , Chakhmouradian Anton R , Brenna Marco , Kynicky Jindrich , Song Wen-Lei 
Published: February 2020

Abstract
Mantle-derived carbonatites emplaced in orogenic belts and some extensional settings are hypothesized to contain recycled crustal material. However, these carbonatites are typically composed of calcite showing a typical mantle range of C–O isotopic values devoid of recognizable sedimentary fingerprints. Here, we report the first known instance of C–Sr isotope decoupling between intimately associated dolomite carbonatites and magnetite–forsterite–calcite carbonatites from the northern Qinling orogen, central China. The calcite-dominant variety is developed at the contact between the dolomite carbonatite and metasomatized wall-rock gneiss. The two types of carbonatites have similar δ18OVSMOW (6·98‰ to 9·96‰), εNd(i) (-3·01 to -6·47) and Pb (206Pb/204Pb(i) = 17·369–17·584, 207Pb/204Pb(i) = 15·443–15·466) isotopic compositions, but significantly different C and Sr isotopic signatures (δ13CVPDB = -3·09 to -3·58‰ and -6·11 to -7·19‰; 87Sr/86Sr(i) = 0·70373 to 0·70565 vs 0·70565 to 0·70624 for the dolomite and calcite rocks, respectively). The relative enrichment of the early-crystallizing dolomite carbonatite in 13C and its depletion in 87Sr are primary isotopic characteristics inherited from its mantle source. The observed field relations, petrographic and geochemical characteristics of the Caotan dolomite and calcite carbonatites imply that the strong C–Sr isotopic decoupling between them could not result from mixing of different mantle reservoirs (e.g. HIMU and EM1), or from magma fractionation processes. We propose that the calcite carbonatites were a by-product of metasomatic reactions between primary dolomitic melts and felsic wall-rock. These reactions involved the loss of Mg and CO2 from the magma, leading to depletion of the evolved calcite-saturated liquid in 13C and its enrichment in radiogenic Sr. We conclude that calcite carbonatites in plate-collision zones may not represent primary melts even if their isotopic signature is recognizably ‘mantle-like’.
Acoustic closed-loop stimulation during sleep improves consolidation of reward-related memory information in healthy children but not in children with attention-deficit hyperactivity disorder
Authors: Prehn-Kristensen Alexander , Ngo Hong-Viet V , Lentfer Luisa , Berghäuser Julia , Brandes Lena , Schulze Larissa , Göder Robert , Mölle Matthias , Baving Lioba 
Published: February 2020

Abstract

Study Objectives
Slow oscillations (SO) during slow-wave sleep foster the consolidation of declarative memory. Children with attention-deficit hyperactivity disorder (ADHD) display deficits in the sleep-associated consolidation of declarative memory, possibly due to an altered function of SO. The present study aimed at enhancing SO activity using closed-looped acoustic stimulation during slow-wave sleep in children with ADHD.

Methods
A total of 29 male children (14 with ADHD; aged 8–12 years) participated in a double-blind, placebo-controlled study trial. Children spent two experimental nights in a sleep lab, one stimulation night and one sham night. A declarative learning task (word-pair learning) with a reward condition was used as a primary outcome. Secondary outcome variables were a procedural memory (serial reaction time) and working memory (WM; n-back) task. Encoding of declarative and procedural memory took place in the evening before sleep. After sleep, the retrieval took place followed by the n-back task.

Results
The stimulation successfully induced SO activity during sleep in children with and without ADHD. After stimulation, only healthy children performed better on high-rewarded memory items (primary outcome). In contrast, there were indications that only children with ADHD benefitted from the stimulation with respect to procedural as well as WM performance (secondary outcome).

Conclusions
We were able to show that the acoustic closed-loop stimulation can be applied to enhance SO activity in children with and without ADHD. Our data indicate that SO activity during sleep interacts with subsequent memory performance (primary outcome: rewarded declarative memory; secondary outcome: procedural and WM) in children with and without ADHD.
Relationship between heifer carcass maturity and beef quality characteristics
Authors: Hoffman Kacie C , Colle Michael J , Nasados James A , Gray Sara J , Rogers Jakobie , Van Buren Jessie B , Puga Kendelle J , Murdoch Gordon K , Richard Ronald P , Doumit Matthew E 
Published: February 2020

