bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolomics reveals a link between homocysteine and lipid metabolism and leukocyte telomere length: the ENGAGE consortium
Authors: van der Spek Ashley , Broer Linda , Draisma Harmen H. M. , Pool René , Albrecht Eva , Beekman Marian , Mangino Massimo , Raag Mait , Nyholt Dale R. , Dharuri Harish K. , Codd Veryan , Amin Najaf , de Geus Eco J. C. , Deelen Joris , Demirkan Ayse , Yet Idil , Fischer Krista , Haller Toomas , Henders Anjali K. , Isaacs Aaron , Medland Sarah E. , Montgomery Grant W. , Mooijaart Simon P. , Strauch Konstantin , Suchiman H. Eka D. , Vaarhorst Anika A. M. , van Heemst Diana , Wang-Sattler Rui , Whitfield John B. , Willemsen Gonneke , Wright Margaret J. , Martin Nicholas G. , Samani Nilesh J. , Metspalu Andres , Eline Slagboom P. , Spector Tim D. , Boomsma Dorret I. , van Duijn Cornelia M. , Gieger Christian
Published: August 2019

Telomere shortening has been associated with multiple age-related diseases such as cardiovascular disease, diabetes, and dementia. However, the biological mechanisms responsible for these associations remain largely unknown. In order to gain insight into the metabolic processes driving the association of leukocyte telomere length (LTL) with age-related diseases, we investigated the association between LTL and serum metabolite levels in 7,853 individuals from seven independent cohorts. LTL was determined by quantitative polymerase chain reaction and the levels of 131 serum metabolites were measured with mass spectrometry in biological samples from the same blood draw. With partial correlation analysis, we identified six metabolites that were significantly associated with LTL after adjustment for multiple testing: lysophosphatidylcholine acyl C17:0 (lysoPC a C17:0, p-value = 7.1 × 10−6), methionine (p-value = 9.2 × 10−5), tyrosine (p-value = 2.1 × 10−4), phosphatidylcholine diacyl C32:1 (PC aa C32:1, p-value = 2.4 × 10−4), hydroxypropionylcarnitine (C3-OH, p-value = 2.6 × 10−4), and phosphatidylcholine acyl-alkyl C38:4 (PC ae C38:4, p-value = 9.0 × 10−4). Pathway analysis showed that the three phosphatidylcholines and methionine are involved in homocysteine metabolism and we found supporting evidence for an association of lipid metabolism with LTL. In conclusion, we found longer LTL associated with higher levels of lysoPC a C17:0 and PC ae C38:4, and with lower levels of methionine, tyrosine, PC aa C32:1, and C3-OH. These metabolites have been implicated in inflammation, oxidative stress, homocysteine metabolism, and in cardiovascular disease and diabetes, two major drivers of morbidity and mortality.
Analysis of circulating cell-free DNA identifies KRAS copy number gain and mutation as a novel prognostic marker in Pancreatic cancer
Authors: Mohan Sumitra , Ayub Mahmood , Rothwell Dominic G. , Gulati Sakshi , Kilerci Bedirhan , Hollebecque Antoine , Sun Leong Hui , Smith Nigel K. , Sahoo Sudhakar , Descamps Tine , Zhou Cong , Hubner Richard A. , McNamara Mairéad G. , Lamarca Angela , Valle Juan W. , Dive Caroline , Brady Ged
Published: August 2019

Serial biopsy of pancreatic ductal adenocarcinoma (PDAC), to chart tumour evolution presents a significant challenge. We examined the utility of circulating free DNA (cfDNA) as a minimally invasive approach across a cohort of 55 treatment-naïve patients with PDAC; 31 with metastatic and 24 with locally advanced disease. Somatic mutations in cfDNA were detected using next generation sequencing in 15/24 (62.5%) and 27/31 (87%) of patients with locally advanced and metastatic disease, respectively. Copy number changes were detected in cfDNA of 10 patients of whom 7 exhibited gain of chromosome 12p harbouring KRAS as well as a canonical KRAS codon 12 mutation. In multivariable Cox Regression analysis, we show for the first time that patients with KRAS copy number gain and KRAS mutation have significantly worse outcomes, suggesting that this may be linked to PDAC progression. The simple cfDNA assay we describe will enable determination of the presence of KRAS copy number gain and KRAS mutations in larger studies and clinical trials.
Pretreatment-Integration for Milk Protein Removal and Device-Facilitated Immunochromatographic Assay for 17 Items
Authors: Qie Zhiwei , Huang Ziwei , Gao Zichen , Meng Wu , Zhu Yanhui , Xiao Rui , Wang Shengqi
Published: August 2019

