bluuebunny/crossref_metadata_2025_split huggingface dataset:
Household Debt Accumulation and the Great Recession of the United States: A Comparative Perspective
Authors: Kim Yun K. 
Published: November 2019

The Great Recession has provided an important intellectual challenge to both post-Keynesian and mainstream economists. In this article we survey some post-Keynesian views on household debt accumulation and the Great Recession of the United States, as well as the Atif Mian and Amir Sufi’s studies, perhaps the most influential and empirically-oriented studies of mainstream economics. We identify and distinguish their policy perspectives, and highlight commonalities and differences between them. By examining both post-Keynesian and Mian and Sufi’s views together, this paper emphasizes that, although there are clear differences between them, a careful examination reveals valuable complementarity which yields a better understanding of household debt accumulation and the Great Recession of the United States. JEL classification: E21, E32, E52, E62
Spinal cord syndromes in patients with systemic lupus erythematosus: differentiating lupus myelitis, neuromyelitis optica, and multiple sclerosis
Authors: Williams J N , Speyer C B , Kreps D J , Kimbrough D J , Costenbader K , Bhattacharyya S 
Published: November 2019

Objective Non-infectious myelitis in systemic lupus erythematosus (SLE) may be due to SLE myelitis, comorbid multiple sclerosis (MS), or neuromyelitis optica (NMO). We compared characteristics of these three conditions in SLE patients at a large academic institution. Methods We searched for neurologic diagnoses of SLE myelitis, NMO myelitis, and MS myelitis among 2297 patients with at least four 1997 American College of Rheumatology revised criteria for SLE between 2000 and 2015. Each subject was reviewed by a neurologist to confirm the underlying neurologic diagnosis. Demographic, clinical, laboratory, and radiographic data were extracted and compared using Fisher's exact test, analysis of variance, and Wilcoxon rank-sum test. Results Fifteen of the 2297 subjects with SLE (0.7%) met criteria for a spinal cord syndrome: seven had SLE myelitis, three had AQP4 seropositive NMO, and five had MS. The median SLE Disease Activity Index 2000 score at time of neurologic syndrome presentation was higher in SLE myelitis subjects (8, interquartile range (IQR) 7–16) compared with subjects with NMO (6, IQR 0–14) or MS (2, IQR 0–4), p = 0.02. Subjects with SLE myelitis were also more likely to have elevated anti-dsDNA antibodies at presentation (86%) compared with subjects with NMO (33%) or MS (0%), p = 0.03. Conclusion Myelitis occurs rarely among patients with SLE. Compared with subjects with SLE + NMO and subjects with SLE + MS, subjects with SLE myelitis had higher SLE disease activity at presentation.
Neurofilament light levels are associated with long-term outcomes in multiple sclerosis
Authors: Kuhle Jens , Plavina Tatiana , Barro Christian , Disanto Giulio , Sangurdekar Dipen , Singh Carol M , de Moor Carl , Engle Bob , Kieseier Bernd C , Fisher Elizabeth , Kappos Ludwig , Rudick Richard A , Goyal Jaya 
Published: November 2019

Background: Neurofilament light chain (NfL) is a promising marker of disease activity/treatment response in multiple sclerosis (MS), although its predictive value for long-term clinical outcomes remains unclear. Objective: We measured NfL from a phase 3 trial in relapsing-remitting MS and investigated its association with outcomes after 8 and 15 years. Methods: NfL concentrations were measured by single molecule array assay in cerebrospinal fluid (CSF) from MS patients ( n = 235) in a 2-year randomized clinical trial (RCT) of intramuscular interferon β-1a, and in serum ( n = 164) from the extension study. Results: Year 2 CSF and Year 3 serum NfL were associated with brain parenchymal fraction (BPF) change over 8 years ( p < 0.0001, r = −0.46; p < 0.05. r = −0.36, respectively) and were predictive of reaching Expanded Disability Status Scale (EDSS) ⩾ 6.0 at Year 8 (odds ratio (OR) (upper vs lower tertile) = 3.4; 95% confidence interval (CI) = 1.2–9.9, p < 0.05; OR = 11.0, 95% CI = 2.0–114.6; p < 0.01, respectively). Serum NfL concentration (Year 4) was predictive of reaching EDSS score ⩾6.0 at 15 years (OR (upper vs lower tertile) = 4.9; 95% CI = 1.4–20.4; p < 0.05). NfL concentrations were complementary to 2-year BPF change in predicting long-term outcomes. Conclusion: Serum and CSF NfL concentrations were associated with long-term clinical outcomes in MS patients and are promising biomarkers for disease severity stratification supporting treatment decisions.
Factors Affecting Caregivers’ Acceptance of the Use of Wearable Devices by Patients With Dementia: An Extension of the Unified Theory of Acceptance and Use of Technology Model
Authors: Dai Baozhen , Larnyo Ebenezer , Tetteh Ebenezer Ababio , Aboagye Abigail Konadu , Musah Abdul-Aziz Ibn 
Published: November 2019

