bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Integrin β3 Gene Expression: Evidence for a Megakaryocytic Cell-Specific cis-Acting Element
Authors: Jin Ying , Wilhide Calvin C. , Dang Chi , Li Lu , Li Su-Xia , Villa-Garcia Manuel , Bray Paul F. 
Published: October 2019

The human integrin β3 participates in a wide range of adhesive biologic functions and is expressed in a selected subset of tissues, but little is known about the cis-acting DNA elements or trans-acting factors responsible for this regulation. Using cell lines characterized for β3 expression, a number of upstream regulatory regions in the β3 gene were identified. (1) The three regions from −1159 to −584, −290 to −146, and −126 to −115 demonstrated positive, negative, and negative activity, respectively. (2) The region from −115 to +29 of the β3 gene was sufficient for cell-specific activity. Deletion of the sequence from −115 to −89 produced a 6- to 40-fold reduction in reporter gene activity in β3-expressing megakaryocytic cell lines (K562, Dami, and HEL), but only a 1.7- and 2.7-fold reduction, respectively, in β3-expressing endothelial and melanoma cell lines, and 1.3- and 2.8-fold reduction, respectively, in non–β3-expressing Chinese hamster ovary and 293 cell lines. This sequence also bound nuclear proteins in a cell-specific manner in electrophoretic mobility shift assays. Mutational analysis indicated that the sequence GAGGGG (positions −113 to −108) is a megakaryocytic cell line-specificcis-acting element. (3) The region from −89 to +29 promoted lower activity in all cell lines. We also provide evidence that a CCCACCC sequence at position −70 has transcriptional activity, most likely through the Sp1 transcription factor. These data supply the first detailed map of the transcriptional regulatory elements of the 5′ region of the β3 gene, define positive regulatory sequences with potent megakaryocyte preferential activity, and indicate that the ubiquitous transcription factor, Sp1, may augment β3 gene expression.© 1998 by The American Society of Hematology.
Prolonged Phenotypic, Functional, and Molecular Change in Group I Burkitt Lymphoma Cells on Short-Term Exposure to CD40 Ligand
Authors: Baker Matthew P. , Eliopoulos Aristides G. , Young Lawrence S. , Armitage Richard J. , Gregory Christopher D. , Gordon John 
Published: October 2019

Group I Burkitt lymphoma (BL) cell lines (L3055, Elijah, Louckes, BL2, and BL29) retaining the original biopsy phenotype were found to undergo prolonged phenotypic, functional, and molecular change on short-term exposure to soluble recombinant CD40L trimer. Sensitivity to, extent of, and duration of change appeared to reflect passage number in that the earliest passaged lines, L3055 and BL29, were generally the most susceptible. Culture of group I BL lines with CD40L resulted in significant growth arrest (without apoptosis) that, for L3055 cells, was sustained for 7 to 9 days after 72 hours of exposure. This was accompanied by the formation of large homotypic aggregates together with gross changes in individual cell morphology and a concomitant upregulation of CD54 (ICAM-1). Three of the five group I BL lines exhibited rapid downregulation of the hallmark CD77 surface antigen, which, for L3055 cells, was maintained for at least 12 days after 72 hours of incubation with CD40L. With the exception of BL2, all group I BL lines were induced to express CD40 homodimers on CD40-stimulation, whereas only monomers were detected in unstimulated cells. Experiments using CD40-transfected Rat-1 fibroblasts showed that the ability to signal for dimer formation required Thr234of CD40. For L3055 and BL29 cells, an initial 72 hours of exposure to CD40L resulted in the maintenance of homodimers for up to 14 and 10 days, respectively. There was a close correlation between the induction and duration of CD40 homodimers and the appearance of Bcl-2. For L3055 cells, which are sensitive to apoptosis-induction on BCR-engagement, exposure to CD40L for 72 hours was found to provide considerable protection from anti-IgM, which was still significant to 20 days. The implications of such sustained effects on relatively short-term exposure of tumor B cells to CD40L are discussed.© 1998 by The American Society of Hematology.
Altered Expression and Activity of Topoisomerases During All-Trans Retinoic Acid-Induced Differentiation of HL-60 Cells
Authors: Aoyama Masako , Grabowski Dale R. , Isaacs Richard J. , Krivacic Kim A. , Rybicki Lisa A. , Bukowski Ronald M. , Ganapathi Mahrukh K. , Hickson Ian D. , Ganapathi Ram 
Published: October 2019

