bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-Shot Multi-Stage Damage and Ablation of Silicon by Femtosecond Mid-infrared Laser Pulses
Authors: Werner Kevin , Gruzdev Vitaly , Talisa Noah , Kafka Kyle , Austin Drake , Liebig Carl M. , Chowdhury Enam
Published: December 2019

Although ultrafast laser materials processing has advanced at a breakneck pace over the last two decades, most applications have been developed with laser pulses at near-IR or visible wavelengths. Recent progress in mid-infrared (MIR) femtosecond laser source development may create novel capabilities for material processing. This is because, at high intensities required for such processing, wavelength tuning to longer wavelengths opens the pathway to a special regime of laser-solid interactions. Under these conditions, due to the λ2 scaling, the ponderomotive energy of laser-driven electrons may significantly exceed photon energy, band gap and electron affinity and can dominantly drive absorption, resulting in a paradigm shift in the traditional concepts of ultrafast laser-solid interactions. Irreversible high-intensity ultrafast MIR laser-solid interactions are of primary interest in this connection, but they have not been systematically studied so far. To address this fundamental gap, we performed a detailed experimental investigation of high-intensity ultrafast modifications of silicon by single femtosecond MIR pulses (λ = 2.7–4.2 μm). Ultrafast melting, interaction with silicon-oxide surface layer, and ablation of the oxide and crystal surfaces were ex-situ characterized by scanning electron, atomic-force, and transmission electron microscopy combined with focused ion-beam milling, electron diffractometry, and μ-Raman spectroscopy. Laser induced damage and ablation thresholds were measured as functions of laser wavelength. The traditional theoretical models did not reproduce the wavelength scaling of the damage thresholds. To address the disagreement, we discuss possible novel pathways of energy deposition driven by the ponderomotive energy and field effects characteristic of the MIR wavelength regime.
Reduction in the Incidence of Urological Cancers after the Ban on Chinese Herbal Products Containing Aristolochic Acid: An Interrupted Time-Series Analysis
Authors: Jhuang Jing-Rong , Chiang Chun-Ju , Su Shih-Yung , Yang Ya-Wen , Lee Wen-Chung
Published: December 2019

Cancer is a public health problem worldwide. Taiwan has a higher incidence rate of urological cancers than many Asian countries do. Aristolochic acid has been considered a potent carcinogen. In this study, we examined whether the cessation of the sales and preparation of aristolochic acid-containing Chinese herbal products (AA-CHPs) in Taiwan contributed to a decline in the incidence rates of bladder cancer, carcinomas of the renal pelvis and other urinary organs, and kidney cancer. We conducted an interrupted time-series analysis of long-term trends in the incidence rates of the aforementioned cancers between 1995 and 2013 in Taiwan. The incidence rates of bladder cancer and carcinomas of the renal pelvis and other urinary organs decreased considerably after 2008 and 2011, respectively. Notably, these change-of-slope time points occurred after the year 2003, when a ban on AA-CHPs was imposed in Taiwan. The ban on AA-CHPs in Taiwan was possibly associated with the reduction in the incidence of bladder cancer and carcinomas of the renal pelvis and other urinary organs.
High prevalence of clarithromycin resistance and effect on Helicobacter pylori eradication in a population from Santiago, Chile: cohort study and meta-analysis
Authors: Arenas A. , Serrano C. , Quiñones L. , Harris P. , Sandoval M. , Lavanderos M. , Sepúlveda R. , Maquilón S. , Echeverría A. , Ríos C. , Fuentes-López E. , Rojas L. , Jorquera A. , Pizarro M. , Camargo M. C. , Riquelme A.
Published: December 2019

Helicobacter pylori (H. pylori) eradication using standard triple therapy (STT) with proton pump inhibitors (PPI), amoxicillin and clarithromycin (CLA) has been the standard in Latin America. However, CLA resistance is a rising problem affecting eradication rates. Genetic polymorphisms of CYP2C19, a PPI metabolizer may also affect eradication. The primary aims of this study were to evaluate the effect of clarithromycin resistance on H. pylori eradication in a population from Santiago, and to establish the pooled clarithromycin resistance in Santiago, Chile. Symptomatic adult patients attending a tertiary hospital in Santiago were recruited for this study. CLA resistance and the polymorphisms of CYP2C19 were determined on DNA extracted from gastric biopsies, using PCR. The STT was indicated for 14 days and eradication was determined by a urea breath test 4–6 weeks after therapy. A meta-analysis of CLA resistance studies among adult residents in Santiago was performed. Seventy-three out of 121 consecutive patients had positive rapid urease test (RUT) and received STT. Sixty-nine patients (95%) completed the study. The H. pylori eradication rate was 63% and the prevalence of CLA resistance was 26%. According to the CYP2C19 polymorphisms, 79.5% of the RUT-positive patients were extensive metabolizers. Multivariable analyses showed that only CLA resistance was significantly and inversely associated with failure of eradication (OR: 0.13; 95% confidence interval [95% CI], 0.04–0.49). A meta-analysis of two previous studies and our sample set (combined n = 194) yielded to a pooled prevalence of CLA resistance of 31.3% (95% CI 23.9–38.7). Our study shows that CLA resistance is associated with failure of H. pylori eradication. Given the high pooled prevalence of CLA resistance, consideration of CLA free therapies in Santiago is warranted. We could recommend bismuth quadruple therapy or high-dose dual therapy, according to bismuth availability. Further studies need to evaluate the best therapy.
KCa3.1 channel blockade attenuates microvascular remodelling in a large animal model of bleomycin-induced pulmonary fibrosis
Authors: Derseh Habtamu B. , Dewage Sasika N. Vithana , Perera Kopiyawaththage U. E. , Pagel Charles N. , Koumoundouros Emmanuel , Organ Louise , Snibson Ken J.
Published: December 2019

