bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of serum inflammatory cytokines on cytochrome P450 drug metabolising activity during breast cancer chemotherapy: a patient feasibility study
Authors: Crake Rebekah L. I. , Strother Matthew R. , Phillips Elisabeth , Doogue Matthew P. , Zhang Mei , Frampton Chris M. A. , Robinson Bridget A. , Currie Margaret J.
Published: March 2021

Individual response to chemotherapy in patients with breast cancer is variable. Obesity and exercise are associated with better and worse outcomes, respectively, and it is known that both impact the systemic cytokine milieu. Cytochrome P450 (CYP) enzymes are responsible for the metabolism of many chemotherapy agents, and CYP enzyme activity has been shown to be modified by inflammatory cytokines in vitro and in vivo. Cytokine-associated changes in CYP metabolism may alter chemotherapy exposure, potentially affecting treatment response and patient survival. Therefore, better understanding of these biological relationships is required. This exploratory single arm open label trial investigated changes in in vivo CYP activity in twelve women treated for stage II or III breast cancer, and demonstrated for the first time the feasibility and safety of utilising the Inje phenotyping cocktail to measure CYP activity in cancer patients receiving chemotherapy. Relative CYP activity varied between participants, particularly for CYP2C9 and CYP2D6, and changes in serum concentrations of the inflammatory cytokine monocyte chemoattractant protein 1 inversely correlated to CYP3A4 activity during chemotherapy. Future use of phenotyping cocktails in a clinical oncology setting may help guide drug dosing and improve chemotherapy outcomes.

Clinical Trial Registration: Trial was retrospectively registered to the Australia New Zealand Clinical Trial Registry (ANZCTR). ACTRN12620000832976, 21 Aug 2020, https://www.anzctr.org.au/ACTRN12620000832976.aspx.
Nanostructure of bioactive glass affects bone cell attachment via protein restructuring upon adsorption
Authors: Thamma Ukrit , Kowal Tia J. , Falk Matthias M. , Jain Himanshu
Published: March 2021

The nanostructure of engineered bioscaffolds has a profound impact on cell response, yet its understanding remains incomplete as cells interact with a highly complex interfacial layer rather than the material itself. For bioactive glass scaffolds, this layer comprises of silica gel, hydroxyapatite (HA)/carbonated hydroxyapatite (CHA), and absorbed proteins—all in varying micro/nano structure, composition, and concentration. Here, we examined the response of MC3T3-E1 pre-osteoblast cells to 30 mol% CaO–70 mol% SiO2 porous bioactive glass monoliths that differed only in nanopore size (6–44 nm) yet resulted in the formation of HA/CHA layers with significantly different microstructures. We report that cell response, as quantified by cell attachment and morphology, does not correlate with nanopore size, nor HA/CHO layer micro/nano morphology, or absorbed protein amount (bovine serum albumin, BSA), but with BSA’s secondary conformation as indicated by its β-sheet/α-helix ratio. Our results suggest that the β-sheet structure in BSA interacts electrostatically with the HA/CHA interfacial layer and activates the RGD sequence of absorbed adhesion proteins, such as fibronectin and vitronectin, thus significantly enhancing the attachment of cells. These findings provide new insight into the interaction of cells with the scaffolds’ interfacial layer, which is vital for the continued development of engineered tissue scaffolds.
Establishment and genomic characterization of a sporadic malignant peripheral nerve sheath tumor cell line
Authors: Longo Jody Fromm , Brosius Stephanie N. , Znoyko Iya , Alers Victoria A. , Jenkins Dorea P. , Wilson Robert C. , Carroll Andrew J. , Wolff Daynna J. , Roth Kevin A. , Carroll Steven L.
Published: March 2021

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive Schwann cell-derived neoplasms that occur sporadically or in patients with neurofibromatosis type 1 (NF1). Preclinical research on sporadic MPNSTs has been limited as few cell lines exist. We generated and characterized a new sporadic MPNST cell line, 2XSB, which shares the molecular and genomic features of the parent tumor. These cells have a highly complex karyotype with extensive chromothripsis. 2XSB cells show robust invasive 3-dimensional and clonogenic culture capability and form solid tumors when xenografted into immunodeficient mice. High-density single nucleotide polymorphism array and whole exome sequencing analyses indicate that, unlike NF1-associated MPNSTs, 2XSB cells have intact, functional NF1 alleles with no evidence of mutations in genes encoding components of Polycomb Repressor Complex 2. However, mutations in other genes implicated in MPNST pathogenesis were identified in 2XSB cells including homozygous deletion of CDKN2A and mutations in TP53 and PTEN. We also identified mutations in genes not previously associated with MPNSTs but associated with the pathogenesis of other human cancers. These include DNMT1, NUMA1, NTRK1, PDE11A, CSMD3, LRP5 and ACTL9. This sporadic MPNST-derived cell line provides a useful tool for investigating the biology and potential treatment regimens for sporadic MPNSTs.
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Authors: Wang Jerry C. , Ramaswami Gokul , Geschwind Daniel H.
Published: March 2021