Regulation of topoisomerase II (TOPO II) isozymes  and β is influenced by the growth and transformation state of cells. Using HL-60 cells induced to differentiate by all-trans retinoic acid (RA), we have investigated the expression and regulation of TOPO II isozymes as well as the levels of topoisomerase I (TOPO I). During RA-induced differentiation of human leukemia HL-60 cells, levels of TOPO I remained unchanged, whereas the levels and phosphorylation of TOPO II and TOPO IIβ proteins were increased twofold to fourfold and fourfold to eightfold, respectively. The elevation of TOPO II ( and β) protein levels and phosphorylation was apparent at 48 hours of treatment with RA and persisted through 96 hours. The increased level of TOPO IIβ protein was also detected in differentiated cells subsequently cultured for 96 hours in RA-free medium. Pulse chase experiments in cells labeled with 35S-methionine showed that the rate of degradation of TOPO IIβ protein in control cells was about twofold faster than that in the differentiated RA-treated cells. The level of decatenation activity of kDNA was comparable in nuclear extracts from control or RA-treated cells. Whereas etoposide (1 to 10 μmol/L) -induced DNA cleavage was not significantly different, apoptosis was significantly lower (P = .012) in RA-treated versus control cells after exposure to 10 μmol/L etoposide. Consistent with unaltered levels of TOPO I, camptothecin (CPT) -induced DNA cleavage was similar in control or RA-treated cells. However, apoptosis after exposure to 1 to 10 μmol/L CPT was significantly lower (P = .003 to P < .001) in RA-treated versus control cells. Results suggest that TOPO IIβ protein levels are posttranscriptionally regulated and that degradation of TOPO IIβ is decreased during RA-induced differentiation. Furthermore, whereas the total level of TOPO II ( + β) is increased with RA, the level of TOPO II catalytic activity and etoposide-stabilized DNA cleavage activity remains unaltered. Thus, TOPO IIβ may have a specific role in transcription of genes involved in differentiation with RA treatment.© 1998 by The American Society of Hematology.
Serum Transferrin Receptor and Transferrin Receptor-Ferritin Index Identify Healthy Subjects With Subclinical Iron Deficits
Authors: Suominen Pauli , Punnonen Kari , Rajamäki Allan , Irjala Kerttu 
Published: October 2019

Despite the established utility of serum transferrin receptor (sTfR), serum ferritin, and the sTfR/log ferritin ratio (TfR-F Index) in the diagnosis of iron deficiency (ID) anemia, the numeric values of these parameters, which are indicative of subclinical ID, remain to be clearly defined. In this study, 65 apparently healthy nonanemic adults (22 men and 43 women) were treated with 3 months of oral iron supplementation to evaluate its effect on parameters reflecting iron status and to determine the prevalence of subclinical iron deficiency in apparently healthy adults. Significant supplementation-induced changes were observed in sTfR, ferritin, and TfR-F Index values in women, whereas in men, none of the studied parameters showed any significant change. Iron-deficient erythropoiesis (IDE) was not observed in men, but was found in 17 women (40%). Although individuals with a compromised iron status may be represented in substantial numbers in conventional reference populations, they can be readily identified using sTfR, ferritin, and TfR-F Index determinations.© 1998 by The American Society of Hematology.
Gi and Gq/11 proteins are involved in dissemination of myeloid leukemia cells to the liver and spleen, whereas bone marrow colonization involves Gq/11 but not Gi
Authors: Soede Ron D. M. , Wijnands Yvonne M. , Kamp Marga , van der Valk Martin A. , Roos Ed 
Published: October 2019