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with limited therapeutic options and poor prognosis. IPF has been associated with aberrant vascular remodelling, however the role of vascular remodelling in pulmonary fibrosis is poorly understood. Here, we used a novel segmental challenge model of bleomycin-induced pulmonary fibrosis in sheep to evaluate the remodelling of the pulmonary vasculature, and to investigate the changes to this remodelling after the administration of the KCa3.1 channel inhibitor, senicapoc, compared to the FDA-approved drug pirfenidone. We demonstrate that in vehicle-treated sheep, bleomycin-infused lung segments had significantly higher blood vessel density when compared to saline-infused control segments in the same sheep. These microvascular density changes were significantly attenuated by senicapoc treatment. The increases in vascular endothelial growth factor (VEGF) expression and endothelial cell proliferation in bleomycin-infused lung segments were significantly reduced in sheep treated with the senicapoc, when compared to vehicle-treated controls. These parameters were not significantly suppressed with pirfenidone treatment. Senicapoc treatment attenuated vascular remodelling through inhibition of capillary endothelial cell proliferation and VEGF expression. These findings suggest a potential new mode of action for the novel drug senicapoc which may contribute to its efficacy in combatting pulmonary fibrosis.
Histone acetyltransferase and Polo-like kinase 3 inhibitors prevent rat galactose-induced cataract
Authors: Kanada Fumito , Takamura Yoshihiro , Miyake Seiji , Kamata Kazuma , Inami Mayumi , Inatani Masaru , Oki Masaya
Published: December 2019

Diabetic cataracts can occur at an early age, causing visual impairment or blindness. The detailed molecular mechanisms of diabetic cataract formation remain incompletely understood, and there is no well-documented prophylactic agent. Galactose-fed rats and ex vivo treatment of lenses with galactose are used as models of diabetic cataract. To assess the role of histone acetyltransferases, we conducted cataract prevention screening with known histone acetyltransferase (HAT) inhibitors. Ex vivo treatment with a HAT inhibitor strongly inhibited the formation of lens turbidity in high-galactose conditions, while addition of a histone deacetylase (HDAC) inhibitor aggravated turbidity. We conducted a microarray to identify genes differentially regulated by HATs and HDACs, leading to discovery of a novel cataract causative factor, Plk3. Plk3 mRNA levels correlated with the degree of turbidity, and Plk3 inhibition alleviated galactose-induced cataract formation. These findings indicate that epigenetically controlled Plk3 influences cataract formation. Our results demonstrate a novel approach for prevention of diabetic cataract using HAT and Plk3 inhibitors.
Bactericidal Activity of Copper-Zinc Hybrid Nanoparticles on Copper-Tolerant Xanthomonas perforans
Authors: Carvalho Renato , Duman Kamil , Jones Jeffrey B. , Paret Mathews L.
Published: December 2019

Bacterial spot of tomato, caused by Xanthomonas perforans, X. euvesicatoria, X. vesicatoria and X. gardneri, is a major disease, contributing to significant yield losses worldwide. Over dependence of conventional copper bactericides over the last decades has led to the prevalence of copper-tolerant strains of Xanthomonas spp., making copper bactericides ineffective. Thus, there is a critical need to develop new strategies for better management of copper-tolerant Xanthomonas spp. In this study, we investigated the antimicrobial activity of a hybrid nanoparticle, copper-zinc (Cu/Zn), on copper-tolerant and sensitive strains. The hybrid nanoparticle significantly reduced bacterial growth in vitro compared to the non-treated and micron-size commercial copper controls. Tomato transplants treated with the hybrid nanoparticle had significantly reduced disease severity compared to the controls, and no phytotoxicity was observed on plants. We also studied the hybrid nanoparticle effect on the bacterial pigment xanthomonadin using Near-Infra Red Raman spectroscopy as an indicator of bacterial degradation. The hybrid nanoparticle significantly affected the ability of X. perforans in its production of xanthomonadin when compared with samples treated with micron-size copper or untreated. This study sheds new light on the potential utilization of this novel multi-site Cu/Zn hybrid nanoparticle for bacterial spot management.
Integrated transcriptomic and functional immunological approach for assessing the invasiveness of bivalve alien species
Authors: Romero Alejandro , Aranguren Raquel , Moreira Rebeca , Novoa Beatriz , Figueras Antonio
Published: December 2019