Abstract
Our objective was to determine the relationship between heifer carcass maturity and beef palatability of the longissimus lumborum (LM) and biceps femoris (BF). Left sides of A (n = 30), B (n = 30), and C (n = 30) maturity heifer carcasses under 30 mo of age by dentition were used. Carcasses were selected to ensure similar marbling scores across maturity groups (Small to Modest). Beef strip loins (LM) and outside rounds (BF) were obtained from these carcasses. Steaks were used to measure color stability, lipid oxidation (thiobarbituric acid reactive substances; TBARS), Warner-Bratzler shear force (WBSF), soluble and insoluble collagen, and consumer sensory perceptions. Heifer carcass maturity did not affect pH, fluid loss, WBSF, or collagen content of LM or BF steaks (P &gt; 0.29). In LM and BF steaks, a maturity × day of retail display interaction occurred for TBARS, in which B maturity steaks had lower levels of lipid oxidation compared with A and C maturity steaks from the fourth day to the end of the retail display (P &lt; 0.01). Nevertheless, LM steaks from B maturity carcasses tended to have lower overall acceptability (P = 0.08) and juiciness (P = 0.09) than steaks from C maturity carcasses, but steaks from B and C maturity carcasses did not differ from LM steaks obtained from A maturity carcasses. No differences in tenderness or flavor were observed due to maturity (P &gt; 0.24). Similarly, maturity had no effect on sensory characteristics of BF steaks (P &gt; 0.30). In conclusion, our results indicate that advanced physiological maturity does not decrease palatability of strip loin or outside round steaks from carcasses of heifers under 30 mo of age.
Pharmaceutic application of vitamin D3 on particle-induced fibrotic effects through induction of Nrf2 signals
Authors: Zhang Hong , Deng Wuquan , Yang Youjing , Wei Shuhui , Xue Lian , Tao Shasha 
Published: February 2020

AbstractFine particulate matter, a major air pollutant across the world, causes a series of pulmonary diseases. Vitamin D is a typical vitamin with emerging roles in inflammation and fibrosis. Different situations and diseases need different doses and modes of vitamin D administration, which challenges the existing vitamin D supplementary rules. Thus, studies of vitamin D applications and their mechanisms in various diseases are important for its future therapeutic applications. In this study, the therapeutic application of vitamin D3 in chronic particle-exposure-associated lung fibrosis and tissue remodeling was investigated. In vivo studies showed that vitamin D3 significantly attenuated fibrosis effects by decreasing α-smooth muscle actin-regulated extracellular matrix deposition and restoring expressions of E-cadherin and N-cadherin. With the importance of activated macrophage in the regulation of local epithelium and fibroblast in the process of tissue fibrosis, two separate in vitro systems of co-culture of macrophages with lung epithelium or fibroblast were built. The results confirmed that vitamin D3 promoted the proliferation of lung epithelium and depressed the fibrosis effects of fibroblasts as well. In addition, our results indicated that the therapeutic effects of vitamin D3 were through Nrf2 signals. Our work provides convincing experimental evidence for vitamin D therapeutic application to promote tissue repair and improve particle-associated lung fibrosis.
Incorporating phylogenetic information in microbiome abundance studies has no effect on detection power and FDR control
Authors: Bichat Antoine , Plassais Jonathan , Ambroise Christophe , Mariadassou Mahendra 
Published: February 2020

AbstractWe consider the problem of incorporating evolutionary information (e.g. taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierachical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non hierachical, Benjamini-Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierachical structure with profit but do not control the False Discovery Rate (FDR)a prioriand remain inferior to a classical Benjamini-Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Although intuition advocates the use of a hierachical structure, be it the phylogeny or the correlation tree, to increase the detection rate in microbiome studies, current hierachical procedures are still inferior to non hierachical ones and effective procedures remain to be invented.
Clinically Applicable Deep Learning Strategy for Pulmonary Nodule Risk Prediction: Insights into HONORS
Authors: Lv Wenhui , Wang Yang , Zhou Changsheng , Huang Sheng , Fang Xiangming , Xu Qiuzhen , Zhang Qirui , Huang Chuxi , Li Xinyu , Zhou Zhen , Yu Yizhou , Wang Yizhou , Lu Mengjie , Xu Qiang , Li Xiuli , Lin Haoliang , Lu Xiaofan , Xu Qinmei , Sun Jing , Tang Yuxia , Song Yong , Yan Fangrong , Zhang Bing , Cheng Zhen , Zhang Longjiang , Lu Guangming 
Published: February 2020

AbstractBackground and PurposeLimited optimization was clinically applicable for reducing missed diagnosis, misdiagnosis and inter-reader variability in pulmonary nodule diagnosis. We aimed to propose a deep learning-based algorithm and a practical strategy to better stratify the risk of pulmonary nodules, thus reducing medical errors and optimizing the clinical workflow.Materials and MethodsA total of 2,348 pulmonary nodules (1,215 with lung cancer) containing screened nodules from National Lung Cancer Screening Trial (NLST) and incidentally detected nodules from Jinling Hospital (JLH) were used to train and evaluate a deep learning algorithm, Filter-guided pyramid network (FGP-NET). Internal and external test of FGP-NET were performed on two independent datasets (n=542). The performance of FGP-NET at Youden point which maximizing the Youden index was compared with 126 board-certificated radiologists. We further proposed Hierarchical Ordered Network ORiented Strategy (HONORS), which manipulates the emphasis either on sensitivity or specificity to target risk-stratified clinical scenarios, directly making decisions for some patients.ResultsFGP-NET achieved a high area under the curve (AUC) of 0.969 and 0.855 for internal and external testing, and was comparable or even outperformed the radiologists when considering sensitivity. HONORS-guided FGP-NET identified benign nodules with a high sensitivity (95.5%) in the screening scenario, and demonstrated satisfactory performance for the rest ambiguous nodules with 0.945 of AUC by the Youden point. FGP-NET also detected lung cancer with a high specificity of 94.5% in routine diagnostic scenario; an AUC of 0.809 was achieved for the rest nodules.ConclusionThe combination of HONORS and FGP-NET provides well-organized stratification for pulmonary nodules and also offers the potential for reducing medical errors.HighlightsPulmonary nodules were managed for both screening and diagnostic scenariosProposal of a hierarchical strategy for targeting risk-stratified clinical scenariosA large scale Human-deep learning contest for reliable performance evaluation
Hippocampal volume in Provisional Tic Disorder predicts tic severity at 12-month follow-up
Authors: Kim Soyoung , Greene Deanna J. , D’Andrea Carolina Badke , Bihun Emily C. , Koller Jonathan M. , O’Reilly Bridget , Schlaggar Bradley L. , Black Kevin J. 
Published: February 2020