Purpose: This study aims to examine the factors affecting caregivers’ acceptance of the use of wearable devices by patients with dementia by extending the Unified Theory of Acceptance and Use of Technology (UTAUT) model with 2 additional constructs: resistance to change (RC) and technology anxiety (TA). Methods: A structured online questionnaire was developed and distributed to caregivers who have either dealt previously with or were currently taking care of patients with dementia in sub-Saharan Africa. The selection of countries for the study was purely based on the availability of caregivers of patients with dementia and their readiness to take part in the survey. Questionnaire data from 350 respondents were analyzed and the hypothesis tested using partial least squares based on structural equation modeling. Result: The results of the extended model show that social influence, effort expectancy, facilitating conditions, and behavioral intention (BI) all had P < .05, thus were statistically significant in explaining the perceived BI and actual use of health-care wearable devices among patients with dementia as reported by caregivers. However, P value for RC and TA was greater than .05, hence were insignificant.
Long-term (>10-year) clinical follow-up after young embolic stroke/TIA of undetermined source
Authors: Nassif M , Annink ME , Yang H , Rettig TCD , Roos YBWEM , van den Brink RBA , Tijssen JGP , Mulder BJM , de Winter RJ , Bouma BJ 
Published: November 2019

Background To date, the pathophysiology of first-ever and recurrent stroke/TIA still remains unclear in young patients with embolic stroke/TIA of undetermined source (ESUS). Clinical studies with long-term follow-up in young ESUS patients are necessary to investigate the underlying pathophysiology of first-ever and recurrent stroke/TIA in this patient population, in particular the role of new-onset atrial fibrillation. Aims Our aim was to study the long-term (>10-year) clinical outcome of young patients (<50 years) with ESUS. Methods This cohort study included all patients aged ≤ 50 years who underwent transoesophageal echocardiography for diagnostic work-up of ESUS during 1996–2008 from one tertiary center. All patients were contacted by telephone between September–November 2018 to update clinical information from medical records. The clinical outcomes of this study were incidence rates of all-cause and cardiovascular mortality, recurrent stroke/TIA, new-onset clinical AF, and ischemic vascular events. Results In total, 108 patients (57% female, mean age 40 ± 7.2 years [range 19–50 years], n = 72 stroke) were included. Across clinical follow-up (median 13[IQR 10–16] years), 24 patients died ( n = 14 cardiovascular). The 15-year incidence rate of recurrent stroke/TIA was 15% (incidence rate = 1.09[95%CI 0.54–1.65]/100 patient-years) and a 5.5% incidence of new-onset clinical AF (incidence rate = 0.44[95%CI 0.09–0.79]/100 patient-years) following ESUS. Conclusions The incidence of recurrent stroke/TIA is relatively high during long-term clinical follow-up of young patients with ESUS. In contrast, new-onset clinical AF is relatively low and therefore may not play an important part in the pathophysiology of first-ever and recurrent stroke/TIA of these patients.
Koryakite, NaKMg2Al2(SO4)6, a new NASICON-related anhydrous sulfate mineral from Tolbachik volcano, Kamchatka, Russia
Authors: Siidra Oleg I. , Nazarchuk Evgeny V. , Zaitsev Anatoly N. , Vlasenko Natalia S. 
Published: November 2019

AbstractExhalative mineral assemblages from fumaroles of Tolbachik volcano are very rich in anhydrous sulfate minerals of alkali and transition metals. Koryakite, ideally NaKMg2Al2(SO4)6, was found in the Yadovitaya fumarole of the Second scoria cone of the North Breach of the Great Tolbachik Fissure Eruption (1975–1976), Tolbachik volcano, Kamchatka Peninsula, Russia. Koryakite occurs as a product of fumarolic activity and closely associates with euchlorine and langbeinite. Koryakite is trigonal, R$\bar{3}$, a = 8.1124(11), c = 22.704(7) Å and V = 1294.0(5) Å3. The chemical composition determined by electron-microprobe analysis is (wt.%): Na2O 4.27, K2O 5.85, ZnO 0.31, СaO 0.31, CuO 0.76, MgO 10.15, Al2O3 11.47, Fe2O3 2.73, SO3 64.33 and SiO2 0.13, total 100.31. The empirical formula calculated on the basis of 24 O apfu is Na1.03K0.93(Mg1.89Cu0.07Ca0.04Zn0.03)Σ2.03(Al1.68Fe3+0.26)Σ1.94(S6.02Si0.02)Σ6.04O24. No natural or synthetic chemical analogues of koryakite are known to date. The topology of the [M2+2M3+2(SO4)6]2– heteropolyhedral framework in koryakite is very similar to the one in millosevichite, Al2(SO4)3 and mikasaite, Fe3+2(SO4)3. Replacement of part of the trivalent cations in the [M3+2(SO4)3]0 framework by divalent cations gives the framework a negative charge for koryakite and allows the incorporation of the alkali species in the channels. This structural mechanism is reminiscent of the concept of stuffed derivative structures. Koryakite is also structurally related to synthetic NaMgFe3+(SO4)3 and to the broader family of NASICON-related phases.
An immunoevasive strategy through clinically-relevant pan-cancer genomic and transcriptomic alterations of JAK-STAT signaling components
Authors: Chang Wai Hoong , Lai Alvina G. 
Published: November 2019