Biological invasions started when humans moved species beyond their normal geographic limits. Bivalves are the most notoriously invasive species in subtidal aquatic environments. Next-generation sequencing technologies are applied to understand the molecular mechanisms involved in the invasion. The ecological immunology focuses on the role of immunity in invasion, and its magnitude could help to predict the invasiveness of alien species. A remarkable case of invasion has been reported in the Ría de Vigo (Spain) by the black pygmy mussel Xenostrobus securis. In Galicia, the Mediterranean mussel Mytilus galloprovincialis is the predominant cultured bivalve species. Can we predict the invasiveness of alien bivalve species by analyzing their immune response? Can X. securis represent a risk for the autochthonous mussel? We evaluated the suitability of the immune-related hypotheses in our model by using an integrated transcriptomic and functional immunological approach. Our analysis suggests lower immune capabilities in X. securis compared to M. galloprovincialis, probably due to the relocation of energetic resources from the immune response to vital physiological processes to cope with salinity stress. This multidisciplinary approach will help us understand how the immune response can be influenced by the adaptive process and how this immune response can influence the invasion process.
Incorporation of humic acid into biomass derived carbon for enhanced adsorption of phenol
Authors: Song Min , Song Bing , Meng Fanyue , Chen Dandan , Sun Fei , Wei Yuexing
Published: December 2019

In the present work, the biomass derived carbon decorated with humic acid (HC), was synthesized through impregnation method for the adsorption of phenol from water environment. Humic acids contain more oxygen-containing functional groups and hydrogen bonds, which promotes the binding between HC and phenol molecules. The results indicated that the adsorption performance of HC to phenol was better than that of commercial activated carbon. Moreover, in addition to physical absorption, the chemical reaction between carboxylic groups on the carbon surface and hydroxyl in phenol also played an important role during the process. The adsorption behavior of HC was described by equilibrium and kinetics parameters. Pseudo-second order model can describe the adsorption process well. Langmuir model was more suitable for the equilibrium adsorption data fitting, indicating that the adsorption mechanism of phenol on carbon surface tends to be monolayer adsorption. Considering practical application, UV254, chemical oxygen demand (COD) and ammonia from raw wastewater were selected as target contaminants and the corresponding adsorption experiments were carried out. The results displayed that HC exhibited excellent adsorption performance, especially for UV254, indicating that as-prepared carbon material had potential application for the control of certain organic pollutants in actual wastewater.
The mechanism of MYB transcriptional regulation by MLL-AF9 oncoprotein
Authors: Cao Lu , Mitra Partha , Gonda Thomas J.
Published: December 2019

Acute leukaemias express high levels of MYB which are required for the initiation and maintenance of the disease. Inhibition of MYB expression or activity has been shown to suppress MLL-fusion oncoprotein-induced acute myeloid leukaemias (AML), which are among the most aggressive forms of AML, and indeed MYB transcription has been reported to be regulated by the MLL-AF9 oncoprotein. This highlights the importance of understanding the mechanism of MYB transcriptional regulation in these leukaemias. Here we have demonstrated that the MLL-AF9 fusion protein regulates MYB transcription directly at the promoter region, in part by recruiting the transcriptional regulator kinase CDK9, and CDK9 inhibition effectively suppresses MYB expression as well as cell proliferation. However, MYB regulation by MLL-AF9 does not require H3K79 methylation mediated by the methyltransferase DOT1L, which has also been shown to be a key mediator of MLL-AF9 leukemogenicity. The identification of specific, essential and druggable transcriptional regulators may enable effective targeting of MYB expression, which in turn could potentially lead to new therapeutic approaches for acute myeloid leukaemia with MLL-AF9.
Quantification of nitrogen oxides emissions from build-up of pollution over Paris with TROPOMI
Authors: Lorente A. , Boersma K. F. , Eskes H. J. , Veefkind J. P. , van Geffen J. H. G. M. , de Zeeuw M. B. , Denier van der Gon H. A. C. , Beirle S. , Krol M. C.
Published: December 2019

Nitrogen dioxide (NO2) is a regulated air pollutant that is of particular concern in many cities, where concentrations are high. Emissions of nitrogen oxides to the atmosphere lead to the formation of ozone and particulate matter, with adverse impacts on human health and ecosystems. The effects of emissions are often assessed through modeling based on inventories relying on indirect information that is often outdated or incomplete. Here we show that NO2 measurements from the new, high-resolution TROPOMI satellite sensor can directly determine the strength and distribution of emissions from Paris. From the observed build-up of NO2 pollution, we find highest emissions on cold weekdays in February 2018, and lowest emissions on warm weekend days in spring 2018. The new measurements provide information on the spatio-temporal distribution of emissions within a large city, and suggest that Paris emissions in 2018 are only 5–15% below inventory estimates for 2011–2012, reflecting the difficulty of meeting NOx emission reduction targets.
Decision-making factors for best supportive care alone and prognostic factors after best supportive care in non-small cell lung cancer patients
Authors: Kitazawa Haruna , Takeda Yuichiro , Naka Go , Sugiyama Haruhito
Published: December 2019