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified, implicating RNA and protein metabolism and intracellular transport, among other biological mechanisms. To achieve a systems-level understanding of the mechanisms governing ALS pathophysiology, we built gene co-expression networks using RNA-sequencing data from control human spinal cord samples, identifying 13 gene co-expression modules, each of which represents a distinct biological process or cell type. Analysis of four RNA-seq datasets from a range of ALS disease-associated contexts reveal dysregulation in numerous modules related to ribosomal function, wound response, and leukocyte activation, implicating astrocytes, oligodendrocytes, endothelia, and microglia in ALS pathophysiology. To identify potentially causal processes, we partitioned heritability across the genome, finding that ALS common genetic risk is enriched within two specific modules, SC.M4, representing genes related to RNA processing and gene regulation, and SC.M2, representing genes related to intracellular transport and autophagy and enriched in oligodendrocyte markers. Top hub genes of this latter module include ALS-implicated risk genes such as KPNA3, TMED2, and NCOA4, the latter of which regulates ferritin autophagy, implicating this process in ALS pathophysiology. These unbiased, genome-wide analyses confirm the utility of a systems approach to understanding the causes and drivers of ALS.
Ankle dorsiflexion deficit in the back leg is a risk factor for shoulder and elbow injuries in young baseball players
Authors: Shitara Hitoshi , Tajika Tsuyoshi , Kuboi Takuro , Ichinose Tsuyoshi , Sasaki Tsuyoshi , Hamano Noritaka , Endo Takafumi , Kamiyama Masataka , Honda Akira , Miyamoto Ryosuke , Nakase Kurumi , Yamamoto Atsushi , Kobayashi Tsutomu , Takagishi Kenji , Chikuda Hirotaka
Published: March 2021

The relationship between ankle joint function and throwing-related injuries has not been demonstrated. We hypothesized that limited ankle joint range of motion (ROM) was related to risk factors for shoulder and elbow injuries in young baseball players. This 12-month prospective cohort study evaluated the age, height, weight, playing position, shoulder, elbow, and ankle function of 228 enrolled baseball players. Shoulder and elbow injuries were tracked during the season. Univariate and multivariate analyses were performed to identify risk factors for shoulder and elbow injuries among participants divided into non-injured and injured groups. Univariate analysis showed that age, height, weight, ROM of elbow flexion in the dominant arm, muscle strength ratio of shoulder abduction, and the likelihood of being a pitcher or a catcher were significantly greater in the injured group than in the non-injured group. ROM of shoulder abduction-external/internal rotation, shoulder total arc on the dominant arm, ankle joint dorsiflexion, and plantar flexion on the back (non-lead) and front (lead) legs were significantly less in the injured group than in the non-injured group. In conclusion, ROM dorsiflexion deficits in the back leg, shoulder abduction-external rotation in the dominant arm, ROM increase in elbow flexion on the dominant side, older age, and being a pitcher were significant independent risk factors for injury.
RETRACTED ARTICLE: MicroRNA-205-5p inhibits skin cancer cell proliferation and increase drug sensitivity by targeting TNFAIP8
Authors: Ge Xinhong , Niture Suryakant , Lin Minghui , Cagle Patrice , Li P. Andy , Kumar Deepak
Published: March 2021

Tumor necrosis factor-α-induced protein 8 (TNFAIP8) is a member of the TIPE/TNFAIP8 family which regulates tumor growth and survival. Our goal is to delineate the detailed oncogenic role of TNFAIP8 in skin cancer development and progression. Here we demonstrated that higher expression of TNFAIP8 is associated with basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and melanoma development in patient tissues. Induction of TNFAIP8 expression by TNFα or by ectopic expression of TNFAIP8 in SCC or melanoma cell lines resulted in increased cell growth/proliferation. Conversely, silencing of TNFAIP8 decreased cell survival/cell migration in skin cancer cells. We also showed that miR-205-5p targets the 3′UTR of TNFAIP8 and inhibits TNFAIP8 expression. Moreover, miR-205-5p downregulates TNFAIP8 mediated cellular autophagy, increased sensitivity towards the B-RAFV600E mutant kinase inhibitor vemurafenib, and induced cell apoptosis in melanoma cells. Collectively our data indicate that miR-205-5p acts as a tumor suppressor in skin cancer by targeting TNFAIP8.
Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing
Authors: Ahmed Syed A. K. Shifat , Rudden Michelle , Elias Sabrina M. , Smyth Thomas J. , Marchant Roger , Banat Ibrahim M. , Dooley James S. G.
Published: March 2021

Pseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.
Canine mammary cancer tumour behaviour and patient survival time are associated with collagen fibre characteristics
Authors: Garcia Ana P. V. , Reis Luana A. , Nunes Fernanda C. , Longford Francis G. J. , Frey Jeremy G. , de Paula Ana M. , Cassali Geovanni D.
Published: March 2021

