bluuebunny/crossref_metadata_2025_split huggingface dataset:
Varicose Veins: A Local or Systemic Hemodynamic Disorder?
Authors: Kalinin Roman E. , Suchkov Igor A. , Laut Marina V. , Mzhavanadze Nina D. , Shanaev Ivan N. 
Published: April 2020

Objective: To determine the capabilities of a sonographic examination to evaluate local and systemic hemodynamic disorders in patients with varicose disease. Materials and Methods: This study included 583 patients with varicose veins, among whom 348 had trophic disorders. All subjects underwent lower limb duplex sonography and superficial, perforator, and deep venous diameter measurements, as well as had a calculated velocity for antegrade and reflux flow. Peripheral resistive index (RI) in the arteries, accompanying perforator veins (PVs), was analyzed. In addition, echocardiography was performed on 46 of the participants. Results: A statistically significant difference in the diameter of the great saphenous vein was obtained between class C2 and C4 varicose veins ( P < .05). Similar findings were obtained for the diameter of the PVs and the velocity reflux flow through PVs. Arteries in the perforator bundles demonstrated low RI, which may be attributed to the presence of arteriovenous shunts. Varicose veins were associated with an increased incidence of nonrestrictive type of blood flow through the tricuspid valve. Conclusions: Sonography demonstrated that additional factors rather than hemodynamics may be attributable to the development of venous ulcers. The most informative parameters of cardiac function, in a patient with varicose veins, are the indicators of diastolic function in both ventricles.
HLA loci predisposing to immune TTP in Japanese: potential role of the shared ADAMTS13 peptide bound to different HLA-DR
Authors: Sakai Kazuya , Kuwana Masataka , Tanaka Hidenori , Hosomichi Kazuyoshi , Hasegawa Atsushi , Uyama Hiroki , Nishio Kenji , Omae Takashi , Hishizawa Masakatsu , Matsui Masashi , Iwato Koji , Okamoto Akinao , Okuhiro Kazuki , Yamashita Yukiko , Itoh Masataka , Kumekawa Hanae , Takezako Naoki , Kawano Noriaki , Matsukawa Toshihiro , Sano Haruna , Ohshiro Kazuiku , Hayashi Kunio , Ueda Yasunori , Mushino Toshiki , Ogawa Yoshiyuki , Yamada Yuji , Murata Mitsuru , Matsumoto Masanori 
Published: April 2020

Abstract
Immune-mediated thrombotic thrombocytopenic purpura (iTTP) is a rare autoimmune disorder caused by neutralizing anti-ADAMTS13 autoantibodies. In white individuals, HLA allele DRB1*11 is a predisposing factor for iTTP, whereas DRB1*04 is a protective factor. However, the role of HLA in Asians is unclear. In this study, we analyzed 10 HLA loci using next-generation sequencing in 52 Japanese patients with iTTP, and the allele frequency in the iTTP group was compared with that in a Japanese control group. We identified the following HLA alleles as predisposing factors for iTTP in the Japanese population: DRB1*08:03 (odds ratio [OR], 3.06; corrected P [Pc] = .005), DRB3/4/5*blank (OR, 2.3; Pc = .007), DQA1*01:03 (OR, 2.25; Pc = .006), and DQB1*06:01 (OR,: 2.41; Pc = .003). The estimated haplotype consisting of these 4 alleles was significantly more frequent in the iTTP group than in the control group (30.8% vs 6.0%; Pc &lt; .001). DRB1*15:01 and DRB5*01:01 were weak protective factors for iTTP (OR, 0.23; Pc = .076; and OR, 0.23, Pc = .034, respectively). On the other hand, DRB1*11 and DRB1*04 were not associated with iTTP in the Japanese. These findings indicated that predisposing and protective factors for iTTP differ between Japanese and white individuals. HLA-DR molecules encoded by DRB1*08:03 and DRB1*11:01 have different peptide-binding motifs, but interestingly, bound to the shared ADAMTS13 peptide in an in silico prediction model.
Coexpression of FOXP3 and a Helios isoform enhances the effectiveness of human engineered regulatory T cells
Authors: Seng Amara , Krausz Kelsey L. , Pei Dong , Koestler Devin C. , Fischer Ryan T. , Yankee Thomas M. , Markiewicz Mary A. 
Published: April 2020