Among patients with non-small cell lung cancer (NSCLC), best supportive care (BSC) is well-known to improve patient’s quality of life and prolong survival. This study aimed to clarify (1) the decision-making factors of BSC alone and (2) the prognostic factors after selection of no further anticancer therapies. We retrospectively reviewed the clinical data of patients with NSCLC between November 2004 and February 2014, who received BSC as only therapy and BSC after completion of anticancer therapies. One hundred eighteen patients received BSC alone. Among 860 patients treated with anticancer therapies, 236 were selected as control group, 160 of whom received BSC after anticancer therapy. The significant reasons for receiving BSC alone were: comorbidities of dementia, poor Eastern Cooperative Oncology Group performance status (ECOG-PS), patients’ wishes, pulmonary comorbidities, wild type epidermal growth factor receptor (EGFR), relevant social background and psychiatric comorbidities. Poor prognostic factors at the start of BSC were poor ECOG-PS, presence of disseminated intravascular coagulation (DIC), and history of anticancer therapy. NSCLC patients with comorbidities, wild type EGFR, and relevant social background factors tended to receive BSC alone. Post-cancer therapy NSCLC patients and those with DIC and declining ECOG-PS have a shorter survival period from the start of BSC.
Proteomic analyses of decellularized porcine ovaries identified new matrisome proteins and spatial differences across and within ovarian compartments
Authors: Henning Nathaniel F. , LeDuc Richard D. , Even Kelly A. , Laronda Monica M.
Published: December 2019

Premature ovarian insufficiency (POI) affects approximately 1% of women. We aim to understand the ovarian microenvironment, including the extracellular matrix (ECM) and associated proteins (matrisome), and its role in controlling folliculogenesis. We mapped the composition of the matrisome of porcine ovaries through the cortical compartment, where quiescent follicles reside and the medullary compartment, where the larger follicles grow and mature. To do this we sliced the ovaries, uniformly in two anatomical planes, enriched for matrisome proteins and performed bottom-up shotgun proteomic analyses. We identified 42 matrisome proteins that were significantly differentially expressed across depths, and 11 matrisome proteins that have not been identified in previous ovarian protein analyses. We validated these data for nine proteins and confirmed compartmental differences with a second processing method. Here we describe a processing and proteomic analysis pipeline that revealed spatial differences and matrisome protein candidates that may influence folliculogenesis.
AAV-mediated expression of HLA-G1/5 reduces severity of experimental autoimmune uveitis
Authors: Crabtree Elizabeth , Song Liujiang , Llanga Telmo , Bower Jacquelyn J. , Cullen Megan , Salmon Jacklyn H. , Hirsch Matthew L. , Gilger Brian C.
Published: December 2019

Non-infectious uveitis (NIU) is an intractable, recurrent, and painful disease that is a common cause of vision loss. Available treatments of NIU, such as the use of topical corticosteroids, are non-specific and have serious side effects which limits them to short-term use; however, NIU requires long-term treatment to prevent vision loss. Therefore, a single dose therapeutic that mediates long-term immunosuppression with minimal side effects is desirable. In order to develop an effective long-term therapy for NIU, an adeno-associated virus (AAV) gene therapy approach was used to exploit a natural immune tolerance mechanism induced by the human leukocyte antigen G (HLA-G). To mimic the prevention of NIU, naïve Lewis rats received a single intravitreal injection of AAV particles harboring codon-optimized cDNAs encoding HLA-G1 and HLA-G5 isoforms one week prior to the induction of experimental autoimmune uveitis (EAU). AAV-mediated expression of the HLA-G-1 and -5 transgenes in the targeted ocular tissues following a single intravitreal injection of AAV-HLA-G1/5 significantly decreased clinical and histopathological inflammation scores compared to untreated EAU eyes (p < 0.04). Thus, localized ocular gene delivery of AAV-HLA-G1/5 may reduce the off-target risks and establish a long-term immunosuppressive effect that would serve as an effective and novel therapeutic strategy for NIU, with the potential for applications to additional ocular immune-mediated diseases.
Evaporation abrupt changes in the Qinghai-Tibet Plateau during the last half-century
Authors: Yao Tianci , Lu Hongwei , Feng Wei , Yu Qing
Published: December 2019

Pan evaporation (Epan) was regarded as a critical indicator of climate change, especially in the Qinghai-Tibet Plateau (QTP). By using the measured daily Epan data of 274 stations in the QTP from 1970 to 2017, the study detected abrupt changes in annual Epan series in different spatial scales, through integrating the Mann-Kendall abrupt change test, moving t-test and piecewise linear fitting model. Results showed that abrupt changes existed generally in the QTP where mean and trend abrupt changes were detected in 76.6% and 97.8% of 274 stations during the last half-century. Major abrupt change time of mean values and trends was respectively in around 1996, 1989 and 2007. In comparison, early abrupt changes were observed in the south (south of 30°N) and north (north of 35°N) but late ones in the midland (30–35°N). Corresponding to the low frequent behaviors, pan evaporation paradox only existed in the QTP as a whole in 1970–1990 and was not apparent at site scale, with less than 9.5% of 274 stations detected in different periods. The results confirmed prevailing abrupt change of pan evaporation and its distinct spatial pattern in the QTP.
Parallel Reaction Monitoring reveals structure-specific ceramide alterations in the zebrafish
Authors: Zhang Tejia , Trauger Sunia A. , Vidoudez Charles , Doane Kim P. , Pluimer Brock R. , Peterson Randall T.
Published: December 2019