AbstractBackgroundSince its discovery almost three decades ago, the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway has paved the road for understanding inflammatory and immunity processes related to a wide range of human pathologies including cancer. Several studies have demonstrated the importance of JAK-STAT pathway components in regulating tumor initiation and metastatic progression, yet, the extent of how genetic alterations influence patient outcome is far from being understood.MethodsFocusing on 133 genes involved in JAK-STAT signaling, we investigated genomic, transcriptomic and clinical profiles of over 18,000 patients representing 21 diverse cancer types. We identified a core set of 28 putative gain- or loss-of-function JAK-STAT genes that correlated with survival outcomes using Cox proportional hazards regression and Kaplan-Meier analyses. Differential expression analyses between high- and low-expressing patient groups were performed to evaluate the consequences of JAK-STAT misexpression.ResultsWe found that copy number alterations underpinning transcriptional dysregulation of JAK-STAT pathway genes differ within and between cancer types. Integrated analyses uniting genomic and transcriptomic datasets revealed a core set of JAK-STAT pathway genes that correlated with survival outcomes in brain, renal, lung and endometrial cancers. High JAK-STAT scores were associated with increased mortality rates in brain and renal cancers, but not in lung and endometrial cancers where hyperactive JAK-STAT signaling is a positive prognostic factor. Patients with aberrant JAK-STAT signaling demonstrated pan-cancer molecular features associated with misexpression of genes in other oncogenic pathways (Wnt, MAPK, TGF-β, PPAR and VEGF). Brain and renal tumors with hyperactive JAK-STAT signaling had increased regulatory T cell gene (Treg) expression. A combined model uniting JAK-STAT and Tregs allowed further delineation of risk groups where patients with high JAK-STAT and Treg scores consistently performed the worst.ConclusionProviding a pan-cancer perspective of clinically-relevant JAK-STAT alterations, this study could serve as a framework for future research investigating anti-tumor immunity using combination therapy involving JAK-STAT and immune checkpoint inhibitors.
A Tunable Dual-Band and Polarization-Insensitive Coherent Perfect Absorber Based on Double-Layers Graphene Hybrid Waveguide
Authors: Luo Xin , Cheng Zi-Qiang , Zhai Xiang , Liu Zhi-Min , Li Si-Qi , Liu Jian-Ping , Wang Ling-Ling , Lin Qi , Zhou Yan-Hong 
Published: November 2019

Abstract
A suspended monolayer graphene has only about 2.3% absorption rate in visible and infrared band, which limits its optoelectronic applications. To significantly increase graphene’s absorption efficiency, a tunable dual-band and polarization-insensitive coherent perfect absorber (CPA) is proposed in the mid-infrared regime, which contains the silicon array coupled in double-layers graphene waveguide. Based on the FDTD methods, dual-band perfect absorption peaks are achieved in 9611 nm and 9924 nm, respectively. Moreover, due to its center symmetric feature, the proposed absorber also demonstrates polarization-insensitive. Meanwhile, the coherent absorption peaks can be all-optically modulated by altering the relative phase between two reverse incident lights. Furthermore, by manipulating the Fermi energies of two graphene layers, two coherent absorption peaks can move over a wide spectrum range, and our designed CPA can also be changed from dual-band CPA to narrowband CPA. Thus, our results can find some potential applications in the field of developing nanophotonic devices with excellent performance working at the mid-infrared regime.
A binning tool to reconstruct viral haplotypes from assembled contigs
Authors: Chen Jiao , Shang Jiayu , Wang Jianrong , Sun Yanni 
Published: November 2019

AbstractBackgroundInfections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed.ResultsWe developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction.ConclusionsIn this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. It competes favorably with other tools on viral contig binning. The source codes are available at:https://github.com/chjiao/VirBin.
Predictive modelling using pathway scores: robustness and significance of pathway collections
Authors: Segura-Lepe Marcelo P. , Keun Hector C. , Ebbels Timothy M. D. 
Published: November 2019

Abstract

Background
Transcriptomic data is often used to build statistical models which are predictive of a given phenotype, such as disease status. Genes work together in pathways and it is widely thought that pathway representations will be more robust to noise in the gene expression levels. We aimed to test this hypothesis by constructing models based on either genes alone, or based on sample specific scores for each pathway, thus transforming the data to a ‘pathway space’. We progressively degraded the raw data by addition of noise and examined the ability of the models to maintain predictivity.