Precise diagnosis and prognosis are key in prevention and reduction of morbidity and mortality in all types of cancers. Here we show that changes in the collagen fibres in the main histological subtypes of canine mammary gland carcinomas are directly associated with the tumour behaviour and the animal survival time and could become a useful tool in helping with diagnosis. Imaging by second harmonic generation and multiphoton excited fluorescence microscopy were performed to evaluate the collagen and cellular segment parameters in cancer biopsies. We present a retrospective study of 45 cases of canine mammary cancer analysing 836 biopsies regions including normal mammary gland tissue, benign mixed tumours, carcinoma in mixed tumour, carcinosarcoma, micropapillary carcinoma and solid carcinoma. The image analyses and the comparison between the tumour types allowed to assess the collagen fibre changes during tumour progression. We demonstrate that the collagen parameters correlate with the clinical and pathological data, the results show that in neoplastic tissues, the collagen fibres are more aligned and shorter as compared to the normal tissues. There is a clear association of the mean fibre length with the dogs survival times, the carcinomas presenting shorter collagen fibres indicate a worse survival rate.
Influence of alkaline modification on selected properties of banana fiber paperbricks
Authors: Akinwande Abayomi A. , Adediran Adeolu A. , Balogun Oluwatosin A. , Olusoju Oluwaseyi S. , Adesina Olanrewaju S.
Published: March 2021

In a bid to develop paper bricks as alternative masonry units, unmodified banana fibers (UMBF) and alkaline (1 Molar aqueous sodium hydroxide) modified banana fibers (AMBF), fine sand, and ordinary Portland cement were blended with waste paper pulp. The fibers were introduced in varying proportions of 0, 0.5, 1.0 1.5, 2.0, and 2.5 wt% (by weight of the pulp) and curing was done for 28 and 56 days. Properties such as water and moisture absorption, compressive, flexural, and splitting tensile strengths, thermal conductivity, and specific heat capacity were appraised. The outcome of the examinations carried out revealed that water absorption rose with fiber loading while AMBF reinforced samples absorbed lesser water volume than UMBF reinforced samples; a feat occasioned by alkaline treatment of banana fiber. Moisture absorption increased with paper bricks doped with UMBF, while in the case of AMBF-paper bricks, property value was noted to depreciate with increment in AMBF proportion. Fiber loading resulted in improvement of compressive, flexural, and splitting tensile strengths and it was noted that AMBF reinforced samples performed better. The result of the thermal test showed that incorporation of UMBF led to depreciation in thermal conductivity while AMBF infusion in the bricks initiated increment in value. Opposite behaviour was observed for specific heat capacity as UMBF enhanced heat capacity while AMBF led to depreciation. Experimental trend analysis carried out indicates that curing length and alkaline modification of fiber were effective in maximizing the properties of paperbricks for masonry construction.
Spatio-temporal alterations in retinal and choroidal layers in the progression of age-related macular degeneration (AMD) in optical coherence tomography
Authors: Vogl Wolf-Dieter , Bogunović Hrvoje , Waldstein Sebastian M. , Riedl Sophie , Schmidt-Erfurth Ursula
Published: March 2021

Age-related macular degeneration (AMD) is the predominant cause of vision loss in the elderly with a major impact on ageing societies and healthcare systems. A major challenge in AMD management is the difficulty to determine the disease stage, the highly variable progression speed and the risk of conversion to advanced AMD, where irreversible functional loss occurs. In this study we developed an optical coherence tomography (OCT) imaging based spatio-temporal reference frame to characterize the morphologic progression of intermediate age-related macular degeneration (AMD) and to identify distinctive patterns of conversion to the advanced stages macular neovascularization (MNV) and macular atrophy (MA). We included 10,040 OCT volumes of 518 eyes with intermediate AMD acquired according to a standardized protocol in monthly intervals over two years. Two independent masked retina specialists determined the time of conversion to MNV or MA. All scans were aligned to a common reference frame by intra-patient and inter-patient registration. Automated segmentations of retinal layers and the choroid were computed and en-face maps were transformed into the common reference frame. Population maps were constructed in the subgroups converting to MNV (n=135), MA (n=50) and in non-progressors (n=333). Topographically resolved maps of changes were computed and tested for statistical significant differences. The development over time was analysed by a joint model accounting for longitudinal and right-censoring aspect. Significantly enhanced thinning of the outer nuclear layer (ONL) and retinal pigment epithelium (RPE)–photoreceptorinner segment/outer segment (PR-IS/OS) layers within the central 3 mm and a faster thinning speed preceding conversion was documented for MA progressors. Converters to MNV presented an accelerated thinning of the choroid and appearance changes in the choroid prior to MNV onset. The large-scale automated image analysis allowed us to distinctly assess the progression of morphologic changes in intermediate AMD based on conventional OCT imaging. Distinct topographic and temporal patterns allow to prospectively determine eyes with risk of progression and thereby greatly improving early detection, prevention and development of novel therapeutic strategies.
Multilayer representation of collaboration networks with higher-order interactions
Authors: Vasilyeva E. , Kozlov A. , Alfaro-Bittner K. , Musatov D. , Raigorodskii A. M. , Perc M. , Boccaletti S.
Published: March 2021