Accurate and comprehensive immunochromatographic assay (ICA) data are urgently required in the daily supervision of plants, schools, testing institutions, and law-enforcing departments. Through pretreatment-integration and device-facilitated operation, a quantitative ICA with high sensitivity and throughput was realized on the basis of a commercialized semi-quantitative ICA strip. Three pretreatment methods, namely, acid base, heavy metal salt, and organic solvent methods, have less than three steps. The pretreatment was established for protein removal. A total of 17 pretreated ICA items in milk were considered for the identification of the most suitable pretreatment method. The items are composed of six items pretreated by the acid-base method, six by the heavy salt method, and five by the organic solvent method. Then, the ICA results with pretreatment were compared with those without pretreatment. After pretreatment, the signal intensity increased by 39%, the detection limit decreased to 12%, the half maximal inhibitory concentration decreased to 18%, and the detection range increased fourfold. A device with mixing and centrifugation functions was designed for the pretreatment-related operations. A pre-incubation sampling device was used to facilitate incubation in batch and high-throughput detection. An ICA reader was used. The detection throughput reached 8 samples per batch or 32 samples per hour. The designed devices were printed through 3D printing and rapid prototyping.
Guideline-conform statin use reduces overall mortality in patients with compensated liver disease
Authors: Unger Lukas W. , Forstner Bernadette , Schneglberger Stephan , Muckenhuber Moritz , Eigenbauer Ernst , Bauer David , Scheiner Bernhard , Mandorfer Mattias , Trauner Michael , Reiberger Thomas
Published: August 2019

Statins reduce cardiovascular risk. However, “real-life” data on statin use in patients with chronic liver disease and its impact on overall and liver-related survival are limited. Therefore, we assessed 1265 CLD patients stratified as advanced (ACLD) or non-advanced (non-ACLD) stage. Statin indication was evaluated according to the 2013 ACC/AHA guidelines and survival-status was verified by national death registry data. Overall, 122 (9.6%) patients had an indication for statin therapy but did not receive statins, 178 (14.1%) patients were on statins and 965 (76.3%) patients had no indication for statins. Statin underutilization was 34.2% in non-ACLD and 48.2% in ACLD patients. In non-ACLD patients, survival was worse without a statin despite indication as compared to patients on statin or without indication (log-rank p = 0.018). In ACLD patients, statin use did not significantly impact on survival (log-rank p = 0.264). Multivariate cox regression analysis confirmed improved overall survival in patients with statin as compared to patients with indication but no statin (HR 0.225; 95%CI 0.053–0.959; p = 0.044) and a trend towards reduced liver-related mortality (HR 0.088; 95%CI 0.006–1.200; p = 0.068). This was not observed in ACLD patients. In conclusion, guideline-confirm statin use is often withhold from  patients with liver disease and this underutilization is associated with impaired survival in non-ACLD patients.
Preparation of MnOx Supported LiOH Activated Soybean Oil Sludge Catalyst and Its Analysis in Denitration Mechanism of Selective Catalytic Oxidation (SCO)
Authors: Lei Zhang , Min Luo , Tingting Kong , Lei Zhang , Huibin He , Yang Jia , Chao Yang , Yan Wu , Mengting Li
Published: August 2019

Treatment with selective catalytic oxidation (SCO) is an effective technology applied recently for conversion of nitrogen oxides pollution control. In order to solve the problems of high cost and difficulties in practical application of SCO catalyst, it was put forward using the solid waste sludge from soybean oil plant as catalyst carrier to prepare denitration catalyst. The sludge was treated by alkaline activation and then MnOx-based sludge was prepared by impregnation. Finally, MnOx-based sludge was calcined in the muffle furnace. The effects of activation and calcination conditions on catalyst activity were investigated. Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to characterize the activity of the sludge based denitration catalyst, and the structure and activity of the sludge based denitration catalyst were furtherly confirmed. According to the achieved results, (1) after activated by LiOH with a mass concentration of 15% for 4 hours, the surface of the sludge catalyst has more alkali functional groups, making the denitration of sludge catalyst the best; (2) the MnOx-based catalyst calcined in the muffle furnace with calcination temperature of 450 °C for 4 hours has obvious denitration efficiency.
The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs
Authors: Van Ghelder Cyril , Parent Geneviève J. , Rigault Philippe , Prunier Julien , Giguère Isabelle , Caron Sébastien , Stival Sena Juliana , Deslauriers Annie , Bousquet Jean , Esmenjaud Daniel , MacKay John
Published: August 2019

The NLRs or NBS-LRRs (nucleotide-binding, leucine-rich-repeat) form the largest resistance gene family in plants, with lineage-specific contingents of TNL, CNL and RNL subfamilies and a central role in resilience to stress. The origin, evolution and distribution of NLR sequences has been unclear owing in part to the variable size and diversity of the RNL subfamily and a lack of data in Gymnosperms. We developed, searched and annotated transcriptomes assemblies of seven conifers and identified a resource of 3816 expressed NLR sequences. Our analyses encompassed sequences data spanning the major groups of land plants and determinations of NLR transcripts levels in response to drought in white spruce. We showed that conifers have among the most diverse and numerous RNLs in tested land plants. We report an evolutionary swap in the formation of RNLs, which emerged from the fusion of an RPW8 domain to a NB-ARC domain of CNL. We uncovered a quantitative relationship between RNLs and TNLs across all land plants investigated, with an average ratio of 1:10. The conifer RNL repertoire harbours four distinct groups, with two that differ from Angiosperms, one of which contained several upregulated sequences in response to drought while the majority of responsive NLRs are downregulated.
Stress-induced phospho-ubiquitin formation causes parkin degradation
Authors: Kovalchuke Lyudmila , Mosharov Eugene V. , Levy Oren A. , Greene Lloyd A.
Published: August 2019