Extensive characterisations of the zebrafish genome and proteome have established a foundation for the use of the zebrafish as a model organism; however, characterisation of the zebrafish lipidome has not been as comprehensive. In an effort to expand current knowledge of the zebrafish sphingolipidome, a Parallel Reaction Monitoring (PRM)-based liquid chromatography–mass spectrometry (LC–MS) method was developed to comprehensively quantify zebrafish ceramides. Comparison between zebrafish and a human cell line demonstrated remarkable overlap in ceramide composition, but also revealed a surprising lack of most sphingadiene-containing ceramides in the zebrafish. PRM analysis of zebrafish embryogenesis identified developmental stage-specific ceramide changes based on long chain base (LCB) length. A CRISPR-Cas9-generated zebrafish model of Farber disease exhibited reduced size, early mortality, and severe ceramide accumulation where the amplitude of ceramide change depended on both acyl chain and LCB lengths. Our method adds an additional level of detail to current understanding of the zebrafish lipidome, and could aid in the elucidation of structure-function associations in the context of lipid-related diseases.
Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches
Authors: Cruz Mariana Vargas , Mori Gustavo Maruyama , Signori-Müller Caroline , da Silva Carla Cristina , Oh Dong-Ha , Dassanayake Maheshi , Zucchi Maria Imaculada , Oliveira Rafael Silva , de Souza Anete Pereira
Published: December 2019

Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.
Applied Precision Cancer Medicine in Neuro-Oncology
Authors: Taghizadeh H. , Müllauer L. , Furtner J. , Hainfellner J. A. , Marosi C. , Preusser M. , Prager G. W.
Published: December 2019

Brain tumours that are refractory to treatment have a poor prognosis and constitute a major challenge in offering effective treatment strategies. By targeting molecular alterations, precision cancer medicine may be a viable option for the treatment of brain tumours. In this retrospective analysis of our PCM platform, we describe the molecular profiling of primary brain tumours from 50 patients. Tumour samples of the patients were examined by a 161-gene next-generation sequencing panel, immunohistochemistry, and fluorescencein situhybridization (FISH). We identified 103 molecular aberrations in 36 (72%) of the 50 patients. The predominant mutations wereTP53(14.6%),IDH1(9.7%) andPIK3CA(6.8%). No mutations were detected in 14 (28%) of the 50 patients. IHC demonstrated frequent overexpression of EGFR and mTOR, in 38 (76%) and 35 (70%) patients, respectively. Overexpression of PDGFRa and PDGFRb were less common and detected in 16 and four patients, respectively. For 35 patients a targeted therapy was recommended. In our database, the majority of patients displayed mutations, against which targeted therapy could be offered. Based on our observations, PCM may be a feasible novel treatment approach in neuro-oncology.
High MAST2 mRNA expression and its role in diagnosis and prognosis of liver cancer
Authors: Jiao Yan , Li Yanqing , Jiang Peiqiang , Fu Zhuo , Liu Yahui
Published: December 2019

Liver cancer is a high morbidity and low survival disease all over the world. Chromosomal instability is hallmark of liver cancer. Microtubule-associated serine and threonine kinase 2 (MAST2), as a microtubule associated protein, may involve in tumorous chromosomal instability and plays important roles in cell proliferation and survival. The role of MAST2 in liver cancer has not been well elucidated, which is the aim of our study. In this study, The Cancer Genome Atlas database was used to study the MAST2 mRNA expression in liver cancer, and Chi-squared tests were performed to test the correlation between clinical features and MAST2 expression. ROC curve was performed to examined the diagnostic capacity. The prognostic value of MAST2 in liver cancer was assessed through Kaplan–Meier curves as well as Cox analysis. Our results showed MAST2 was upregulated in liver cancer, and the area under the curve (AUC) was 0.925 and indicated powerful diagnostic capability. High MAST2 expression was associated with advanced clinical status such as histological type (p = 0.0059), histologic grade (p = 0.0142), stage (p = 0.0008), T classification (p = 0.0028), N classification (p = 0.0107), survival status (p = 0.0062), and poor prognosis of patients. Importantly, MAST2 was an independent risk factor for patients’ prognosis after adjusting for other risk factors including stage, T classification, and residual tumor. In total, MAST2 is a potential diagnostic and prognostic biomarker of liver cancer.
Efficacy and Safety of Nivestim Versus Neupogen for Mobilization of Peripheral Blood Stem Cells for Autologous Stem Cell Transplantation
Authors: Chew Cindy , Ng Hong Yen
Published: December 2019

A retrospective cohort study was conducted in Singapore General Hospital to study the safety and efficacy of biosimilar granulocyte-colony stimulating factor (G-CSF) Nivestim for chemo-mobilization of stem cells for autologous stem cell transplant (autoSCT). All patients who underwent an autoSCT between January 2011 and December 2016 were screened for eligibility. A total of 194 patients were screened, and 131 were included. Nivestim was used in 65 patients and the originator G-CSF (Neupogen) in 66. Patient characteristics were similar between both arms except for chemo-mobilization regimen used (p < 0.0001). Mobilization success rates were found to be comparable, at 96.9% (Nivestim) and 97% (Neupogen). Adverse events rates were also similar. Median duration of G-CSF use and hospitalization were both found to be shorter in the Nivestim arm. Median drug acquisition cost per mobilization cycle was significantly lower in the Nivestim arm at $533.40 (range $213.40–$1280.20) as compared to $1261.90 (range $574–$2755.20) in the Neupogen arm (p < 0.0001). No difference was observed for neutrophil and platelet engraftment after autoSCT. Nivestim was found to be safe and non-inferior to Neupogen for chemo-mobilization of stem cells for autoSCT, and associated with lower cost and shorter length of hospitalization.
Divergent expression patterns of pituitary gonadotropin subunit and GnRH receptor genes to continuous GnRH in vitro and in vivo
Authors: Janjic Marija M. , Prévide Rafael M. , Fletcher Patrick A. , Sherman Arthur , Smiljanic Kosara , Abebe Daniel , Bjelobaba Ivana , Stojilkovic Stanko S.
Published: December 2019

