bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volatility Estimation and Forecasts Based on Price Durations
Authors: Hong Seok Young , Nolte Ingmar , Taylor Stephen J , Zhao Xiaolu 
Published: February 2021

Abstract
We investigate price duration variance estimators that have long been neglected in the literature. In particular, we consider simple-to-construct non-parametric duration estimators, and parametric price duration estimators using autoregressive conditional duration specifications. This paper shows (i) how price duration estimators can be used for the estimation and forecasting of the integrated variance of an underlying semi-martingale price process and (ii) how they are affected by discrete and irregular spacing of observations, market microstructure noise, and finite price jumps. Specifically, we contribute to the literature by constructing the asymptotic theory for the non-parametric estimator with and without the presence of bid/ask spread and time discreteness. Further, we provide guidance about how our estimators can best be implemented in practice by appropriately selecting a threshold parameter that defines a price duration event, or by averaging over a range of non-parametric duration estimators. We also provide simulation and forecasting evidence that price duration estimators can extract relevant information from high-frequency data better and produce more accurate forecasts than competing realized volatility and option-implied variance estimators, when considered in isolation or as part of a forecasting combination setting.
Facsimile narratives: Researching the past in the age of digital reproduction
Authors: Fafinski Mateusz 
Published: February 2021

AbstractTaking a cue from the reflections and contributions made by manuscript, archival and historical studies, this paper proposes a new approach to the methodology of digital facsimiles. It asks how we research the past in the age of digital facsimiles and what are our biggest challenges and opportunities. By broadening the definition of what digital facsimiles are and re-evaluating their relationship with databases seeing databases as primarily aggregations of digital facsimiles the paper argues that the key methodological challenge lies in acknowledging the narrative within them. This can only be achieved if we incorporate the existing humanities methodologies in any data-related pursuits. The article demonstrates how notions of objective thresholds in data aggregations are in reality failures to notice and acknowledge the inherent narratives within the digital facsimiles that constitute them. At the same time, while deeply connected, digital facsimiles have to be recognised as ontologically separate from their exemplars. This influences greatly the way we research the past and a failure to recognize both the inherent narrativity and the cognitive gap will always lead to questionable results.
BRCA1-BARD1 regulates transcription through BRD4 in Xenopus nucleoplasmic extract
Authors: Barrows John K , Fullbright George , Long David T 
Published: February 2021

Abstract
The tumor suppressor BRCA1 is considered a master regulator of genome integrity. Although widely recognized for its DNA repair functions, BRCA1 has also been implicated in various mechanisms of chromatin remodeling and transcription regulation. However, the precise role that BRCA1 plays in these processes has been difficult to establish due to the widespread consequences of its cellular dysfunction. Here, we use nucleoplasmic extract derived from the eggs of Xenopus laevis to investigate the role of BRCA1 in a cell-free transcription system. We report that BRCA1-BARD1 suppresses transcription initiation independent of DNA damage signaling and its established role in histone H2A ubiquitination. BRCA1-BARD1 acts through a histone intermediate, altering acetylation of histone H4K8 and recruitment of the chromatin reader and oncogene regulator BRD4. Together, these results establish a functional relationship between an established (BRCA1) and emerging (BRD4) regulator of genome integrity.
The branched-chain amino acid aminotransferase TaBCAT1 modulates amino acid metabolism and positively regulates wheat rust susceptibility
Authors: Corredor-Moreno Pilar , Minter Francesca , Davey Phoebe E , Wegel Eva , Kular Baldeep , Brett Paul , Lewis Clare M , Morgan Yvie M L , Macías Pérez Luis A , Korolev Andrey V , Hill Lionel , Saunders Diane G O 
Published: February 2021