AbstractRegulatory T cells (Tregs) are a subset of immune cells that suppress the immune response. Treg therapy for inflammatory diseases is being tested in the clinic, with moderate success. However, it is difficult to isolate and expand Tregs to sufficient numbers. Engineered Tregs (eTregs) can be generated in larger quantities by genetically manipulating conventional T cells to express FOXP3. These eTregs can suppress in vitro and in vivo but not as effectively as endogenous Tregs. We hypothesized that ectopic expression of the transcription factor Helios along with FOXP3 is required for optimal eTreg immunosuppression. To test this theory, we generated eTregs by retrovirally transducing total human T cells (CD4+ and CD8+) with FOXP3 alone or with each of the 2 predominant isoforms of Helios. Expression of both FOXP3 and the full-length isoform of Helios was required for eTreg-mediated disease delay in a xenogeneic graft-versus-host disease model. In vitro, this corresponded with superior suppressive function of FOXP3 and full-length Helios-expressing CD4+ and CD8+ eTregs. RNA sequencing showed that the addition of full-length Helios changed gene expression in cellular pathways and the Treg signature compared with FOXP3 alone or the other major Helios isoform. Together, these results show that functional human CD4+ and CD8+ eTregs can be generated from total human T cells by coexpressing FOXP3 and full-length Helios.
Modulating the rate of fibrin formation and clot structure attenuates microvascular thrombosis in systemic inflammation
Authors: Valladolid Christian , Martinez-Vargas Marina , Sekhar Nitin , Lam Fong , Brown Cameron , Palzkill Timothy , Tischer Alexander , Auton Mathew , Vijayan K. Vinod , Rumbaut Rolando E. , Nguyen Trung C. , Cruz Miguel A. 
Published: April 2020

AbstractSystemic inflammation can lead to coagulopathy and disseminated intravascular coagulation (DIC). In prior studies, the recombinant A2 domain of human von Willebrand factor (VWF; A2 protein) attenuated DIC and decreased mortality in lipopolysaccharide (LPS)-treated mice. Here, we performed studies to dissect the mechanism by which the A2 protein moderates DIC. We used confocal microscopy to analyze the fibrin clot structure in plasma from healthy humans and endotoxemic mice, turbidity assays to examine fibrin polymerization, and a murine model for LPS-induced DIC and introduced a loss-of-function mutation into the A2 protein for fibrin. The mutation of the residue E1567 located in the α2 helix of the folded A2 domain of VWF inhibited binding activity for fibrin, possibly mapping a novel region containing a putative binding site for fibrin. The A2 protein increased the initial rate of change of fibrin polymerization, intercalated into the fibrin network, and modified the resultant clot structure in vitro. Furthermore, ex vivo experiments using plasma from mice with endotoxemia treated with the A2 protein revealed an increased rate of fibrin formation and an altered clot structure as compared with plasma from nontreated sick animals. Moreover, and in contrast to the A2 mutant, the A2 protein improved survival and reduced fibrin deposition and microvascular thrombosis in mice with endotoxemia-induced DIC. Importantly, in vivo and in vitro studies indicated that the A2 protein did not affect experimental thrombosis. Thus, we provide evidence for a novel treatment to attenuate systemic inflammation-induced coagulopathy/DIC via targeting fibrin formation, without an increased risk for bleeding.
The possible use of surian tree (Toona sinensis Roem) branches as an alternative raw material in the production of composite boards
Authors: Alamsyah Eka Mulya , Sutrisno  , Sumardi Ihak , Darwis Atmawi , Suhaya Yoyo , Hidayat Yayat 
Published: April 2020