AbstractThe migration of leukocytes into tissues is regulated by chemokines and other chemotactic factors that act on receptors that signal through Gi proteins. It seems likely that the colonization of tissues during dissemination of hematopoietic tumor cells is similarly regulated. In fact, dissemination of a T-cell hybridoma, a model for T lymphoma, was blocked when Gi proteins were inactivated by the S1 catalytic subunit of pertussis toxin that had been transfected into those cells. Pertussis toxin S1 blocked dissemination of MDAY-D2 murine myeloid leukemia cells to the liver and spleen, as in T-cell hybridoma cells, but it did not prevent bone marrow colonization. In contrast, overexpression of a function-defective mutant of the Gq/11 protein blocked dissemination to the bone marrow and also prevented Gq/11 dissemination to the liver and spleen. This indicates that the influx of these myeloid cells into all tissues requires the Gq/11 protein in addition to the Gi protein in the liver and spleen.
Magnetic Field-Enhancing Photocatalytic Reaction in Micro Optofluidic Chip Reactor
Authors: Huang Hung Ji , Wang Yen Han , Chau Yuan-Fong Chou , Chiang Hai-Pang , Wu Jeffrey Chi-Sheng 
Published: October 2019

Abstract
A small external magnetic field (100–1000 Oe) was demonstrated to enhance the photocatalytic degradation of methyl orange (MO) using TiO2 NPs in micro optofluidic chip (MOFC) reactors. The rectangular shape of the fluidic channel and TiO2 deposited only onto the lower glass substrate leads to a selectively enhancing photocatalytic reactions by magnetic field in specific directions. Utilizing ethyl alcohol as a scavenger presented the difference between generated hot-hole (hVB+) and hot-electron (eCB−) pathways of photocatalytic reactions. Effects of dissolved oxygen (DO) and hydroxyl ions (OH−) are all demonstrated in a magnetic field-enhancing photocatalytic reaction. The experimental results demonstrate great potential for practical applications utilizing low-price fixed magnets in the field of green chemistry.
Intrinsic bubbles and Granger causality in the Hong Kong residential property market
Authors: Lan Ting 
Published: October 2019

AbstractThis study uses the intrinsic bubbles detection method to identify housing bubbles in the Hong Kong residential property market. By using sample period data from 1993 to 2019, the empirical results show evidence of intrinsic bubbles. Based on the unit root and co-integration tests, I found that there are no rational speculative bubbles in the Hong Kong residential property market. Furthermore, by using the Granger causality tests of the corresponding asymmetric VECM specification, there is no causality from lagged changes in the rental price returns to changes in the property price returns. However, there is strong evidence to show that changes in the property price index returns can Granger cause changes in the rental price index returns.
Response-based methods to measure road surface irregularity: a state-of-the-art review
Authors: Nguyen Teron , Lechner Bernhard , Wong Yiik Diew 
Published: October 2019

Abstract

Purpose
With the development of smart technologies, Internet of Things and inexpensive onboard sensors, many response-based methods to evaluate road surface conditions have emerged in the recent decade. Various techniques and systems have been developed to measure road profiles and detect road anomalies for multiple purposes such as expedient maintenance of pavements and adaptive control of vehicle dynamics to improve ride comfort and ride handling. A holistic review of studies into modern response-based techniques for road pavement applications is found to be lacking. Herein, the focus of this article is threefold: to provide an overview of the state-of-the-art response-based methods, to highlight key differences between methods and thereby to propose key focus areas for future research.

Methods
Available articles regarding response-based methods to measure road surface condition were collected mainly from “Scopus” database and partially from “Google Scholar”. The search period is limited to the recent 15 years. Among the 130 reviewed documents, 37% are for road profile reconstruction, 39% for pothole detection and the remaining 24% for roughness index estimation.

Results
The results show that machine-learning techniques/data-driven methods have been used intensively with promising results but the disadvantages on data dependence have limited its application in some instances as compared to analytical/data processing methods. Recent algorithms to reconstruct/estimate road profiles are based mainly on passive suspension and quarter-vehicle-model, utilise fewer key parameters, being independent on speed variation and less computation for real-time/online applications. On the other hand, algorithms for pothole detection and road roughness index estimation are increasingly focusing on GPS accuracy, data aggregation and crowdsourcing platform for large-scale application. However, a novel and comprehensive system that is comparable to existing International Roughness Index and conventional Pavement Management System is still lacking.
Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature
Authors: Weber Zendrera Adèle , Sokolovska Nataliya , Soula Hédi A. 
Published: October 2019

Abstract

Background
Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to study fluxes through the reactions, or to relate the graph structure to environmental characteristics and phenotypes. About ten years ago, Takemoto et al. (2007) stated that the structure of prokaryotic metabolic networks represented as undirected graphs, is correlated to their living environment. Although metabolic networks are naturally directed graphs, they are still usually analysed as undirected graphs.