Mutations in the E3 ubiquitin ligase parkin are the most common known cause of autosomal recessive Parkinson’s disease (PD), and parkin depletion may play a role in sporadic PD. Here, we sought to elucidate the mechanisms by which stress decreases parkin protein levels using cultured neuronal cells and the PD-relevant stressor, L-DOPA. We find that L-DOPA causes parkin loss through both oxidative stress-independent and oxidative stress-dependent pathways. Characterization of the latter reveals that it requires both the kinase PINK1 and parkin’s interaction with phosphorylated ubiquitin (phospho-Ub) and is mediated by proteasomal degradation. Surprisingly, autoubiquitination and mitophagy do not appear to be required for such loss. In response to stress induced by hydrogen peroxide or CCCP, parkin degradation also requires its association with phospho-Ub, indicating that this mechanism is broadly generalizable. As oxidative stress, metabolic dysfunction and phospho-Ub levels are all elevated in PD, we suggest that these changes may contribute to a loss of parkin expression.
Reproducibility via coordinated standardization: a multi-center study in a Shank2 genetic rat model for Autism Spectrum Disorders
Authors: Arroyo-Araujo María , Graf Radka , Maco Martine , van Dam Elsbeth , Schenker Esther , Drinkenburg Wilhelmus , Koopmans Bastijn , de Boer Sietse F. , Cullum-Doyle Michaela , Noldus Lucas P. J. J. , Loos Maarten , van Dommelen Wil , Spooren Will , Biemans Barbara , Buhl Derek L. , Kas Martien J.
Published: August 2019

Inconsistent findings between laboratories are hampering scientific progress and are of increasing public concern. Differences in laboratory environment is a known factor contributing to poor reproducibility of findings between research sites, and well-controlled multisite efforts are an important next step to identify the relevant factors needed to reduce variation in study outcome between laboratories. Through harmonization of apparatus, test protocol, and aligned and non-aligned environmental variables, the present study shows that behavioral pharmacological responses in Shank2 knockout (KO) rats, a model of synaptic dysfunction relevant to autism spectrum disorders, were highly replicable across three research centers. All three sites reliably observed a hyperactive and repetitive behavioral phenotype in KO rats compared to their wild-type littermates as well as a dose-dependent phenotype attenuation following acute injections of a selective mGluR1 antagonist. These results show that reproducibility in preclinical studies can be obtained and emphasizes the need for high quality and rigorous methodologies in scientific research. Considering the observed external validity, the present study also suggests mGluR1 as potential target for the treatment of autism spectrum disorders.
Hydrogels formed by anammox extracellular polymeric substances: structural and mechanical insights
Authors: Lotti Tommaso , Carretti Emiliano , Berti Debora , Montis Costanza , Del Buffa Stefano , Lubello Claudio , Feng Cuijie , Malpei Francesca
Published: August 2019

The recovery of biopolymers from the waste sludge produced in wastewater treatments and their application in other industrial sectors, would substantially increase the environmental and economical sustainability of the process, promoting the development of a circular economy. In this study, extracellular polymeric substances (EPS) extracted from anammox granular waste sludge, were investigated and characterized. Rheological and differential scanning calorimetry measurements on EPS aqueous dispersions indicate the formation of an extended 3-D network above a threshold concentration, with a clear dependence of the mechanical and water retention properties on EPS content. The structural characterization, performed with transmission electron microscopy and small angle X-ray scattering, reveals the presence of functional amyloids as putative structural units, observed for the first time in an EPS-based hydrogel. As a proof of concept of the applicative potential, we explored the water and grease resistance provided to paper by an EPS coating. These results shed light on the structural details of EPS-based hydrogels, and pave the way for the possible use of EPS-based materials as a cheap, eco-friendly alternative to commonly adopted paper coatings, in line with a circular economy pattern for wastewater treatment.
Interplay of strain and intermixing effects on direct-bandgap optical transition in strained Ge-on-Si under thermal annealing
Authors: Lee Chulwon , Yoo Yang-Seok , Ki Bugeun , Jang Min-Ho , Lim Seung-Hyuk , Song Hyun Gyu , Cho Jong-Hoi , Oh Jungwoo , Cho Yong-Hoon
Published: August 2019

The influence of thermal annealing on the properties of germanium grown on silicon (Ge-on-Si) has been investigated. Depth dependencies of strain and photoluminescence (PL) were compared for as-grown and annealed Ge-on-Si samples to investigate how intermixing affects the optical properties of Ge-on-Si. The tensile strain on thermally annealed Ge-on-Si increases at the deeper region, while the PL wavelength becomes shorter. This unexpected blue-shift is attributed to Si interdiffusion at the interface, which is confirmed by energy dispersive X-ray spectroscopy and micro-Raman experiments. Not only Γ- and L-valley emissions but also Δ2-valley related emission could be found from the PL spectra, showing a possibility of carrier escape from Γ valley. Temperature-dependent PL analysis reveals that the thermal activation energy of Γ-valley emission increases at the proximity of the Ge/Si interface. By comparing the PL peak energies and their activation energies, both SiGe intermixing and shallow defect levels are found to be responsible for the activation energy increase and consequent efficiency reduction at the Ge/Si interface. These results provide an in-depth understanding of the influence of strain and Si intermixing on the direct-bandgap optical transition in thermally annealed Ge-on-Si.
Binarized Neural Network with Silicon Nanosheet Synaptic Transistors for Supervised Pattern Classification
Authors: Kim Sungho , Choi Bongsik , Yoon Jinsu , Lee Yongwoo , Kim Hee-Dong , Kang Min-Ho , Choi Sung-Jin
Published: August 2019