AbstractThe current research focuses on the utilization of branches and twigs of surian as raw material for making composite boards in an effort to utilize the waste part of surian stem wood waste. The types of particle board and oriented strand board were bonded with phenol formaldehyde (PF) of 10% resin content. Variations of board density and board types were focused in this research. The boards were evaluated based on Japanese Industrial Standard (JIS). The results showed that the density of the board affected the physical and mechanical properties of the composite board. Strand boards were better than particle boards with regard to mechanical properties. Physical properties that met the testing standards were moisture content, density, water absorption and thickness swell for both after soaking 2 h in water, while for the mechanical properties test, only modulus of elasticity (MOE) met the standards. However, for further study, it seemed that generally this initial study informed that it was possible to make composite boards from the raw materials, both branches and twigs, with the additional treatment such as changing the size of particles and strands that could improve the properties of the board.
Application of Chemically Exfoliated Boron Nitride Nanosheets Doped with Co to Remove Organic Pollutants Rapidly from Textile Water
Authors: Hassan J. , Ikram M. , Ul-Hamid A. , Imran M. , Aqeel M. , Ali S. 
Published: April 2020

AbstractTwo-dimensional layered materials doped with transition metals exhibit enhanced magnetization and improved catalytic stability during water treatment leading to potential environmental applications across several industrial sectors. In the present study, cobalt (Co)-doped boron nitride nanosheets (BN-NS) were explored for such an application. Chemical exfoliation process was used to exfoliate BN-NS and the hydrothermal route was adopted to incorporate Co dopant in various concentrations (e.g., 2.5, 5, 7.5, and 10 wt%). X-ray diffraction (XRD) study indicated that crystallinity improved upon doping with the formation of a hexagonal phase of the synthesized material. Selected area electron diffraction (SAED) confirmed enhanced crystallinity, which corroborates XRD results. Interlayer spacing was evaluated through a high-resolution transmission electron microscope (HR-TEM) equipped with Gatan digital micrograph software. Compositional and functional group analysis was undertaken with energy dispersive X-ray (EDS) and Fourier transform infrared (FTIR) spectroscopy, respectively. Field emission scanning electron microscope (FE-SEM) and HR-TEM were utilized to probe surface morphologies of prepared samples. Bonding modes in the sample were identified through Raman analysis. Optical properties were examined using UV-vis spectroscopy. Photoluminescence spectra were acquired to estimate the separation and recombination of excitons. Magnetic properties were studied by means of hysteresis loop acquired using VSM measurements. Methylene blue dye was degraded with as-prepared host and doped nanosheets used as catalysts and investigated through absorption spectra ranging from 250 to 800 nm. The experimental results of this study indicate that Co-doped BN-NS showed enhanced magnetic properties and can be used to degrade dyes present as an effluent in industrial wastewater.
Exposure to low-dose nanopolystyrene induces the response of neuronal JNK MAPK signaling pathway in nematode Caenorhabditis elegans
Authors: Qu Man , Li Dan , Zhao Yunli , Yuan Yujie , Wang Dayong 
Published: April 2020

Abstract
Background
The response of organisms to nanoplastic exposure has gradually received the attention. Nevertheless, the role of neurons in response to nanoplastic exposure and the underlying mechanism are still largely unclear. We here examined the role of neuronal JNK MAPK signaling in response to low-dose of polystyrene (100 nm) in Caenorhabditis elegans.

Results
Exposure to nanopolystyrene in the range of μg/L could increase the expression of genes (jkk-1, mek-1, and jnk-1) encoding JNK MAPK signaling pathway. Meanwhile, RNAi knockdown of any of these genes induced a susceptibility to nanopolystyrene toxicity. In the neurons, SNB-1/synaptobrevin was identified as the downstream target of JNK-1/JNK, suggesting the alteration in neurotransmitter signals in nanopolystyrene-exposed nematodes. In nanopolystyrene-exposed nematodes, JNK-1 modulated TBH-1-mediated octopamine signal and CAT-2-mediated dopamine signal. TBH-1 and CAT-2 further regulated the response to nanopolystyrene by affecting the function of corresponding intestinal octopamine receptors (SER-6 and OCTR-1) and intestinal dopamine receptor (DOP-1). In the intestine, DOP-1 regulated the response to nanopolystyrene by activating the downstream signaling cascade in p38 MAPK signaling pathway.