Results
Models in the pathway space indeed had higher predictive robustness than models in the gene space. This result was independent of the workflow, parameters, classifier and data set used. Surprisingly, randomised pathway mappings produced models of similar accuracy and robustness to true mappings, suggesting that the success of pathway space models is not conferred by the specific definitions of the pathway. Instead, predictive models built on the true pathway mappings led to prediction rules with fewer influential pathways than those built on randomised pathways. The extent of this effect was used to differentiate pathway collections coming from a variety of widely used pathway databases.

Conclusions
Prediction models based on pathway scores are more robust to degradation of gene expression information than the equivalent models based on ungrouped genes. While models based on true pathway scores are not more robust or accurate than those based on randomised pathways, true pathways produced simpler prediction rules, emphasizing a smaller number of pathways.
ProTstab – predictor for cellular protein stability
Authors: Yang Yang , Ding Xuesong , Zhu Guanchen , Niroula Abhishek , Lv Qiang , Vihinen Mauno 
Published: November 2019

Abstract

Background
Stability is one of the most fundamental intrinsic characteristics of proteins and can be determined with various methods. Characterization of protein properties does not keep pace with increase in new sequence data and therefore even basic properties are not known for far majority of identified proteins. There have been some attempts to develop predictors for protein stabilities; however, they have suffered from small numbers of known examples.

Results
We took benefit of results from a recently developed cellular stability method, which is based on limited proteolysis and mass spectrometry, and developed a machine learning method using gradient boosting of regression trees. ProTstab method has high performance and is well suited for large scale prediction of protein stabilities.

Conclusions
The Pearson’s correlation coefficient was 0.793 in 10-fold cross validation and 0.763 in independent blind test. The corresponding values for mean absolute error are 0.024 and 0.036, respectively. Comparison with a previously published method indicated ProTstab to have superior performance. We used the method to predict stabilities of all the remaining proteins in the entire human proteome and then correlated the predicted stabilities to protein chain lengths of isoforms and to localizations of proteins.
Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection
Authors: Ma Xuelian , Zhao Xiaomin , Wang Kaili , Tang Xiaoyi , Guo Jianxiong , Mi Mi , Qi Yanping , Chang Lingling , Huang Yong , Tong Dewen 
Published: November 2019

AbstractBackgroundTransmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown.ResultsIn this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML).ConclusionsThe data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.
Transcriptome analysis of the differential effect of the NADPH oxidase gene RbohB in Phaseolus vulgaris roots following Rhizobium tropici and Rhizophagus irregularis inoculation
Authors: Fonseca-García Citlali , Zayas Alejandra E. , Montiel Jesús , Nava Noreide , Sánchez Federico , Quinto Carmen 
Published: November 2019

AbstractBackgroundReactive oxygen species (ROS) are generated by NADPH oxidases known as respiratory burst oxidase homologs (RBOHs) in plants. ROS regulate various cellular processes, including the mutualistic interactions between legumes and nitrogen-fixing bacteria or arbuscular mycorrhizal (AM) fungi.Rbohis a multigene family comprising nine members (RbohA–I) in common bean (Phaseolus vulgaris).The RNA interference-mediated silencing ofRbohB(PvRbohB-RNAi) in this species diminished its ROS production and greatly impaired nodulation. By contrast, thePvRbohB-RNAi transgenic roots showed early hyphal root colonization with enlarged fungal hypopodia; therefore, we proposed thatPvRbohBpositively regulates rhizobial infection (Rhizobium tropici) and inhibits AM colonization byRhizophagus irregularisinP. vulgaris.ResultsTo corroborate this hypothesis, an RNA-Seq transcriptomic analysis was performed to identify the differentially expressed genes in thePvRbohB-RNAi roots inoculated withRhizobium tropiciorRhizophagus irregularis. We found that, in the early stages, root nodule symbioses generated larger changes of the transcriptome than did AM symbioses inP. vulgaris. Genes related to ROS homeostasis and cell wall flexibility were markedly upregulated in the early stages of rhizobial colonization, but not during AM colonization. Compared with AM colonization, the rhizobia induced the expression of a greater number of genes encoding enzymes involved in the metabolism of auxins, cytokinins, and ethylene, which were typically repressed in thePvRbohB-RNAi roots.ConclusionsOur research provides substantial insights into the genetic interaction networks in the early stages of rhizobia and AM symbioses withP. vulgaris, as well as the differential roles thatRbohBplays in processes related to ROS scavenging, cell wall remodeling, and phytohormone homeostasis during nodulation and mycorrhization in this legume.