In the biological neural network, the learning process is achieved through massively parallel synaptic connections between neurons that can be adjusted in an analog manner. Recent developments in emerging synaptic devices and their networks can emulate the functionality of a biological neural network, which will be the fundamental building block for a neuromorphic computing architecture. However, on-chip implementation of a large-scale artificial neural network is still very challenging due to unreliable analog weight modulation in current synaptic device technology. Here, we demonstrate a binarized neural network (BNN) based on a gate-all-around silicon nanosheet synaptic transistor, where reliable digital-type weight modulation can contribute to improve the sustainability of the entire network. BNN is applied to three proof-of-concept examples: (1) handwritten digit classification (MNIST dataset), (2) face image classification (Yale dataset), and (3) experimental 3 × 3 binary pattern classifications using an integrated synaptic transistor network (total 9 × 9 × 2   162 cells) through a supervised online training procedure. The results consolidate the feasibility of binarized neural networks and pave the way toward building a reliable and large-scale artificial neural network by using more advanced conventional digital device technologies.
Low infiltration of tumor-associated macrophages in high c-Myb-expressing breast tumors
Authors: Volodko Nataliya , Gutor Taras , Petronchak Orest , Huley Roman , Dúcka Monika , Šmarda Jan , Borsig Lubor , Beneš Petr , Knopfová Lucia
Published: August 2019

Tumor-associated macrophages (TAMs) are prominent components of tumor stroma that promotes tumorigenesis. Many soluble factors participate in the deleterious cross-talk between TAMs and transformed cells; however mechanisms how tumors orchestrate their production remain relatively unexplored. c-Myb is a transcription factor recently described as a negative regulator of a specific immune signature involved in breast cancer (BC) metastasis. Here we studied whether c-Myb expression is associated with an increased presence of TAMs in human breast tumors. Tumors with high frequency of c-Myb-positive cells have lower density of CD68-positive macrophages. The negative association is reflected by inverse correlation between MYB and CD68/CD163 markers at the mRNA levels in evaluated cohorts of BC patients from public databases, which was found also within the molecular subtypes. In addition, we identified potential MYB-regulated TAMs recruiting factors that in combination with MYB and CD163 provided a valuable clinical multigene predictor for BC relapse. We propose that identified transcription program running in tumor cells with high MYB expression and preventing macrophage accumulation may open new venues towards TAMs targeting and BC therapy.
Plasmid DNA nicking- a Novel Activity of Soybean Trypsin Inhibitor and Bovine Aprotinin
Authors: Islam M. Rafiq , Ihenacho Kelvin , Park Jae Whan , Islam I. Sakif
Published: August 2019

Protease inhibitors, such as trypsin inhibitor, serum alpha-1 antitrypsin, or liver aprotinin, are a class of proteins that competitively bind and block the catalytic activity of proteolytic enzymes with wide ranging biological functions. A significant number of protease inhibitors have also been shown to possess antimicrobial activity, presumed to contribute in defense against pathogenic microorganisms as plants with higher levels of protease inhibitors tend to exhibit increased resistance towards pathogens. Two proposed mechanisms for the antimicrobial activity are combating microbial proteases that play roles in disease development and disruption of microbial cell wall & membrane necessary for survival. Here we show for the first time a novel activity of soybean trypsin inhibitor and bovine aprotinin that they nick supercoiled, circular plasmid DNA. A number of experiments conducted to demonstrate the observed DNA nicking activity is inherent, rather than a co-purified, contaminating nuclease. The nicking of the plasmid results in markedly reduced efficiencies in transformation of E. coli and transfection of HEK293T cells. Thus, this work reveals yet a new mechanism for the antimicrobial activity by protease inhibitors.
Outcome and Prognosis of Patients With Lupus Nephritis Submitted to Renal Transplantation
Authors: Albuquerque Bruna Coelho , Salles Vivian Brito , Tajra Rodrigo Dib de Paulo , Rodrigues Carlos Ewerton Maia
Published: August 2019

This stydy aimed to evaluate the epidemiological and clinical profile and outcome of patients with lupus nephritis (LN) submitted to renal transplantation. Retrospective cohort study based on the records of 35 LN patients submitted to renal transplantation at a single center in Brazil between July 1996 and May 2016. The Kaplan-Meier method was used to estimate 6-month, 1-year and 5-year graft survival. The sample included 38 transplantations (3 of which retransplantations). The mean age at the time of SLE diagnosis was 23.7 ± 9.0 years. Most patients were female (94.7%) and 68.4% were non-Caucasian. Twenty-two (57.9%) underwent renal biopsy prior to transplantation. The mean time from SLE diagnosis to transplantation was 10.3 ± 6.4 years. The mean pre-transplantation dialysis time was 3.8 ± 3.7 years. The grafts came from living related (n = 11) or deceased (n = 27) donors. Three (7.9%) patients experienced acute rejection in the first year. Graft and patient survival rates were, respectively, 97.1% and 100% at 6 months, 84.9% and 96.9% at 1 year, and 76.3% and 92.5% at 5 years. One (2.6%) patient had SLE recurrence. Venous thrombosis (p = 0.017) and antiphospholipid syndrome (APS) (p = 0.036) were more prevalent in patients with graft loss. In our cohort of LN patients submitted to renal transplantation, the 5-year survival rate was high, and APS was an important predictor of poor renal outcome (graft loss).
Peripheral sounds elicit stronger activity in contralateral occipital cortex in blind than sighted individuals
Authors: Amadeo Maria Bianca , Störmer Viola S. , Campus Claudio , Gori Monica
Published: August 2019