Conclusions
Exposure to low-dose of nanopolystyrene could induce the response of neuronal JNK MAPK signaling pathway in nematodes. Our data further highlight the crucial role of neuronal JNK MAPK signaling-activated alteration in octopamine and dopamine signals in regulating the response to nanopolystyrene in organisms.
Which factors affect willingness-to-pay for automated vehicle services? Evidence from public road deployment in Stockholm, Sweden
Authors: Chee Pei Nen Esther , Susilo Yusak O. , Wong Yiik Diew , Pernestål Anna 
Published: April 2020

Abstract
Introduction
Travel demand and travel satisfaction of a transport service are affected by user perceptions of the service quality attributes, and such perceptions should be included in studying user willingness-to-pay (WTP) for automated vehicle (AV) services. This study applied structural equation modelling with service quality attribute perceptions as latent variables affecting WTP.

Objectives
We investigated how WTP AV services are affected by socio-demographic characteristics, knowledge and experiences with AV, existing travel modes and particularly, perceptions of the associated service quality attributes. The AV services are: 1) on-demand personalised AV (PAV) service, 2) demand responsive shared AV (SAV) service, and 3) first−/last-mile automated bus (AB) service.

Methods
The data were collected from 584 potential users of a first−/last-mile AB service trial operated in Kista, Stockholm.

Results
Results show people hold different expectations towards each type of AV service. These expectations act as the minimum requirements for people to pay for the AV services. Respondents are found to be willing to pay more for PAV service if it is safe, provides good ride comfort, and is competitively priced relative to the price travelling by metro and train over a same distance. Other than service quality attribute perceptions, income level, existing travel modes for daily trips, familiarity with automated driving technology and AB ride experience are important factors affecting WTP for the AV services.

Conclusion
The developed model can be applied to understand expectations of potential users towards a new AV service, and to identify user groups who are willing to pay the service. New AV services can thus be designed sensibly according to users’ actual needs.
ORdensity: user-friendly R package to identify differentially expressed genes
Authors: Martínez-Otzeta José María , Irigoien Itziar , Sierra Basilio , Arenas Concepción 
Published: April 2020

Abstract
Background
Microarray technology provides the expression level of many genes. Nowadays, an important issue is to select a small number of informative differentially expressed genes that provide biological knowledge and may be key elements for a disease. With the increasing volume of data generated by modern biomedical studies, software is required for effective identification of differentially expressed genes. Here, we describe an R package, called , that implements a recent methodology (Irigoien and Arenas, 2018) developed in order to identify differentially expressed genes. The benefits of parallel implementation are discussed.

Results
gives the user the list of genes identified as differentially expressed genes in an easy and comprehensible way. The experimentation carried out in an off-the-self computer with the parallel execution enabled shows an improvement in run-time. This implementation may also lead to an important use of memory load. Results previously obtained with simulated and real data indicated that the procedure implemented in the package is robust and suitable for differentially expressed genes identification.

Conclusions
The new package, , offers a friendly and easy way to identify differentially expressed genes, which is very useful for users not familiar with programming.

Availability
Using multiple reference genomes to identify and resolve annotation inconsistencies
Authors: Monnahan Patrick J. , Michno Jean-Michel , O’Connor Christine , Brohammer Alex B. , Springer Nathan M. , McGaugh Suzanne E. , Hirsch Candice N. 
Published: April 2020

Abstract
Background
Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ. Of particular concern are split-gene misannotations, in which a single gene is incorrectly annotated as two distinct genes or two genes are incorrectly annotated as a single gene. These misannotations can have major impacts on functional prediction, estimates of expression, and many downstream analyses.

Results
We developed a high-throughput method based on pairwise comparisons of annotations that detect potential split-gene misannotations and quantifies support for whether the genes should be merged into a single gene model. We demonstrated the utility of our method using gene annotations of three reference genomes from maize (B73, PH207, and W22), a difficult system from an annotation perspective due to the size and complexity of the genome. On average, we found several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3–5% of gene models across annotations. To determine which state (i.e. one gene or multiple genes) is biologically supported, we utilized RNAseq data from 10 tissues throughout development along with a novel metric and simulation framework. The methods we have developed require minimal human interaction and can be applied to future assemblies to aid in annotation efforts.