Continuous, as opposed to pulsatile, delivery of hypothalamic gonadotropin-releasing hormone (GnRH) leads to a marked decrease in secretion of pituitary gonadotropins LH and FSH and impairment of reproductive function. Here we studied the expression profile of gonadotropin subunit and GnRH receptor genes in rat pituitary in vitro and in vivo to clarify their expression profiles in the absence and continuous presence of GnRH. Culturing of pituitary cells in GnRH-free conditions downregulated Fshb, Cga, and Gnrhr expression, whereas continuous treatment with GnRH agonists upregulated Cga expression progressively and Gnrhr and Fshb expression transiently, accompanied by a prolonged blockade of Fshb but not Gnrhr expression. In contrast, Lhb expression was relatively insensitive to loss of endogenous GnRH and continuous treatment with GnRH, probably reflecting the status of Egr1 and Nr5a1 expression. Similar patterns of responses were observed in vivo after administration of a GnRH agonist. However, continuous treatment with GnRH stimulated LH secretion in vitro and in vivo, leading to decrease in LH cell content despite high basal Lhb expression. These data suggest that blockade of Fshb expression and depletion of the LH secretory pool are two major factors accounting for weakening of the gonadotroph secretory function during continuous GnRH treatment.
TDP-43 aggregation inside micronuclei reveals a potential mechanism for protein inclusion formation in ALS
Authors: Droppelmann Cristian A. , Campos-Melo Danae , Moszczynski Alexander J. , Amzil Hind , Strong Michael J.
Published: December 2019

Amyotrophic lateral sclerosis (ALS) is a devastating progressive neurodegenerative disease with no known etiology. The formation of pathological protein inclusions, including RNA-binding proteins such as TDP-43 and rho guanine nucleotide exchange factor (RGNEF) are a hallmark of ALS. Despite intensive research, the mechanisms behind protein aggregate formation in ALS remains unclear. We have investigated the role of metabolic stress in protein aggregate formation analyzing how it is relevant to the co-aggregation observed between RGNEF and TDP-43 in motor neurons of ALS patients. Metabolic stress was able to induce formation of micronuclei, small nuclear fragments, in cultured cells. Notably, we observed the formation TDP-43 protein inclusions within micronuclei that co-aggregate with RGNEF and can be released to the cytoplasm. We observed that the leucine-rich domain of RGNEF is critical for its interaction with TDP-43 and localization in micronuclei. Finally, we described that micronuclei-like structures can be found in brain and spinal cord of ALS patients. This work is the first description of protein inclusion formation within micronuclei which also is linked with a neurodegenerative disease. The formation of TDP-43 inclusions within micronuclei induced by metabolic stress is a novel mechanism of protein aggregate formation which may have broad relevance for ALS and other neurodegenerative diseases.
Increase in bone metabolic markers and circulating osteoblast-lineage cells after orthognathic surgery
Authors: Abe Yoko , Chiba Mirei , Yaklai Sanicha , Pechayco Roan Solis , Suzuki Hikari , Takahashi Tetsu
Published: December 2019

Increased mineralisation rate and bone formation after surgery or fracture is the regional acceleratory phenomenon (RAP), and its systemic impact is the systemic acceleratory phenomenon (SAP). The proportion of circulating osteoblast lineage cells, including osteocalcin-positive (OCN+) cells, in the peripheral blood is markedly higher during pubertal growth and in patients with bone fractures. This study aimed to elucidate the dynamic changes in bone metabolic activity after orthognathic surgery by longitudinal prospective observation. Peripheral venous blood samples were collected from patients who had undergone orthognathic surgery, and serum bone metabolic markers and the proportion of OCN+ cells were measured. Orthognathic surgery induces systemic dynamic changes in bone metabolic activity by targeting steps in the bone healing process and related proteins, such as surgical stress/inflammation (C-reactive protein), bone resorption (type I collagen C-telopeptide), and bone formation (alkaline phosphatase and bone-specific alkaline phosphatase). During the early post-operative period, the population of OCN+ cells significantly increased. Confocal microscopy revealed that OCN proteins were localised in the cytoplasm in Triton X-100-treated OCN+ cells. Furthermore, OCN, ALP, and COL1A1 gene expression was detected in OCN+ cells, suggesting the contribution of the local maturation of bone marrow-derived OCN+ cells at the site of bone healing.
Statistical Analysis of Dual-task Gait Characteristics for Cognitive Score Estimation
Authors: Matsuura Taku , Sakashita Kazuhiro , Grushnikov Andrey , Okura Fumio , Mitsugami Ikuhisa , Yagi Yasushi
Published: December 2019