Previous research has shown that peripheral, task-irrelevant sounds elicit activity in contralateral visual cortex of sighted people, as revealed by a sustained positive deflection in the event-related potential (ERP) over the occipital scalp contralateral to the sound’s location. This Auditory-evoked Contralateral Occipital Positivity (ACOP) appears between 200–450 ms after sound onset, and is present even when the task is entirely auditory and no visual stimuli are presented at all. Here, we investigate whether this cross-modal activation of contralateral visual cortex is influenced by visual experience. To this end, ERPs were recorded in 12 sighted and 12 blind subjects during a unimodal auditory task. Participants listened to a stream of sounds and pressed a button every time they heard a central target tone, while ignoring the peripheral noise bursts. It was found that task-irrelevant noise bursts elicited a larger ACOP in blind compared to sighted participants, indicating for the first time that peripheral sounds can enhance neural activity in visual cortex in a spatially lateralized manner even in visually deprived individuals. Overall, these results suggest that the cross-modal activation of contralateral visual cortex triggered by peripheral sounds does not require any visual input to develop, and is rather enhanced by visual deprivation.
Genomic Polymorphism Associated with the Emergence of Virulent Isolates of Mycobacterium bovis in the Nile Delta
Authors: Abdelaal Hazem F. M. , Spalink Daniel , Amer Ali , Steinberg Howard , Hashish Emad A. , Nasr Essam A. , Talaat Adel M.
Published: August 2019

Mycobacterium bovis is responsible for bovine tuberculosis in both animals and humans. Despite being one of the most important global zoonotic disease, data related to the ecology and pathogenicity of bovine tuberculosis is scarce, especially in developing countries. In this report, we examined the dynamics of M. bovis transmission among dairy cattle in the Nile Delta of Egypt. Animals belonging to 27 herds from 7 governorates were tested by the Single Intradermal Comparative Skin Tuberculin (SICST), as a preliminary screen for the presence of bovine tuberculosis. Positive SICST reactors were identified in 3% of the animals spread among 40% of the examined herds. Post-mortem examination of slaughtered reactors confirmed the presence of both pulmonary and/or digestive forms of tuberculosis in > 50% of the examined animals. Targeted and whole-genome analysis of M. bovis isolates indicated the emergences of a predominant spoligotype (SB0268) between 2013–2015, suggesting a recent clonal spread of this isolate within the Nile Delta. Surprisingly, 2 isolates belonged to M. bovis BCG group, which are not allowed for animal vaccination in Egypt, while the rest of isolates belonged to the virulent M. bovis clonal complex European 2 present in Latin America and several European countries. Analysis of strain virulence in the murine model of tuberculosis indicated the emergence of a more virulent strain (MBE4) with a specific genotype. More analysis is needed to understand the molecular basis for successful spread of virulent isolates of bovine tuberculosis among animals and to establish genotype/phenotype association.
Brief oxygenation events in locally anoxic oceans during the Cambrian solves the animal breathing paradox
Authors: Dahl Tais W. , Siggaard-Andersen Marie-Louise , Schovsbo Niels H. , Persson Daniel O. , Husted Søren , Hougård Iben W. , Dickson Alexander J. , Kjær Kurt , Nielsen Arne T.
Published: August 2019

Oxygen is a prerequisite for all large and motile animals. It is a puzzling paradox that fossils of benthic animals are often found in black shales with geochemical evidence for deposition in marine environments with anoxic and sulfidic bottom waters. It is debated whether the geochemical proxies are unreliable, affected by diagenesis, or whether the fossils are transported from afar or perhaps were not benthic. Here, we improved the stratigraphic resolution of marine anoxia records 100–1000 fold using core-scanning X-Ray Fluorescence and established a centennial resolution record of oxygen availability at the seafloor in an epicontinental sea that existed ~501–494 million years ago. The study reveals that anoxic bottom-water conditions, often with toxic hydrogen sulfide present, were interrupted by brief oxygenation events of 600–3000 years duration, corresponding to 1–5 mm stratigraphic thickness. Fossil shells occur in some of these oxygenated intervals suggesting that animals invaded when conditions permitted an aerobic life style at the seafloor. Although the fauna evidently comprised opportunistic species adapted to low oxygen environments, these findings reconcile a long-standing debate between paleontologists and geochemists, and shows the potential of ultra-high resolution analyses for reconstructing redox conditions in past oceans.
Curcumin diethyl disuccinate, a prodrug of curcumin, enhances anti-proliferative effect of curcumin against HepG2 cells via apoptosis induction
Authors: Muangnoi Chawanphat , Ratnatilaka Na Bhuket Pahweenvaj , Jithavech Ponsiree , Supasena Wiwat , Paraoan Luminita , Patumraj Suthiluk , Rojsitthisak Pornchai
Published: August 2019