BackgroundPrevious studies have investigated differences in the volumes of subcortical structures (e.g., caudate nucleus, putamen, thalamus, amygdala, hippocampus) between individuals with and without Tourette syndrome (TS), as well as the relationships between these volumes and tic symptom severity. These volumes may also predict clinical outcome in Provisional Tic Disorder (PTD), but that hypothesis has never been tested.ObjectiveThis study aimed to examine whether the volumes of subcortical structures measured shortly after tic onset can predict tic symptom severity at one year post tic onset, when TS can first be diagnosed.MethodsWe obtained T1-weighted structural MRI scans from 41 children with PTD (25 with prospective motion correction [vNavs]) whose tics had begun less than 9 months (median 3.7 months) prior to the first study visit (baseline). We re-examined them at the 12-month anniversary of their first tic (follow-up), assessing tic severity using the Yale Global Tic Severity Scale. We quantified the volumes of subcortical structures using volBrain software.ResultsBaseline hippocampal volume was correlated with tic severity at the 12-month follow-up, with a larger hippocampus at baseline predicting worse tic severity at follow-up. This result was confirmed in the subgroup scanned with prospective motion correction. The volumes of other subcortical structures did not significantly predict tic severity at follow-up.ConclusionThese findings suggest that hippocampal volume may be an important marker in predicting prognosis in Provisional Tic Disorder.
External error attribution dampens efferent-based predictions but not proprioceptive changes in hand localization
Authors: Gastrock Raphael Q. , Modchalingam Shanaathanan , ’t Hart Bernard Marius , Henriques Denise Y. P. 
Published: February 2020

AbstractIn learning and adapting movements in changing conditions, people attribute the errors they experience to a combined weighting of internal or external sources. As such, error attribution that places more weight on external sources should lead to decreased updates in our internal models for movement of the limb or estimating the position of the effector, i.e. there should be reduced implicit learning. However, measures of implicit learning are the same whether or not we induce explicit adaptation with instructions about the nature of the perturbation. Here we evoke clearly external errors by either demonstrating the rotation on every trial, or showing the hand itself throughout training. Implicit reach aftereffects persist, but are reduced in both groups. Only for the group viewing the hand, changes in hand position estimates suggest that predicted sensory consequences are not updated, but only rely on recalibrated proprioception. Our results show that estimating the position of the hand incorporates source attribution during motor learning, but recalibrated proprioception is an implicit process unaffected by external error attribution.
Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity
Authors: Deng Lei , Cai Yideng , Zhang Wenhao , Yang Wenyi , Gao Bo , Liu Hui 
Published: February 2020

AbstractMotivationTo efficiently save cost and reduce risk in drug research and development, there is a pressing demand to developin-silicomethods to predict drug sensitivity to cancer cells. With the exponentially increasing number of multi-omics data derived from high-throughput techniques, machine learning-based methods have been applied to the prediction of drug sensitivities. However, these methods have drawbacks either in the interpretability of mechanism of drug action or limited performance in modeling drug sensitivity.ResultsIn this paper, we presented a pathway-guided deep neural network model, referred to as pathDNN, to predict the drug sensitivity to cancer cells. Biological pathways describe a group of molecules in a cell that collaborates to control various biological functions like cell proliferation and death, thereby abnormal function of pathways can result in disease. To make advantage of both the excellent predictive ability of deep neural network and the biological knowledge of pathways, we reshape the canonical DNN structure by incorporating a layer of pathway nodes and their connections to input gene nodes, which makes the DNN model more interpretable and predictive compared to canonical DNN. We have conducted extensive performance evaluations on multiple independent drug sensitivity data sets, and demonstrate that pathDNN significantly outperformed canonical DNN model and seven other classical regression models. Most importantly, we observed remarkable activity decreases of disease-related pathway nodes during forward propagation upon inputs of drug targets, which implicitly corresponds to the inhibition effect of disease-related pathways induced by drug treatment on cancer cells. Our empirical experiments show that pathDNN achieves pharmacological interpretability and predictive ability in modeling drug sensitivity to cancer cells.AvailabilityThe web server, as well as the processed data sets and source codes for reproducing our work, is available athttp://pathdnn.denglab.org