Traditional approaches for the screening of cognitive function are often based on paper tests, such as Mini-Mental State Examination (MMSE), that evaluate the degree of cognitive impairment and provide a score of patient’s mental ability. Procedures for conducting paper tests require time investment involving a questioner and not suitable to be carried out frequently. Previous studies showed that dementia impaired patients are not capable of multi-tasking efficiently. Based on this observation an automated system utilizing Kinect device for collecting primarily patient’s gait data who carry out locomotion and calculus tasks individually (i.e., single-tasks) and then simultaneously (i.e., dual-task) was introduced. We installed this system in three elderly facilities and collected 10,833 behavior data from 90 subjects. We conducted analyses of the acquired information extracting 12 features of single- and dual-task performance developed a method for automatic dementia score estimation to investigate determined which characteristics are the most important. In result, a machine learning algorithm using single and dual-task performance classified subjects with an MMSE score of 23 or lower with a recall 0.753 and a specificity 0.799. We found the gait characteristics were important features in the score estimation, and referring to both single and dual-task features was effective.
Diversity of SpaP in genetic and salivary agglutinin mediated adherence among Streptococcus mutans strains
Authors: Yang Jingmei , Deng Dongmei , Brandt Bernd W. , Nazmi Kamran , Wu Yafei , Crielaard Wim , Ligtenberg Antoon J. M.
Published: December 2019

Streptococcus mutans SpaP mediates the binding of this cariogenic bacteria to tooth surfaces. It was reported that the SpaP of S. mutans clinical isolates could be classified to 2 genotypes, type A and B. Our aims are to examine spaP genotypes in often-used S. mutans laboratory strains as well as clinical isolates and to explore the relationship between the genotypes of S. mutans strains and their adherence to salivary-agglutinin (SAG). The sequences of SpaP of 11 S. mutans strains were analyzed with alignment tools. Out of these strains, 9 strains were examined for their adherence to SAG-coated surfaces. The SpaP expression on the cell surfaces and in the spent media of 9 strains were examined by a dot-blot assay. Based on the alignment of the variable V region of SpaP, 9 strains were classified as previously-defined type-A and 3 strains type-B. Among type-B strains, the SpaPs of GS5 and HG723 contain a premature stop codon which resulted in loss of adherence and absence of SpaP expression on the cell surfaces. However, clear SpaP expression was observed in the spent media of both strains. The type-B strain UA159 demonstrated low SpaP expression on the cell surface, but it showed similar adherence ability as the type-A strains. In conclusion, the presence of SpaP on the cell surface determines the adherence of S. mutans to SAG. No difference in SAG-mediated adherence could be seen between type A and B strains, probably due to the limited number of type B strain tested.
A multiple coefficient of determination-based method for parsing SNPs that correlate with mRNA expression
Authors: Song Fan , Tao Yu , Sun Yue , Saffen David
Published: December 2019

In this study, we present a novel, multiple coefficient of determination (R2M)-based method for parsing SNPs located within the chromosomal neighborhood of a gene into semi-independent families, each of which corresponds to one or more functional variants that regulate transcription of the gene. Specifically, our method utilizes a matrix equation framework to calculate R2M values for SNPs within a chromosome region of interest (ROI) based upon the choices of 1-4 “index” SNPs (iSNPs) that serve as proxies for underlying regulatory variants. Exhaustive testing of sets of 1–4 candidate iSNPs identifies iSNP models that best account for estimated R2 values derived from single-variable linear regression analysis of correlations between mRNA expression and genotypes of individual SNPs. Subsequent genotype-based estimation of pairwise r2 linkage disequilibrium (LD) coefficients between each iSNP and the other ROI SNPs allows the SNPs to be parsed into semi-independent families. Analysis of mRNA expression and genotypes data downloaded from Gene Expression Omnibus (GEO) and database for Genotypes and Phenotypes (dbGAP) demonstrates the usefulness of this method for parsing SNPs based on experimental data. We believe that this method will be widely applicable for the analysis of the genetic basis of mRNA expression and visualizing the contributions of multiple genetic variants to the regulation of individual genes.
Optical decomposition of DNA gel and modification of object mobility on micrometre scale
Authors: Shimomura Suguru , Nishimura Takahiro , Ogura Yusuke , Tanida Jun
Published: December 2019

DNA gels can be engineered to exhibit specific properties through the choice of DNA sequences and modification with dye molecules, and can therefore be useful in biomedical applications such as the detection of biomolecules. State transitions of DNA gels on the micrometre scale can generate a viscosity gradient, which can be used to modify the mobility of micrometre-sized objects. In this paper, we propose a method for changing the viscosity of DNA gels using optical decomposition. The use of light allows for decomposition on the micrometre scale, which can be used to achieve patterned viscosity changes within DNA gels. Decomposition was induced by thermal energy released through non-radiative relaxation of excited quenchers. We demonstrated the decomposition of DNA gels in response to irradiation patterns on the micrometre scale. In addition, as a result of changes in DNA gel viscosity due to decomposition, the mobility of polystyrene beads was shown to increase. This technique could provide a new optical approach for controlling the mobility of micrometre-sized objects.
Potential of electrospun cationic BSA fibers to guide osteogenic MSC differentiation via surface charge and fibrous topography
Authors: Raic Annamarija , Friedrich Frank , Kratzer Domenic , Bieback Karen , Lahann Joerg , Lee-Thedieck Cornelia
Published: December 2019