Curcumin (Cur) has been reported to have anti-hepatocellular carcinoma activity but its poor oral bioavailability limits its further development as a chemotherapeutic agent. We synthesized previously a succinate ester prodrug of Cur, curcumin diethyl disuccinate (CurDD) with better chemical stability in a buffer solution pH 7.4. Here, we further investigated and compared the cellular transport and anti-proliferative activity against HepG2 cells of CurDD and Cur. Transport of CurDD across the Caco-2 monolayers provided a significantly higher amount of the bioavailable fraction (BF) of Cur with better cytotoxicity against HepG2 cells compared to that of Cur (p < 0.05). Flow cytometric analysis showed that the BF of CurDD shifted the cell fate to early and late apoptosis to a higher extent than that of Cur. The Western blot analysis revealed that CurDD increased Bax protein expression, downregulated Bcl-2 protein, activated caspase-3 and -9 and increased LC3-II protein level in HepG2 cells. Flow cytometric and immunoblotting results suggest that CurDD can induce HepG2 cell death via an apoptotic pathway. We suggest that CurDD can overcome the limitations of Cur in terms of cellular transport with a potential for further extensive in vitro and in vivo studies of anti-hepatocellular carcinoma effects.
Tiotropium inhibits proinflammatory microparticle generation by human bronchial and endothelial cells
Authors: Neri Tommaso , Scalise Valentina , Passalacqua Ilaria , Sanguinetti Chiara , Lombardi Stefania , Pergoli Laura , Bollati Valentina , Pedrinelli Roberto , Paggiaro Pierluigi , Celi Alessandro
Published: August 2019

Tiotropium is a muscarinic antagonist that reduces the risk of acute exacerbations of chronic obstructive pulmonary disease, possibly through an as yet incompletely characterized anti-inflammatory activity. We hypothesized that muscarinic activation of bronchial epithelial cells and endothelial cells causes the release of proinflammatory microparticles and that tiotropium inhibits the phenomenon. Microparticle generation was assessed by a functional assay, by flow cytometry and by NanoSight technology. Immortalized bronchial epithelial cells (16HBE) and umbilical vein endothelial cells were treated with acetylcholine in the presence of varying concentrations of tiotropium. Intracellular calcium concentration, extracellular regulated kinase phosphorylation and chemokine content in the conditioned media were assessed by commercial kits. Acetylcholine causes microparticle generation that is completely inhibited by tiotropium (50 pM). Microparticles generated by acetylcholine-stimulated cells increase the synthesis of proinflammatory mediators in an autocrine fashion. Acetylcholine-induced upregulation of microparticle generation is inhibited by an inhibitor of extracellular regulated kinase phosphorylation and by a phospholipase C inhibitor. Tiotropium blocks both extracellular regulated kinase phosphorylation and calcium mobilization, consistent with the hypothesis that the drug prevents microparticle generation through inhibition of these critical pathways. These results might contribute to explain the effect of tiotropium in reducing acute exacerbations of chronic obstructive pulmonary disease.
Identification of a factor controlling lysosomal homeostasis using a novel lysosomal trafficking probe
Authors: Ishii Shunsuke , Matsuura Akira , Itakura Eisuke
Published: August 2019

Lysosomes are largely responsible for significant degradation of intracellular and extracellular proteins via the secretory pathway, autophagy, and endocytosis. Therefore, dysregulation of lysosomal homeostasis influences diverse cellular functions. However, a straightforward and quantitative method to measure the integrity of the lysosomal pathway has not been developed. Here, we report the plasmid-based lysosomal-METRIQ (MEasurement of protein Transporting integrity by RatIo Quantification) probe that enables simple quantification of lysosomal integrity by lysosomal green and cytosolic red fluorescent proteins using a flow cytometer. In cultured cells, the lysosomal-METRIQ probe detected not only suppression of the lysosomal pathway but also upregulation of lysosomal activity such as lysosomal biogenesis. To identify factors involved in lysosomal homeostasis, we carried out compound screening and found that the cyclin-dependent kinase (CDK) inhibitors kenpaullone and purvalanol A induce synthesis of cathepsin D and an increase in the number of lysosomes. Subsequent studies revealed that CDK5 maintains lysosomal homeostasis independently of cell cycle arrest. Our results suggest that the lysosomal-METRIQ probe is an effective and efficient tool for measuring lysosomal activity in mammalian cells.
Exosomal miR-16-5p as a target for malignant mesothelioma
Authors: Munson Phillip B. , Hall Elizabeth M. , Farina Nicholas H. , Pass Harvey I. , Shukla Arti
Published: August 2019