Collaboration patterns offer important insights into how scientific breakthroughs and innovations emerge in small and large research groups. However, links in traditional networks account only for pairwise interactions, thus making the framework best suited for the description of two-person collaborations, but not for collaborations in larger groups. We therefore study higher-order scientific collaboration networks where a single link can connect more than two individuals, which is a natural description of collaborations entailing three or more people. We also consider different layers of these networks depending on the total number of collaborators, from one upwards. By doing so, we obtain novel microscopic insights into the representativeness of researchers within different teams and their links with others. In particular, we can follow the maturation process of the main topological features of collaboration networks, as we consider the sequence of graphs obtained by progressively merging collaborations from smaller to bigger sizes starting from the single-author ones. We also perform the same analysis by using publications instead of researchers as network nodes, obtaining qualitatively the same insights and thus confirming their robustness. We use data from the arXiv to obtain results specific to the fields of physics, mathematics, and computer science, as well as to the entire coverage of research fields in the database.
PRYNT: a tool for prioritization of disease candidates from proteomics data using a combination of shortest-path and random walk algorithms
Authors: Boizard Franck , Buffin-Meyer Bénédicte , Aligon Julien , Teste Olivier , Schanstra Joost P. , Klein Julie
Published: March 2021

The urinary proteome is a promising pool of biomarkers of kidney disease. However, the protein changes observed in urine only partially reflect the deregulated mechanisms within kidney tissue. In order to improve on the mechanistic insight based on the urinary protein changes, we developed a new prioritization strategy called PRYNT (PRioritization bY protein NeTwork) that employs a combination of two closeness-based algorithms, shortest-path and random walk, and a contextualized protein–protein interaction (PPI) network, mainly based on clique consolidation of STRING network. To assess the performance of our approach, we evaluated both precision and specificity of PRYNT in prioritizing kidney disease candidates. Using four urinary proteome datasets, PRYNT prioritization performed better than other prioritization methods and tools available in the literature. Moreover, PRYNT performed to a similar, but complementary, extent compared to the upstream regulator analysis from the commercial Ingenuity Pathway Analysis software. In conclusion, PRYNT appears to be a valuable freely accessible tool to predict key proteins indirectly from urinary proteome data. In the future, PRYNT approach could be applied to other biofluids, molecular traits and diseases. The source code is freely available on GitHub at: https://github.com/Boizard/PRYNT and has been integrated as an interactive web apps to improved accessibility (https://github.com/Boizard/PRYNT/tree/master/AppPRYNT).
Epidermal and fibroblast growth factors incorporated polyvinyl alcohol electrospun nanofibers as biological dressing scaffold
Authors: Asiri Amnah , Saidin Syafiqah , Sani Mohd Helmi , Al-Ashwal Rania Hussien
Published: March 2021

In this study, single, mix, multilayer Polyvinyl alcohol (PVA) electrospun nanofibers with epidermal growth factor (EGF) and fibroblast growth factor (FGF) were fabricated and characterized as a biological wound dressing scaffolds. The biological activities of the synthesized scaffolds have been verified by in vitro and in vivo studies. The chemical composition finding showed that the identified functional units within the produced nanofibers (O–H and N–H bonds) are attributed to both growth factors (GFs) in the PVA nanofiber membranes. Electrospun nanofibers' morphological features showed long protrusion and smooth morphology without beads and sprayed with an average range of 198–286 nm fiber diameter. The fiber diameters decrement and the improvement in wettability and surface roughness were recorded after GFs incorporated within the PVA Nanofibers, which indicated potential good adoption as biological dressing scaffolds due to the identified mechanical properties (Young’s modulus) in between 18 and 20 MPa. The MTT assay indicated that the growth factor release from the PVA nanofibers has stimulated cell proliferation and promoted cell viability. In the cell attachment study, the GFs incorporated PVA nanofibers stimulated cell proliferation and adhered better than the PVA control sample and presented no cytotoxic effect. The in vivo studies showed that compared to the control and single PVA-GFs nanofiber, the mix and multilayer scaffolds gave a much more wound reduction at day 7 with better wound repair at day 14–21, which indicated to enhancing tissue regeneration, thus, could be a projected as a suitable burn wound dressing scaffold.
Development of a two-step nucleic acid amplification test for accurate diagnosis of the Mycobacterium tuberculosis complex
Authors: Lin Chien-Ru , Wang Hsin-Yao , Lin Ting-Wei , Lu Jang-Jih , Hsieh Jason Chia-Hsun , Wu Min-Hsien
Published: March 2021