Abstract
Plant pathogens suppress defense responses to evade recognition and promote successful colonization. Although identifying the genes essential for pathogen ingress has traditionally relied on screening mutant populations, the post-genomic era provides an opportunity to develop novel approaches that accelerate identification. Here, RNA-seq analysis of 68 pathogen-infected bread wheat (Triticum aestivum) varieties, including three (Oakley, Solstice and Santiago) with variable levels of susceptibility, uncovered a branched-chain amino acid aminotransferase (termed TaBCAT1) as a positive regulator of wheat rust susceptibility. We show that TaBCAT1 is required for yellow and stem rust infection and likely functions in branched-chain amino acid (BCAA) metabolism, as TaBCAT1 disruption mutants had elevated BCAA levels. TaBCAT1 mutants also exhibited increased levels of salicylic acid (SA) and enhanced expression of associated defense genes, indicating that BCAA regulation, via TaBCAT1, has a key role in SA-dependent defense activation. We also identified an association between the levels of BCAAs and resistance to yellow rust infection in wheat. These findings provide insight into SA-mediated defense responses in wheat and highlight the role of BCAA metabolism in the defense response. Furthermore, TaBCAT1 could be manipulated to potentially provide resistance to two of the most economically damaging diseases of wheat worldwide.
Spatiotemporal control of miR398 biogenesis, via chromatin remodeling and kinase signaling, ensures proper ovule development
Authors: Cai Hanyang , Liu Liping , Zhang Man , Chai Mengnan , Huang Youmei , Chen Fangqian , Yan Maokai , Su Zhenxia , Henderson Ian , Palanivelu Ravishankar , Chen Xuemei , Qin Yuan 
Published: February 2021

AbstractThe coordinated development of sporophytic and gametophytic tissues is essential for proper ovule patterning and fertility. However, the mechanisms regulating their integrated development remain poorly understood. Here, we report that the Swi2/Snf2-Related1 (SWR1) chromatin-remodeling complex acts with the ERECTA receptor kinase-signaling pathway to control female gametophyte and integument growth in Arabidopsis thaliana by inhibiting transcription of the microRNA gene MIR398c in early-stage megagametogenesis. Moreover, pri-miR398c is transcribed in the female gametophyte but is then translocated to and processed in the ovule sporophytic tissues. Together, SWR1 and ERECTA also activate ARGONAUTE10 (AGO10) expression in the chalaza; AGO10 sequesters miR398, thereby ensuring the expression of three AGAMOUS-LIKE (AGL) genes (AGL51, AGL52, and AGL78) in the female gametophyte. In the context of sexual organ morphogenesis, these findings suggest that the spatiotemporal control of miRNA biogenesis, resulting from coordination between chromatin remodeling and cell signaling, is essential for proper ovule development in Arabidopsis.
STUDY ON A SPECIFIC TEST METHOD FOR DOSIMETRIC CHARACTERIZATION OF ULTRA-WIDE DETECTOR COMPUTED TOMOGRAPHY
Authors: Lu Heqing , Ye Xiangqun , Zhang Haowei , Sun Si 
Published: February 2021

Abstract
The purpose of this study was to establish a specific test method for dosimetric characterization of wide-beam computed tomography (CT). For a wide beam, the dose distribution curve and the area of the curve were obtained by using pencil-like ionization chamber, a long CT dose profiler probe, a head phantom and a body phantom. The absolute dose conversion coefficient was multiplied to obtain the total integration integral of the absolute dose distribution, and then the computed tomography dose index (CTDI) value under any wide beam condition was obtained by dividing the collimation width. It was calculated that the absolute dose conversion coefficient was 1.135 under the narrow beam of 8 mm. To a 160 mm-wide beam, the value of CTDI was 7.57 mGy/100mAs after normalized in the head 80 kV CT scanning, and it was 9.80 mGy/100mAs after normalized in the body 120 kV CT scanning. The specific test method solves the problem that the previous measurement method underestimates the CTDI value.
The Impact of Employment on Immigrant Mental Health: Results from a National Survey
Authors: Disney Lindsey 
Published: February 2021

AbstractMental illness and unemployment are both well documented in the literature as potentially having harmful and even detrimental impacts on individuals’ lives. However, less is known about the intersections of mental illness and unemployment in the U.S. immigrant population. This study examined whether unemployment is a predictor of mental illness in a sample of immigrants in the United States (N = 3,732). Data were from the National Epidemiologic Survey on Alcohol and Related Conditions, a three-wave, nationally representative dataset. Multivariate logistical regression analysis examined whether the main effects of a negative employment status were associated with a mental health diagnosis at Wave 2. Negative employment status was a significant predictor of all mental health diagnoses in the multivariate logistic regression models. The results from this study indicate that unemployment is associated with mental health problems among immigrants. This article presents discussion and implications for social work practice, policy, and research.
Circular functional analysis of OCT data for precise identification of structural phenotypes in the eye
Authors: Ali Md. Hasnat , Wainwright Brian , Petersen Alexander , Jonnadula Ganesh B. , Aruru Meghana , Rao Harsha L. , Srinivas M. B. , Jammalamadaka S. Rao , Senthil Sirisha , Pyne Saumyadipta 
Published: February 2021