Results
We implemented a pipeline to reconstruct metabolic networks from genome data and confirmed some of the results of Takemoto et al. (2007) with today data using up-to-date databases. However, Takemoto et al. (2007) used only a fraction of all available enzymes from the genome and taking into account all the enzymes we fail to reproduce the main results. Therefore, we introduce three robust measures on directed representations of graphs, which lead to similar results regardless of the method of network reconstruction. We show that the size of the largest strongly connected component, the flow hierarchy and the Laplacian spectrum are strongly correlated to the environmental conditions.

Conclusions
We found a significant negative correlation between the size of the largest strongly connected component (a cycle) and the optimal growth temperature of the considered prokaryotes. This relationship holds true for the spectrum, high temperature being associated with lower eigenvalues. The hierarchy flow shows a negative correlation with optimal growth temperature. This suggests that the dynamical properties of the network are dependant on environmental factors.
EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm
Authors: Hua Kang-Jian , Ma Bin-Guang 
Published: October 2019

AbstractBackgroundMore and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need.ResultsWe have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs.ConclusionsEVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.
Protective role of berberine in isoprenaline-induced cardiac fibrosis in rats
Authors: Che Yan , Shen Di-Fei , Wang Zhao-Peng , Jin Ya-Ge , Wu Qing-Qing , Wang Sha-Sha , Yuan Yuan 
Published: October 2019

Abstract

Background
Cardiac fibrosis is a crucial aspect of cardiac remodeling that can severely affect cardiac function. Cardiac fibroblasts surely influence this process. Besides, macrophage plays an essential role in cardiac remodeling after heart injury. However, whether macrophage influence fibroblasts remain a question worth exploring. This study aimed to define the role of berberine (BBR) on isoprenaline (ISO)-induced cardiac fibrosis in an in vivo rat model and try to figure out the mechanism in vitro study.

Methods
The Sprague-Dawley rats were divided into five groups: control group, ISO-treated group, and ISO + BBR (10 mg/kg/d, 30 mg/kg/d, and 60 mg/kg/d orally)-pretreatment groups. Fibrosis was induced by ISO administration (5 mg/kg/d subcutaneously) for 10 days. One day after the last injection, all of the rats were sacrificed. Using picrosirius red (PSR) straining, immunohistochemistry, immunofluorescence, flow cytometry, western blot, RT-qPCR and cell co-culture, we explored the influence of pretreatment by BBR on ISO-induced cardiac fibrosis.

Results
Our results showed that BBR pretreatment greatly limited ISO-induced cardiac fibrosis and dysfunction. Moreover, BBR administration reduced macrophage infiltration into the myocardium of ISO-treated rats and inhibited transforming growth factor (TGF)-β1/smads signaling pathways in comparison to that seen in the ISO group. Besides, in vitro study showed that BBR-pretreatment reduced ISO-induced TGF-β1 mRNA expression in macrophages and ISO stimulation of macrophages significantly increased the expression of fibrotic markers in fibroblasts, but BBR-pretreatment blocked this increase.

Conclusion
Our results showed that BBR may have a protective role to cardiac injury via reducing of macrophage infiltration and forbidding fibroblasts transdifferent into an ‘activated’ secretory phenotype, myofibroblasts.
First insights into the genetic characteristics and drug resistance of Mycobacterium tuberculosis population collected during the first national tuberculosis prevalence survey of Lao PDR (2010–2011)
Authors: Somphavong Silaphet , Berland Jean-Luc , Gauthier Marie , Vu Thi Thuong , Nguyen Quang Huy , Iem Vibol , Vongvichit Phouvang , Inthavong Donekham , Akkhavong Vanthala , Chanthavilay Phetsavanh , Soundala Sengaloun , Keovichit Inthalaphone , Paranhos-Baccalà Glaucia , Paboriboune Phimpha , Nguyen Thi Van Anh , Bañuls Anne-Laure 
Published: October 2019

Abstract

Background
In Lao People’s Democratic Republic (PDR), tuberculosis (TB) prevalence was estimated at 540/100,000 in 2011. Nevertheless, little is known about the genetic characteristics and anti-TB drug resistance of the Mycobacterium tuberculosis population. The main objective of this work was to study the genetic characteristics and drug resistance of M. tuberculosis population collected during the first National TB Prevalence Survey (TBPS) of Lao PDR (2010–2011).