The Mycobacterium tuberculosis complex (MTBC) remains one of the top 10 leading causes of death globally. The early diagnosis of MTBC can reduce mortality and mitigate disease transmission. However, current nucleic acid amplification diagnostic test methods are generally time-consuming and show suboptimal diagnostic performance, especially in extrapulmonary MTBC samples or acid-fast stain (AFS)-negative cases. Thus, development of an accurate assay for the diagnosis of MTBC is necessary, particularly under the above mentioned conditions. In this study, a single-tube nested real-time PCR assay (N-RTP) was developed and compared with a newly in-house-developed high-sensitivity real-time PCR assay (HS-RTP) using 134 clinical specimens (including 73 pulmonary and 61 extrapulmonary specimens). The amplification efficiency of HS-RTP and N-RTP was 99.8% and 100.7%, respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in these specimens were 97.5% (77/79) versus 94.9% (75/79) and 80.0% (44/55) versus 89.1% (49/55), respectively. The sensitivity and specificity of HS-RTP and N-RTP for the diagnosis of MTBC in pulmonary specimens were 96.3% (52/54) versus 96.3% (52/54) and 73.7.0% (14/19) versus 89.5% (17/19), respectively; in extrapulmonary specimens, the sensitivity and specificity of HS-RTP and N-RTP were 100% (25/25) versus 92% (23/25) and 83.3% (30/36) versus 88.9% (32/36), respectively. Among the AFS-negative cases, the sensitivity and specificity of HS-RTP and N-RTP were 97.0% (32/33) versus 90.9% (30/33) and 88.0% (44/50) versus 92.0% (46/50), respectively. Overall, the sensitivity of HS-RTP was higher than that of N-RTP, and the performance was not compromised in extrapulmonary specimens and under AFS-negative conditions. In contrast, the specificity of the N-RTP assay was higher than that of the HS-RTP assay in all types of specimens. In conclusion, the HS-RTP assay would be useful for screening patients suspected of exhibiting an MTBC infection due to its higher sensitivity, while the N-RTP assay could be used for confirmation because of its higher specificity. Our results provide a two-step method (screen to confirm) that simultaneously achieves high sensitivity and specificity in the diagnosis of MTBC.
Apelin promotes blood and lymph vessel formation and the growth of melanoma lung metastasis
Authors: Berta Judit , Török Szilvia , Tárnoki-Zách Júlia , Drozdovszky Orsolya , Tóvári József , Paku Sándor , Kovács Ildikó , Czirók András , Masri Bernard , Megyesfalvi Zsolt , Oskolás Henriett , Malm Johan , Ingvar Christian , Markó-Varga György , Döme Balázs , László Viktória
Published: March 2021

Apelin, a ligand of the APJ receptor, is overexpressed in several human cancers and plays an important role in tumor angiogenesis and growth in various experimental systems. We investigated the role of apelin signaling in the malignant behavior of cutaneous melanoma. Murine B16 and human A375 melanoma cell lines were stably transfected with apelin encoding or control vectors. Apelin overexpression significantly increased melanoma cell migration and invasion in vitro, but it had no impact on its proliferation. In our in vivo experiments, apelin significantly increased the number and size of lung metastases of murine melanoma cells. Melanoma cell proliferation rates and lymph and blood microvessel densities were significantly higher in the apelin-overexpressing pulmonary metastases. APJ inhibition by the competitive APJ antagonist MM54 significantly attenuated the in vivo pro-tumorigenic effects of apelin. Additionally, we detected significantly elevated circulating apelin and VEGF levels in patients with melanoma compared to healthy controls. Our results show that apelin promotes blood and lymphatic vascularization and the growth of pulmonary metastases of skin melanoma. Further studies are warranted to validate apelin signaling as a new potential therapeutic target in this malignancy.
A two-stream convolutional neural network for microRNA transcription start site feature integration and identification
Authors: Cha Mingyu , Zheng Hansi , Talukder Amlan , Barham Clayton , Li Xiaoman , Hu Haiyan
Published: March 2021

MicroRNAs (miRNAs) play important roles in post-transcriptional gene regulation and phenotype development. Understanding the regulation of miRNA genes is critical to understand gene regulation. One of the challenges to study miRNA gene regulation is the lack of condition-specific annotation of miRNA transcription start sites (TSSs). Unlike protein-coding genes, miRNA TSSs can be tens of thousands of nucleotides away from the precursor miRNAs and they are hard to be detected by conventional RNA-Seq experiments. A number of studies have been attempted to computationally predict miRNA TSSs. However, high-resolution condition-specific miRNA TSS prediction remains a challenging problem. Recently, deep learning models have been successfully applied to various bioinformatics problems but have not been effectively created for condition-specific miRNA TSS prediction. Here we created a two-stream deep learning model called D-miRT for computational prediction of condition-specific miRNA TSSs (http://hulab.ucf.edu/research/projects/DmiRT/). D-miRT is a natural fit for the integration of low-resolution epigenetic features (DNase-Seq and histone modification data) and high-resolution sequence features. Compared with alternative computational models on different sets of training data, D-miRT outperformed all baseline models and demonstrated high accuracy for condition-specific miRNA TSS prediction tasks. Comparing with the most recent approaches on cell-specific miRNA TSS identification using cell lines that were unseen to the model training processes, D-miRT also showed superior performance.
Cycling hypoxia selects for constitutive HIF stabilization
Authors: Pressley Mariyah , Gallaher Jill A. , Brown Joel S. , Tomaszewski Michal R. , Borad Punit , Damaghi Mehdi , Gillies Robert J. , Whelan Christopher J.
Published: March 2021