Large or complex bone fractures often need clinical treatments for sufficient bone repair. New treatment strategies have pursued the idea of using mesenchymal stromal cells (MSCs) in combination with osteoinductive materials to guide differentiation of MSCs into bone cells ensuring complete bone regeneration. To overcome the challenge of developing such materials, fundamental studies are needed to analyze and understand the MSC behavior on modified surfaces of applicable materials for bone healing. For this purpose, we developed a fibrous scaffold resembling the bone/bone marrow extracellular matrix (ECM) based on protein without addition of synthetic polymers. With this biomimetic in vitro model we identified the fibrous structure as well as the charge of the material to be responsible for its effects on MSC differentiation. Positive charge was introduced via cationization that additionally supported the stability of the scaffold in cell culture, and acted as nucleation point for mineralization during osteogenesis. Furthermore, we revealed enhanced focal adhesion formation and osteogenic differentiation of MSCs cultured on positively charged protein fibers. This pure protein-based and chemically modifiable, fibrous ECM model allows the investigation of MSC behavior on biomimetic materials to unfold new vistas how to direct cells’ differentiation for the development of new bone regenerating strategies.
Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
Authors: Haehnel Susann , Reiche Kristin , Loeffler Dennis , Horn Andreas , Blumert Conny , Puppel Sven-Holger , Kaiser Nicole , Rapp Felicitas , Rade Michael , Horn Friedemann , Meixensberger Juergen , Bechmann Ingo , Gaunitz Frank , Winter Karsten
Published: December 2019

Cancer research requires models closely resembling the tumor in the patient. Human tissue cultures can overcome interspecies limitations of animal models or the loss of tissue architecture inin vitromodels. However, analysis of tissue slices is often limited to histology. Here, we demonstrate that slices are also suitable for whole transcriptome sequencing and present a method for automated histochemistry of whole slices. Tumor and peritumoral tissue from a patient with glioblastoma was processed to slice cultures, which were treated with standard therapy including temozolomide and X-irradiation. Then, RNA sequencing and automated histochemistry were performed. RNA sequencing was successfully accomplished with a sequencing depth of 243 to 368 x 106reads per sample. Comparing tumor and peritumoral tissue, we identified 1888 genes significantly downregulated and 2382 genes upregulated in tumor. Treatment significantly downregulated 2017 genes, whereas 1399 genes were upregulated. Pathway analysis revealed changes in the expression profile of treated glioblastoma tissue pointing towards downregulated proliferation. This was confirmed by automated analysis of whole tissue slices stained for Ki67. In conclusion, we demonstrate that RNA sequencing of tissue slices is possible and that histochemical analysis of whole tissue slices can be automated which increases the usability of this preclinical model.
Assessment of congruence between co-occurrence and functional networks: A new framework for revealing community assembly rules
Authors: Legras Gaëlle , Loiseau Nicolas , Gaertner Jean-Claude , Poggiale Jean-Christophe , Ienco Dino , Mazouni Nabila , Mérigot Bastien
Published: December 2019

Describing how communities change over space and time is crucial to better understand and predict the functioning of ecosystems. We propose a new methodological framework, based on network theory and modularity concept, to determine which type of mechanisms (i.e. deterministicversusstochastic processes) has the strongest influence on structuring communities. This framework is based on the computation and comparison of two networks: the co-occurrence (based on species abundances) and the functional networks (based on the species traits values). In this way we can assess whether the species belonging to a given functional group also belong to the same co-occurrence group. We adapted the Dg index of Gauzenset al. (2015) to analyze congruence between both networks. This offers the opportunity to identify which assembly rule(s) play(s) the major role in structuring the community. We illustrate our framework with two datasets corresponding to different faunal groups and ecosystems, and characterized by different scales (spatial and temporal scales). By considering both species abundance and multiple functional traits, our framework improves significantly the ability to discriminate the main assembly rules structuring the communities. This point is critical not only to understand community structuring but also its response to global changes and other disturbances.
Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis
Authors: Ebrecht Ana C. , van der Bergh Naadia , Harrison Susan T. L. , Smit Martha S. , Sewell B. Trevor , Opperman Diederik J.
Published: December 2019

Cytochrome P450 reductases (CPRs) are diflavin oxidoreductases that supply electrons to type II cytochrome P450 monooxygenases (CYPs). In addition, it can also reduce other proteins and molecules, including cytochrome c, ferricyanide, and different drugs. Although various CPRs have been functionally and structurally characterized, the overall mechanism and its interaction with different redox acceptors remain elusive. One of the main problems regarding electron transfer between CPRs and CYPs is the so-called “uncoupling”, whereby NAD(P)H derived electrons are lost due to the reduced intermediates’ (FAD and FMN of CPR) interaction with molecular oxygen. Additionally, the decay of the iron-oxygen complex of the CYP can also contribute to loss of reducing equivalents during an unproductive reaction cycle. This phenomenon generates reactive oxygen species (ROS), leading to an inefficient reaction. Here, we present the study of the CPR from Candida tropicalis (CtCPR) lacking the hydrophobic N-terminal part (Δ2–22). The enzyme supports the reduction of cytochrome c and ferricyanide, with an estimated 30% uncoupling during the reactions with cytochrome c. The ROS produced was not influenced by different physicochemical conditions (ionic strength, pH, temperature). The X-ray structures of the enzyme were solved with and without its cofactor, NADPH. Both CtCPR structures exhibited the closed conformation. Comparison with the different solved structures revealed an intricate ionic network responsible for the regulation of the open/closed movement of CtCPR.