Methods
Two hundred and twenty two isolates collected during TBPS (2010–2011) were analyzed with the GenoType MTBDRplus test for M. tuberculosis identification and drug resistance detection. Then, 206 of the 222 isolates were characterized by spoligotyping and MIRU-VNTR typing.

Results
Among the 222 M. tuberculosis isolates, 11 were mono-resistant to isoniazid and 2 were resistant to isoniazid and rifampicin (MDR-TB), using the GenoType MTBDRplus test. Among the 202 genetically characterized isolates, the East African-Indian (EAI) family was predominant (76.7%) followed by the Beijing (14.4%) and T (5.5%) families. EAI isolates came from all the country provinces, whereas Beijing isolates were found mainly in the northern and central provinces. A higher proportion of Beijing isolates was observed in people younger than 35 years compared to EAI. Moreover, the percentage of drug resistance was higher among Beijing (17.2%) than EAI (5.2%) isolates, and the two MDR-TB isolates belonged to the Beijing family. Combined analysis of the MIRU-VNTR and spoligotyping results (n = 202 isolates) revealed an estimated clustering rate of 11% and the occurrence of mini-outbreaks of drug-resistant TB caused by Beijing genotypes.

Conclusions
The EAI family, the ancient and endemic family in Asia, is predominant in Lao PDR whereas the prevalence of Beijing, the most harmful M. tuberculosis family for humans, is still low, differently from neighboring countries. However, its association with drug resistance, its presence in young patients and its potential association with recent transmission suggest that the Beijing family could change TB epidemiological pattern in Lao PDR. Therefore, efficient TB control and surveillance systems must be maintained and reinforced to prevent the emergence of highly transmissible and drug-resistant strains in Lao PDR, as observed in neighboring countries.
CD40 polymorphisms were associated with HCV infection susceptibility among Chinese population
Authors: Tian Ting , Huang Peng , Wu Jingjing , Wang Chunhui , Fan Haozhi , Zhang Yun , Yu Rongbin , Wu Chao , Xia Xueshan , Fu Zuqiang , Li Jun , Yue Ming 
Published: October 2019

AbstractBackgroundCD40, encoded byTNFRSF5, participates in the survival of B cells, process of antigen presentation and generation of CD8+ T cell memory. It also has an important effect on HCV antiviral immune response. This study aims to investigate whetherTNFRSF5gene polymorphisms are associated with HCV infection outcomes among Chinese population.MethodsThree single nucleotide polymorphism (SNPs) (rs1535045, rs1883832, rs4810485) onTNFRSF5were genotyped by TaqMan assay among Chinese population, including 1513 uninfected subjects, 496 spontaneous viral clearance subjects and 768 persistent HCV-infected subjects. Logistic analysis was used to compare these SNPs among different groups in this cross-sectional study. Functional annotations of the identified SNPs were further evaluated by bioinformatics analysis.ResultsAfter adjusted by age, gender and routes of infection, the results of logistic analysis indicated that individuals carrying rs1535045 T allele had a higher risk to infect HCV compared with C allele (in recessive model, adjusted OR = 1.368, 95%CI = 1.070-1.749,P = 0.012). Subjects carried rs1535045 TT genotype were more likely to infect HCV than wild CC genotype (adjusted OR = 1.397, 95%CI = 1.078-1.809,P = 0.011). For rs1883832, T allele was significantly associated with an increased risk of HCV infection (in recessive model, adjusted OR = 1.337, 95%CI = 1.069-1.673,P = 0.011). Subjects with TT genotype had more possibility to infect HCV (adjusted OR = 1.351, 95%CI = 1.060-1.702,P = 0.015). In the stratified analysis, rs1535045 and rs1883832 were remained in various subgroups and the heterogeneity test showed no pronounced heterogeneity in any pairwise comparison (allP > 0.05). In addition, the results of the cumulative effects showed a tendency of that the more risk alleles (rs1535045 T and rs1883832 T) subjects carried, the more possibility of HCV infection exhibited (P<0.001). In haplotype analyses, compared with the CC haplotype, CT, TC and TT was correlated with an increased risk to infect HCV (P = 0.029,P = 0.047 andP<0.001, respectively).ConclusionsIn conclusion,CD40polymorphisms were significantly associated with the susceptibility to HCV among Chinese populations.