Tumors experience temporal and spatial fluctuations in oxygenation. Hypoxia inducible transcription factors (HIF-α) respond to low levels of oxygen and induce re-supply oxygen. HIF-α stabilization is typically facultative, induced by hypoxia and reduced by normoxia. In some cancers, HIF-α stabilization becomes constitutive under normoxia. We develop a mathematical model that predicts how fluctuating oxygenation affects HIF-α stabilization and impacts net cell proliferation by balancing the base growth rate, the proliferative cost of HIF-α expression, and the mortality from not expressing HIF-α during hypoxia. We compare optimal net cell proliferation rate between facultative and constitutive HIF-α regulation in environments with different oxygen profiles. We find that that facultative HIF-α regulation promotes greater net cell proliferation than constitutive regulation with stochastic or slow periodicity in oxygenation. However, cell fitness is nearly identical for both HIF-α regulation strategies under rapid periodic oxygenation fluctuations. The model thus indicates that cells constitutively expressing HIF-α may be at a selective advantage when the cost of expression is low. In cancer, this condition is known aspseudohypoxiaor the “Warburg Effect”. We conclude that rapid and regular cycling of oxygenation levels selects for pseudohypoxia, and that this is consistent with the ecological theory of optimal defense.
Streptococcus mutans induces IgA nephropathy-like glomerulonephritis in rats with severe dental caries
Authors: Naka Shuhei , Wato Kaoruko , Misaki Taro , Ito Seigo , Matsuoka Daiki , Nagasawa Yasuyuki , Nomura Ryota , Matsumoto-Nakano Michiyo , Nakano Kazuhiko
Published: March 2021

The mechanisms underlying immunoglobulin A nephropathy (IgAN), the most common chronic form of primary glomerulonephritis, remain poorly understood. Streptococcus mutans, a Gram-positive facultatively anaerobic oral bacterium, is a common cause of dental caries. In previous studies, S. mutans isolates that express Cnm protein on their cell surface were frequently detected in IgAN patients. In the present study, inoculation of Cnm-positive S. mutans in the oral cavities of 2-week-old specific-pathogen free Sprague–Dawley rats fed a high-sucrose diet for 32 weeks produced severe dental caries in all rats. Immunohistochemical analyses of the kidneys using IgA- and complement C3-specific antibodies revealed positive staining in the mesangial region. Scanning electron microscopy revealed a wide distribution of electron dense deposits in the mesangial region and periodic acid-Schiff staining demonstrated prominent proliferation of mesangial cells and mesangial matrix. These results suggest that IgAN-like glomerulonephritis was induced in rats with severe dental caries by Cnm-positive S. mutans.
Philadelphia chromosome-negative B-cell acute lymphoblastic leukaemia with kinase fusions in Taiwan
Authors: Hsu Yin-Chen , Yu Chih-Hsiang , Chen Yan-Ming , Roberts Kathryn G. , Ni Yu-Ling , Lin Kai-Hsin , Jou Shiann-Tarng , Lu Meng-Yao , Chen Shu-Huey , Wu Kang-Hsi , Chang Hsiu-Hao , Lin Dong-Tsamn , Lin Shu-Wha , Lin Ze-Shiang , Chiu Wei-Tzu , Chang Chia-Ching , Ho Bing-Ching , Mullighan Charles G. , Yu Sung-Liang , Yang Yung-Li
Published: March 2021

Philadelphia chromosome-like (Ph-like) acute lymphoblastic leukaemia (ALL), a high-risk subtype characterised by genomic alterations that activate cytokine receptor and kinase signalling, is associated with inferior outcomes in most childhood ALL clinical trials. Half of the patients with Ph-like ALL have kinase rearrangements or fusions. We examined the frequency and spectrum of these fusions using a retrospective cohort of 212 newly diagnosed patients with childhood B-cell ALL. Samples without known chromosomal alterations were subject to multiplex reverse transcription polymerase chain reaction to identify known Ph-like kinase fusions. Immunoglobulin heavy chain locus (IGH) capture and kinase capture were applied to samples without known kinase fusions. We detected known kinase fusions in five of 212 patients, comprising EBF1-PDGFRB, ETV6-ABL1, ZC3HAV1-ABL2, EPOR-IGH, and CNTRL-ABL1. Two patients with P2RY8-CRLF2 were identified. Patients with non-Ph kinase fusions had inferior 5-year event-free survival and overall survival compared with patients with other common genetic alterations. The prevalence of non-Ph kinase fusions in our Taiwanese cohort was lower than that reported in Caucasian populations. Future clinical trials with tyrosine kinase inhibitors may be indicated in Taiwan because of the inferior outcomes for B-cell ALL with kinase fusions.
High Jc and low anisotropy of hydrogen doped NdFeAsO superconducting thin film
Authors: Iida Kazumasa , Hänisch Jens , Kondo Keisuke , Chen Mingyu , Hatano Takafumi , Wang Chao , Saito Hikaru , Hata Satoshi , Ikuta Hiroshi
Published: March 2021