Conclusions
Split-gene misannotations occur at appreciable frequency in maize annotations. We have developed a method to easily identify and correct these misannotations. Importantly, this method is generic in that it can utilize any type of short-read expression data. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.
Morpho-physiological integrators, transcriptome and coexpression network analyses signify the novel molecular signatures associated with axillary bud in chrysanthemum
Authors: Ahmad Sagheer , Yuan Cunquan , Yang Qingqing , Yang Yujie , Cheng Tangren , Wang Jia , Pan Huitang , Zhang Qixiang 
Published: April 2020

AbstractBackgroundAxillary bud is an important agronomic and economic trait in cut chrysanthemum. Bud outgrowth is an intricate process controlled by complex molecular regulatory networks, physio-chemical integrators and environmental stimuli. Temperature is one of the key regulators of bud’s fate. However, little is known about the temperature-mediated control of axillary bud at molecular levels in chrysanthemum. A comprehensive study was designed to study the bud outgrowth at normal and elevated temperature in cut chrysanthemum. Leaf morphology, histology, physiological parameters were studied to correlate the leaf activity with bud morphology, sucrose and hormonal regulation and the molecular controllers.ResultsTemperature caused differential bud outgrowth along bud positions. Photosynthetic leaf area, physiological indicators and sucrose utilization were changed considerable due to high temperature. Comparative transcriptome analysis identified a significant proportion of bud position-specific genes.Weighted Gene Co-expression Network Analysis (WGCNA) showed that axillary bud control can be delineated by modules of coexpressed genes; especially, MEtan3, MEgreen2 and MEantiquewhite presented group of genes specific to bud length. A comparative analysis between different bud positions in two temperatures revealed the morpho-physiological traits associated with specific modules. Moreover, the transcriptional regulatory networks were configured to identify key determinants of bud outgrowth. Cell division, organogenesis, accumulation of storage compounds and metabolic changes were prominent during the bud emergence.ConclusionsRNA-seq data coupled with morpho-physiological integrators from three bud positions at two temperature regimes brings a robust source to understand bud outgrowth status influenced by high temperature in cut chrysanthemum. Our results provide helpful information for elucidating the regulatory mechanism of temperature on axillary bud growth in chrysanthemum.
Epidemiological characteristics and transmissibility of shigellosis in Hubei Province, China, 2005 – 2017
Authors: Chen Qi , Rui Jia , Hu Qingqing , Peng Ying , Zhang Hao , Zhao Zeyu , Tong Yeqing , Wu Yang , Su Yanhua , Zhao Benhua , Guan Xuhua , Chen Tianmu 
Published: April 2020

AbstractBackgroundShigellosis is one of the main diarrhea diseases in developing countries. However, the transmissibility of shigellosis remains unclear.MethodsWe used the dataset of shigellosis cases reported between January 2005 and December 2017, from Hubei Province, China. A mathematical model was developed based on the natural history and the transmission mechanism of the disease. By fitting the data using the model, transmission relative rate from person to person (b) and from reservoir to person (bw), and the effective reproduction number (Reff) were estimated. To simulate the contribution ofbandbwduring the transmission, we performed a “knock-out” simulation in four scenarios: A)b = 0 andbw = 0; B)b = 0; C)bw = 0; D) control (no intervention).ResultsA total of 130,770 shigellosis cases were reported in Hubei province, among which 13 cases were dead. The median annual incidence was 19.96 per 100,000 persons (range: 5.99 per 100,000 persons – 29.47 per 100,000 persons) with a decreased trend (trendχ2 = 25,470.27,P < 0.001). The mean values ofbandbwwere 0.0898 (95% confidence interval [CI]: 0.0851–0.0946) and 1.1264 × 10− 9(95% CI: 4.1123 × 10− 10–1.8416 × 10− 9), respectively. The “knock-out” simulation showed that the number of cases simulated by scenario A was almost the same as scenario B, and scenario C was almost the same as scenario D. The mean value ofReffof shigellosis was 1.19 (95% CI: 1.13–1.25) and decreased slightly with a Linear model until it decreased to an epidemic threshold of 0.99 (95% CI: 0.65–1.34) in 2029.ConclusionsThe incidence of shigellosis is still in high level. The transmissibility of the disease is low in Hubei Province. The transmission would be interrupted in the year of 2029.