AbstractProgressive optic neuropathies such as glaucoma are major causes of blindness globally. Multiple sources of subjectivity and analytical challenges are often encountered by the clinicians in the process of early diagnosis and clinical management of these diseases. In glaucoma, the structural damage is often characterized by neuroretinal rim (NRR) thinning of the optic nerve head, and other clinical parameters. Optical coherence tomography (OCT) is a popular and quantitative eye imaging platform for precise and reproducible measurement of such parameters in the clinic.Baseline structural heterogeneity in the eyes can play a key role in the progression of optic neuropathies, and thus present challenges to clinical decision-making. To address this, large and diverse normative OCT databases with mathematically precise description of phenotypes can help with early detection and characterization of the different phenotypes that are encountered in the clinic. In this study, we generated a new large dataset of OCT generated high-resolution circular data on NRR phenotypes, along with other clinical covariates, of nearly 4,000 healthy eyes as part of a well-established clinical cohort (LVPEI-GLEAMS) of Asian Indian participants.In this study, we (1) generated high-resolution circular OCT measurements of NRR thickness in a given eye, (2) introduced CIFU, a new computational pipeline for CIrcular FUnctional data modeling and analysis that is demonstrated using the OCT dataset, and (3) addressed the disparity of representation of the Asian Indian population in normative OCT databases. We demonstrated CIFU by unsupervised circular functional clustering of the OCT NRR data, meta-clustering to characterize the clustering output using clinical covariates, and presenting a circular visualization of the results. Upon stratification by age, we identified a healthy NRR phenotype cluster in the age group 40-49 years with predictive potential for glaucoma.
The Construction and Analysis of ceRNA Network and Immune Infiltration in Kidney Renal Clear Cell Carcinoma
Authors: Deng Lugang , Qu Zhi , Wang Peixi , Liu Nan 
Published: February 2021

AbstractBackgroundKidney renal clear cell carcinoma (KIRC) has the highest invasion, mortality and metastasis of the renal cell carcinomas and seriously affects patients’ quality of life. However, the composition of the immune microenvironment and regulatory mechanisms at transcriptomic level such as ceRNA of KIRC are still unclear.MethodsWe constructed a ceRNA network associated with KIRC by analyzing the long noncoding RNA (lncRNA), miRNA and mRNA expression data of 506 tumor tissue samples and 71 normal adjacent tissue samples downloaded from the Cancer Genome Atlas (TCGA) database. In addition, we estimated the proportion of 22 immune cell types in these samples through “The Cell Type Identification by Estimating Relative Subsets of RNA Transcripts”. Based on the ceRNA network and immune cells screened by univariate Cox analysis and Lasso regression, two nomograms were constructed to predict the prognosis of patients with KIRC. Receiver operating characteristic curves (ROC) and calibration curves were employed to assess the discrimination and accuracy of the nomograms. Consequently, co-expression analysis was carried out to explore the relationship between each prognostic gene in a Cox proportional hazards regression model of ceRNA and each survival-related immune cell in a Cox proportional hazards regression model of immune cell types to reveal the potential regulatory mechanism.ResultsWe established a ceRNA network consisting of 12 lncRNAs, 25 miRNAs and 136 mRNAs. Two nomograms containing seven prognostic genes and two immune cells, respectively, were successfully constructed. Both ROC [Area Under Curves (AUCs) of 1, 3 and 5-year survival in the nomogram based on ceRNA network: 0.779, 0.747 and 0.772; AUCs of 1, 3 and 5-year survivals in nomogram based on immune cells: 0.603, 0.642 and 0.607] and calibration curves indicated good accuracy and clinical application value of both models. Through co-correlation analysis between ceRNA and immune cells, we found both LINC00894 and KIAA1324 were positively correlated with follicular helper T (Tfh) cells and negatively correlated with resting mast cells.ConclusionsBased on the ceRNA network and tumor-infiltrating immune cells, we constructed two nomograms to predict the survival of KIRC patients and demonstrated their value in improving the personalized management of KIRC.
Identification of endothelial-derived proteins in plasma associated with cardiovascular risk factors
Authors: Iglesias MJ , Kruse LD , Sanchez-Rivera L , Enge L , Dusart P , Hong MG , Uhlén M , Renné T , Schwenk JM , Bergstrom G , Odeberg J , Butler LM 
Published: February 2021