Malignant mesothelioma (MM) is an asbestos-induced cancer arising on the mesothelial surface of organ cavities. MM is essentially incurable without a means of early diagnosis and no successful standard of care. These facts indicate a deep chasm of knowledge that needs to be filled. Our group recently delved into MM tumor biology from the perspective of exosome-contained microRNAs (miRNAs). We discovered that the most abundant miRNAs in MM cancer exosomes were tumor suppressors, particularly miR-16-5p. This observation lead us to hypothesize that MM cells preferentially secreted tumor-suppressor miRNAs via exosomes. Through separate avenues of potential therapeutic advance, we embarked on an innovative strategy to kill MM tumor cells. We employed small molecule inhibitors to block exosome secretion, thereby reducing miR-16-5p exosome loss and replenishing cellular miR-16-5p leading to reduced tumorigenic capacity and miR-16-5p target oncoproteins CCND1 and BCL2. Additionally, we force-fed MM tumor exosomes back to MM tumor cells, which led to cell death, and a reduction in the same oncoproteins. We recapitulated these results with direct transfection of miR-16-5p, confirmed that this is a cancer-cell specific effect, and elucidated a part of the miR-16-5p mechanism of exosome loading.
Enrichment of intracellular sulphur cycle –associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis
Authors: Salonen I. S. , Chronopoulou P. -M. , Bird C. , Reichart G. -J. , Koho K. A.
Published: August 2019

Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammoniasp. (T6),Haynesinasp. (S16) andElphidiumsp. (S5)), using a metabarcoding approach targeting the 16S rRNA andaprA-genes. The most abundant intracellular bacterial groups included the genusSulfurovumand the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA andaprA–gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.
A New Method for Intense Cavitation Bubble Generation on Layer-by-Layer Assembled SLIPS
Authors: Aghdam Araz Sheibani , Ghorbani Morteza , Deprem Gokberk , Cebeci Fevzi Çakmak , Koşar Ali
Published: August 2019

The importance of surface topology for the generation of cavitating flows in micro scale has been emphasized during the last decade. In this regard, the utilization of surface roughness elements is not only beneficial in promoting mass transportation mechanisms, but also in improving the surface characteristics by offering new interacting surface areas. Therefore, it is possible to increase the performance of microfluidic systems involving multiphase flows via modifying the surface. In this study, we aim to enhance generation and intensification of cavitating flows inside microfluidic devices by developing artificial roughness elements and trapping hydrophobic fluorinated lubricants. For this, we employed different microfluidic devices with various hydraulic diameters, while roughness structures with different lengths were formed on the side walls of microchannel configurations. The surface roughness of these devices was developed by assembling various sizes of silica nanoparticles using the layer-by-layer technique (D2). In addition, to compare the cavitating flow intensity with regular devices having plain surfaces (D1), highly fluorinated oil was trapped within the pores of the existing thin films in the configuration D2 via providing the Slippery Liquid-Infused Porous Surface (D3). The microfluidic devices housing the short microchannel and the extended channel were exposed to upstream pressures varying from 1 to 7.23 MPa. Cavitation inception and supercavitation condition occured at much lower upstream pressures for the configurations of D2 and D3. Interestingly, hydraulic flip, which rarely appears in the conventional conical nozzles at high pressures, was observed at moderate upstream pressures for the configuration D2 proving the air passage existence along one side of the channel wall.
Evidence for a link between the Atlantic Multidecadal Oscillation and annual asthma mortality rates in the US
Authors: Bonomo Sergio , Ferrante Giuliana , Palazzi Elisa , Pelosi Nicola , Lirer Fabrizio , Viegi Giovanni , La Grutta Stefania
Published: August 2019

An association between climatic conditions and asthma mortality has been widely assumed. However, it is unclear whether climatic variations have a fingerprint on asthma dynamics over long time intervals. The aim of this study is to detect a possible correlation between climatic indices, namely the Atlantic Multidecadal Oscillation and Pacific Decadal Oscillation, and asthma mortality rates over the period from 1950 to 2015 in the contiguous US. To this aim, an analysis of non-stationary and non-linear signals was performed on time series of US annual asthma mortality rates, AMO and PDO indices to search for characteristic periodicities. Results revealed that asthma death rates evaluated for four different age groups (5–14 yr; 15–24 yr; 25–34 yr; 35–44 yr) share the same pattern of fluctuation throughout the 1950–2015 time interval, but different trends, i.e. a positive (negative) trend for the two youngest (oldest) categories. Annual asthma death rates turned out to be correlated with the dynamics of the AMO, and also modulated by the PDO, sharing the same averaged ∼44 year-periodicity. The results of the current study suggest that, since climate patterns have proved to influence asthma mortality rates, they could be advisable in future studies aimed at elucidating the complex relationships between climate and asthma mortality.
Antiretroviral therapy partially improves the abnormalities of dendritic cells and lymphoid and myeloid regulatory populations in recently infected HIV patients
Authors: Márquez-Coello Mercedes , Montes de Oca Arjona Montserrat , Martín-Aspas Andrés , Guerrero Sánchez Francisca , Fernández-Gutiérrez del Álamo Clotilde , Girón-González José A.
Published: August 2019