The recent realisations of hydrogen doped LnFeAsO (Ln = Nd and Sm) superconducting epitaxial thin films call for further investigation of their structural and electrical transport properties. Here, we report on the microstructure of a NdFeAs(O,H) epitaxial thin film and its temperature, field, and orientation dependencies of the resistivity and the critical current density Jc. The superconducting transition temperature Tc is comparable to NdFeAs(O,F). Transmission electron microscopy investigation supported that hydrogen is homogenously substituted for oxygen. A high self-field Jc of over 10 MA/cm2 was recorded at 5 K, which is likely to be caused by a short London penetration depth. The anisotropic Ginzburg–Landau scaling for the angle dependence of Jc yielded temperature-dependent scaling parameters γJ that decreased from 1.6 at 30 K to 1.3 at 5 K. This is opposite to the behaviour of NdFeAs(O,F). Additionally, γJ of NdFeAs(O,H) is smaller than that of NdFeAs(O,F). Our results indicate that heavily electron doping by means of hydrogen substitution for oxygen in LnFeAsO is highly beneficial for achieving high Jc with low anisotropy without compromising Tc, which is favourable for high-field magnet applications.
Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation
Authors: Okuda Aya , Shimizu Masahiro , Morishima Ken , Inoue Rintaro , Sato Nobuhiro , Urade Reiko , Sugiyama Masaaki
Published: March 2021

Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.
Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells
Authors: Pimenta Andreia I. , Bernardes Nuno , Alves Marta M. , Mil-Homens Dalila , Fialho Arsenio M.
Published: March 2021

Burkholderia cenocepacia is known for its capacity of adherence and interaction with the host, causing severe opportunistic lung infections in cystic fibrosis patients. In this work we produced Giant Plasma Membrane Vesicles (GPMVs) from a bronchial epithelial cell line and validated their use as a cell-like alternative to investigate the steps involved in the adhesion process of B. cenocepacia. RNA-sequencing was performed and the analysis of the B. cenocepacia K56-2 transcriptome after the first contacts with the surface of host cells allowed the recognition of genes implicated in bacterial adaptation and virulence-associated functions. The sensing of host membranes led to a transcriptional shift that caused a cascade of metabolic and physiological adaptations to the host specific environment. Many of the differentially expressed genes encode proteins related with central metabolic pathways, transport systems, cellular processes, and virulence traits. The understanding of the changes in gene expression that occur in the early steps of infection can uncover new proteins implicated in B. cenocepacia-host cell adhesion, against which new blocking agents could be designed to control the progression of the infectious process.
Development of a drug screening system using three-dimensional cardiac tissues containing multiple cell types
Authors: Takeda Maki , Miyagawa Shigeru , Ito Emiko , Harada Akima , Mochizuki-Oda Noriko , Matsusaki Michiya , Akashi Mitsuru , Sawa Yoshiki
Published: March 2021

We hypothesized that an appropriate ratio of cardiomyocytes, fibroblasts, endothelial cells, and extracellular matrix (ECM) factors would be required for the development of three-dimensional cardiac tissues (3D-CTs) as drug screening systems. To verify this hypothesis, ECM-coated human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), ECM-coated cardiac fibroblasts (CFs), and uncoated cardiac endothelial cells (CEs) were mixed in the following ratios: 10:0:0 (10CT), 7:2:1 (7CT), 5:4:1 (5CT), and 2:7:1 (2CT). The expression of cardiac-, fibroblasts-, and endothelial-specific markers was assessed by FACS, qPCR, and immunostaining while that of ECM-, cell adhesion-, and ion channel-related genes was examined by qPCR. Finally, the contractile properties of the tissues were evaluated in the absence or presence of E-4031 and isoproterenol. The expression of ECM- and adhesion-related genes significantly increased, while that of ion channel-related genes significantly decreased with the CF proportion. Notably, 7CT showed the greatest contractility of all 3D-CTs. When exposed to E-4031 (hERG K channel blocker), 7CT and 5CT showed significantly decreased contractility and increased QT prolongation. Moreover, 10CT and 7CT exhibited a stronger response to isoproterenol than did the other 3D-CTs. Finally, 7CT showed the highest drug sensitivity among all 3D-CTs. In conclusion, 3D-CTs with an appropriate amount of fibroblasts/endothelial cells (7CT in this study) are suitable drug screening systems, e.g. for the detection of drug-induced arrhythmia.
Hepatoprotective effect of Thymus vulgaris extract on sodium nitrite-induced changes in oxidative stress, antioxidant and inflammatory marker expression
Authors: Soliman Mohamed Mohamed , Aldhahrani Adil , Metwally Mohammed M. M.
Published: March 2021

The herb thyme (Thymus vulgaris) has multiple therapeutic uses. In this study, we explored how T. vulgaris leaf extract protects liver cells against sodium nitrite-(NaNO2) induced oxidative stress. Mice were divided into four groups; each group received one of the following treatments orally: saline; T. vulgaris extract alone; NaNO2 alone; or T. vulgaris extract + NaNO2. Alanine aminotransferase (ALT), aspartate aminotransferase (AST), reduced glutathione (GSH), superoxide dismutase (SOD), malondialdehyde (MDA), IL-1β, IL-6, TNF-α, and total proteins were measured in serum using standard methods. TNF-α, hemooxygenase-1 (HO-1), thioredoxin, SOD, and GSH synthase, all of which are linked to oxidative stress, were measured using quantitative real-time PCR (qRT-PCR). In mice treated with T. vulgaris extract, the effect of NaNO2 on ALT and AST levels and total proteins was reduced, and its effect on antioxidant levels was reversed. Normally, NaNO2 causes hepatocyte congestion and severe hepatic central vein congestion. Tissues in the mice treated with T. vulgaris were restored to normal conditions. Our results demonstrate that NaNO2-induced hepatic injury is significantly reduced by pretreatment with T. vulgaris extract, which protects against hepatic oxidative stress and its associated genes at the biochemical, molecular, and cellular levels.
Association of early failure of arteriovenous fistula with mortality in hemodialysis patients
Authors: Yap Yit-Sheung , Chi Wen-Che , Lin Cheng-Hao , Liu Yi-Chun , Wu Yi-Wen
Published: March 2021