ABSTRACTEndothelial cell (EC) dysfunction is a well-established response to cardiovascular disease (CVD) risk factors, such as smoking and obesity. Risk factor exposure can modify EC signalling and behaviour, leading to arterial and venous disease development. Biomarker panels to assess EC dysfunction are lacking, but could be useful for risk stratification and to monitor treatment response. Here, we used affinity proteomics to identify EC-derived proteins circulating in plasma that were associated with CVD risk factor exposure. 216 proteins, known to be expressed in ECs across vascular beds, were measured in plasma samples (n=1005) from the population-basedSwedish CArdioPulmonary bioImage Study(SCAPIS) pilot. We identified 38 EC-derived proteins that were associated with body mass index, total cholesterol, low density lipoprotein, smoking, hypertension or diabetes. Sex-specific analysis revealed female- and male-only associations were most frequently observed with BMI, or total cholesterol, respectively. We showed a relationship between individual CVD risk, calculated with the Framingham risk score, and the corresponding biomarker profiles; presenting the concept of measuring EC-derived proteins in plasma to infer vascular status.
Global warming readiness: Feasibility of enhanced biological phosphorus removal from wastewater at 35°C
Authors: Qiu Guanglei , Law Yingyu , Zuniga-Montanez Rogelio , Lu Yang , Roy Samarpita , Thi Sara Swa , Hoon Huiyi , Nguyen Thi Quynh Ngoc , Eganathan Kaliyamoorthy , Liu Xianghui , Nielsen Per H. , Williams Rohan B.H. , Wuertz Stefan 
Published: February 2021

AbstractRecent research has shown enhanced biological phosphorus removal (EBPR) from municipal wastewater at warmer temperatures around 30°C to be stable in both laboratory-scale reactors and full-scale treatment plants. In the context of a changing climate, the feasibility of EBPR at even higher temperatures is of interest. We operated two lab-scale EBPR sequencing batch reactors with alternating anaerobic and aerobic phases for over 300 days at 30°C and 35°C, respectively, and followed the dynamics of the communities of phosphorus accumulating organisms (PAOs) and competing glycogen accumulating organisms (GAOs) using a combination of 16S rRNA gene metabarcoding, quantitative PCR and fluorescent in-situ hybridization analyses. Stable and nearly complete P removal was achieved at 30°C; similarly, long term P removal was stable at 35°C with effluent PO43−-P concentrations < 0.5 mg/L on half of all monitored days. Diverse and abundantCa.Accumulibacter amplicon sequence variants were closely related to those found in temperate environments, suggesting that EBPR at this temperature does not require a highly specialized PAO community. The slow-feeding strategy used effectively limited the carbon uptake rates of GAOs, allowing PAOs to outcompete GAOs at both temperatures.CandidatusCompetibacter was the main GAO, along with cluster IIIDefluviicoccusmembers. These organisms withstood the slow-feeding regime, suggesting that their bioenergetic characteristics of carbon uptake differ from those of their tetrad-forming relatives. This specific lineage of GAOs warrants further study to establish how complete P removal can be maintained. Comparative cycle studies at two temperatures for each reactor revealed higher activity ofCa. Accumulibacter when the temperature was increased from 30°C to 35°C, suggesting that the stress was a result of the higher carbon (and/or P) metabolic rates of PAOs and GAOs, the resultant carbon deficiency, and additional community competition. An increase in the TOC to PO43--P ratio (from 25:1 to 40:1) effectively eased the carbon deficiency and benefited the proliferation of PAOs. In general, the slow-feeding strategy and sufficiently high carbon input benefited a high and stable EBPR at elevated temperature and represent basic conditions for full-scale applications.
NEIL1 and NEIL2 DNA glycosylases regulate anxiety and learning in a cooperative manner
Authors: Hildrestrand Gunn A. , Rolseth Veslemøy , Kunath Nicolas , Suganthan Rajikala , Jensen Vidar , Bugaj Anna M. , Fernandez-Berrocal Marion S. , Bøe Sikko Sunniva , Vetlesen Susanne , Kuśnierczyk Anna , Olsen Ann-Karin , Gützkow Kristine Bjerve , Rowe Alexander D. , Wang Wei , Moldestad Olve , Syrstad Monica Dahl , Slupphaug Geir , Eide Lars , Klungland Arne , Sætrom Pål , Luna Luisa , Ye Jing , Scheffler Katja , Bjørås Magnar 
Published: February 2021

AbstractOxidative DNA damage in the brain has been implicated in neurodegeneration and cognitive decline. DNA glycosylases initiate base excision repair (BER), the main pathway for oxidative DNA base lesion repair. NEIL1 and NEIL3 DNA glycosylases alter cognition in mice, the role of NEIL2 remains unclear. Here, we investigate the impact of NEIL2 and its potential overlap with NEIL1 on behavior in single and double knock-out mouse models.Neil1-/-Neil2-/-mice displayed hyperactivity, reduced anxiety and improved learning. Hippocampal oxidative DNA base lesion levels were comparable between genotypes, no mutator phenotype was found. Impaired canonical repair was thus not the cause of altered behavior. Electrophysiology indicated reduced stratum oriens afferents in the hippocampal CA1 region inNeil1-/-Neil2-/-. Within CA1, NEIL1 and NEIL2 jointly regulated transcription in genes relevant for synaptic function. Thus, we postulate a cooperative function of NEIL1 and NEIL2 in genome regulation beyond canonical BER modulating memory formation and anxiety.
Reliability of web-based affective auditory stimulus presentation
Authors: Seow Tricia X.F. , Hauser Tobias U. 
Published: February 2021

AbstractWeb-based experimental testing has seen an exponential growth in psychology and cognitive neuroscience. However, paradigms involving affective auditory stimuli have yet to adapt to the online approach due to concerns about the lack of experimental control and other technical challenges. In this study, we assessed if sounds commonly used to evoke affective responses in-lab can be used online. Using recent developments to increase sound presentation quality, we selected 15 commonly used sound stimuli and assessed their impact on valence and arousal states in a web-based experiment. Our results reveal good test-retest reliability and good internal consistency, with results comparable to in-lab studies. Additionally, we compared a variety of previously used unpleasant stimuli, allowing us to identify the most aversive of these sounds. Our findings demonstrate that affective sounds can be reliably delivered through web-based platforms, which helps facilitate the development of new auditory paradigms for affective online experiments.
Force-dependent activation of actin elongation factor mDia1 protects the cytoskeleton from mechanical damage and facilitates stress fiber repair
Authors: Valencia Fernando R. , Sandoval Eduardo , Liu Jian , Plotnikov Sergey V. 
Published: February 2021

ABSTRACTPlasticity of cell mechanics underlies a wide range of cell and tissue behaviors allowing cells to migrate through narrow spaces, resist shear forces, and safeguard against mechanical damage. Such plasticity depends on spatiotemporal regulation of the actomyosin cytoskeleton, but mechanisms of adaptive change in cell mechanics remain elusive. Here, we report a mechanism of mechanically activated actin polymerization at focal adhesions, specifically requiring the actin elongation factor mDia1. By combining live-cell imaging with mathematical modelling, we show that actin polymerization at focal adhesions exhibits pulsatile dynamics where spikes of mDia1 activity are triggered by contractile forces. The suppression of mDia1-mediated actin polymerization increases tension on stress fibers leading to an increased frequency of spontaneous stress fiber damage and decreased efficiency of zyxin-mediated stress fiber repair. We conclude that tension-controlled actin polymerization acts as a safety valve dampening excessive tension on the actin cytoskeleton and safeguarding stress fibers against mechanical damage.SUMMARYValenciaet al.report that tension-controlled actin polymerization at focal adhesions mediated by formin mDia1 controls mechanical tension on stress fibers. Suppression of mDia1 increases tension on the actin cytoskeleton leading to a higher rate of stress fiber damage and less efficient stress fiber repair.