Arteriovenous fistula (AVF) is prone to early dysfunction and relates to poor outcome. However, little is known about the role of early AVF dysfunction as an independent risk factor for death in hemodialysis patients. A retrospective cohort study was performed using data of patients who underwent initial AVF surgery at a single institution. Demographic, clinical, biochemistry and AVF parameters were extracted from the electronic records, and the association between these variables and mortality was analyzed by Cox proportional hazards model. A total of 501 patients on hemodialysis (63.4 ± 12.7 years, 57.3% male) were included, and the median observation period was 3.66 years. In multivariate analysis, early failure of AVF (hazard ratio (95% confidence interval): 1.54 (1.06–2.24); p = 0.023) was associated with overall mortality but not cardiovascular mortality. Other identified predictors of overall mortality included older age, peripheral artery disease (PAD), cardiomegaly, higher white blood cell (WBC) count and corrected calcium level, and lower total cholesterol level, while predictors of cardiovascular mortality included older age, coronary artery disease (CAD), PAD and lower hemoglobin level. In conclusion, patients with early AVF failure were associated with increased risk of overall mortality.
Co-application of high temperature biochar with 3,4-dimethylpyrazole-phosphate treated ammonium sulphate improves nitrogen use efficiency in maize
Authors: Hailegnaw Niguss Solomon , Mercl Filip , Kulhánek Martin , Száková Jiřina , Tlustoš Pavel
Published: March 2021

This study aimed on the increasing nitrogen use efficiency (NUE) of maize via the use of high temperature produced biochar (700 °C). Maize was grown to maturity on two contrasting soils (acidic Cambisol and neutral Chernozem) in pots with a treatment of biochar co-applied with ammonium sulphate stabilised by a nitrification inhibitor (3,4-dimethylpyrazole-phosphate, DMPP) or un-stabilised. The combination of biochar with ammonium sulphate containing DMPP increased maize biomass yield up to 14%, N uptake up to 34% and NUE up to 13.7% compared to the sole application of ammonium sulphate containing DMPP. However, the combination of biochar with un-stabilised ammonium sulphate (without DMPP) had a soil-specific influence and increased maize biomass only by 3.8%, N uptake by 27% and NUE by 11% only in acidic Cambisol. Further, the biochar was able to increase the uptake of phosphorus (P) and potassium (K) in both stabilised and un-stabilised treatments of ammonium sulphate. Generally, this study demonstrated a superior effect from the combined application of biochar with ammonium sulphate containing DMPP, which improved NUE, uptake of P, K and increased maize biomass yield. Such a combination may lead to higher efficiency of fertilisation practices and reduce the amount of N fertiliser to be applied.
RAGE ligands stimulate angiotensin II type I receptor (AT1) via RAGE/AT1 complex on the cell membrane
Authors: Yokoyama Serina , Kawai Tatsuo , Yamamoto Koichi , Yibin Huang , Yamamoto Hiroko , Kakino Akemi , Takeshita Hikari , Nozato Yoichi , Fujimoto Taku , Hongyo Kazuhiro , Takahashi Toshimasa , Nakagami Futoshi , Akasaka Hiroshi , Takami Yoichi , Takeya Yasushi , Sugimoto Ken , Sawamura Tatsuya , Rakugi Hiromi
Published: March 2021

The receptor for advanced glycation end-products (RAGE) and the G protein-coupled angiotensin II (AngII) type I receptor (AT1) play a central role in cardiovascular diseases. It was recently reported that RAGE modifies AngII-mediated AT1 activation via the membrane oligomeric complex of the two receptors. In this study, we investigated the presence of the different directional crosstalk in this phenomenon, that is, the RAGE/AT1 complex plays a role in the signal transduction pathway of RAGE ligands. We generated Chinese hamster ovary (CHO) cells stably expressing RAGE and AT1, mutated AT1, or AT2 receptor. The activation of two types of G protein α-subunit, Gq and Gi, was estimated through the accumulation of inositol monophosphate and the inhibition of forskolin-induced cAMP production, respectively. Rat kidney epithelial cells were used to assess RAGE ligand-induced cellular responses. We determined that RAGE ligands activated Gi, but not Gq, only in cells expressing RAGE and wildtype AT1. The activation was inhibited by an AT1 blocker (ARB) as well as a RAGE inhibitor. ARBs inhibited RAGE ligand-induced ERK phosphorylation, NF-κB activation, and epithelial–mesenchymal transition of rat renal epithelial cells. Our findings suggest that the activation of AT1 plays a central role in RAGE-mediated cellular responses and elucidate the role of a novel molecular mechanism in the development of cardiovascular diseases.