This study aimed to evaluate the effects of antiretroviral therapy on plasmacytoid (pDC) and myeloid (mDC) dendritic cells as well as regulatory T (Treg) and myeloid-derived suppressor (MDSC) cells in HIV-infected patients. Forty-five HIV-infected patients (20 of them with detectable HIV load −10 recently infected and 10 chronically infected patients-, at baseline and after antiretroviral therapy, and 25 with undetectable viral loads) and 20 healthy controls were studied. The influence of HIV load, bacterial translocation (measured by 16S rDNA and lipopolysaccharide-binding protein) and immune activation markers (interleukin –IL- 6, soluble CD14, activated T cells) was analyzed. The absolute numbers and percentages of pDC and mDC were significantly increased in patients. Patients with detectable viral load exhibited increased intracellular expression of IL-12 by mDCs and interferon -IFN- α by pDCs. Activated population markers were elevated, and the proportion of Tregs was significantly higher in HIV-infected patients. The MDSC percentage was similar in patients and controls, but the intracellular expression of IL-10 was significantly higher in patients. The achievement of undetectable HIV load after therapy did not modify bacterial translocation parameters, but induce an increase in pDCs, mDCs and MDSCs only in recently infected patients. Our data support the importance of early antiretroviral therapy to preserve dendritic and regulatory cell function in HIV-infected individuals.
Targeted sequencing of linkage region in Dominican families implicates PRIMA1 and the SPATA7-PTPN21-ZC3H14-EML5-TTC8 locus in carotid-intima media thickness and atherosclerotic events
Authors: Wang Liyong , Dueker Nicole , Beecham Ashley , Blanton Susan H. , Sacco Ralph L. , Rundek Tatjana
Published: August 2019

Carotid intima-media thickness (cIMT) is a subclinical marker for atherosclerosis. Previously, we reported a quantitative trait locus (QTL) for total cIMT on chromosome 14q and identified PRiMA1, FOXN3 and CCDC88C as candidate genes using a common variants (CVs)-based approach. Herein, we further evaluated the genetic contribution of the QTL to cIMT by resequencing. We sequenced all exons within the QTL and genomic regions of PRiMA1, FOXN3 and CCDC88C in Dominican families with evidence for linkage to the QTL. Unrelated Dominicans from the Northern Manhattan Study (NOMAS) were used for validation. Single-variant-based and gene-based analyses were performed for CVs and rare variants (RVs). The strongest evidence for association with CVs was found in PRiMA1 (p = 8.2 × 10−5 in families, p = 0.01 in NOMAS at rs12587586), and in the five-gene cluster SPATA7-PTPN21-ZC3H14-EML5-TTC8 locus (p = 1.3 × 10−4 in families, p = 0.01 in NOMAS at rs2274736). No evidence for association with RVs was found in PRiMA1. The top marker from previous study in PRiMA1 (rs7152362) was associated with fewer atherosclerotic events (OR = 0.67; p = 0.02 in NOMAS) and smaller cIMT (β = −0.58, p = 2.8 × 10−4 in Family). Within the five-gene cluster, evidence for association was found for exonic RVs (p = 0.02 in families, p = 0.28 in NOMAS), which was enriched among RVs with higher functional potentials (p = 0.05 in NOMAS for RVs in the top functional tertile). In summary, targeted resequencing provided validation and novel insights into the genetic architecture of cIMT, suggesting stronger effects for RVs with higher functional potentials. Furthermore, our data support the clinical relevance of CVs associated with subclinical atherosclerosis.
Targeting PFKFB3 alleviates cerebral ischemia-reperfusion injury in mice
Authors: Burmistrova Olga , Olias-Arjona Ana , Lapresa Rebeca , Jimenez-Blasco Daniel , Eremeeva Tatiana , Shishov Dmitry , Romanov Sergei , Zakurdaeva Kristina , Almeida Angeles , Fedichev Peter O. , Bolaños Juan P.
Published: August 2019

The glycolytic rate in neurons is low in order to allow glucose to be metabolized through the pentose-phosphate pathway (PPP), which regenerates NADPH to preserve the glutathione redox status and survival. This is controlled by 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3), the pro-glycolytic enzyme that forms fructose-2,6-bisphosphate, a powerful allosteric activator of 6-phosphofructo-1-kinase. In neurons, PFKFB3 protein is physiologically inactive due to its proteasomal degradation. However, upon an excitotoxic stimuli, PFKFB3 becomes stabilized to activate glycolysis, thus hampering PPP mediated protection of redox status leading to neurodegeneration. Here, we show that selective inhibition of PFKFB3 activity by the small molecule AZ67 prevents the NADPH oxidation, redox stress and apoptotic cell death caused by the activation of glycolysis triggered upon excitotoxic and oxygen-glucose deprivation/reoxygenation models in mouse primary neurons. Furthermore, in vivo administration of AZ67 to mice significantly alleviated the motor discoordination and brain infarct injury in the middle carotid artery occlusion ischemia/reperfusion model. These results show that pharmacological inhibition of PFKFB3 is a suitable neuroprotective therapeutic strategy in excitotoxic-related disorders such as stroke.
HER2, chromosome 17 polysomy and DNA ploidy status in breast cancer; a translational study
Authors: Halilovic Altuna , Verweij Dagmar I. , Simons Annet , Stevens-Kroef Marian J. P. L. , Vermeulen Susan , Elsink Janet , Tops Bastiaan B. J. , Otte-Höller Irene , van der Laak Jeroen A. W. M. , van de Water Carlijn , Boelens Oliver B. A. , Schlooz-Vries Margrethe S. , Dijkstra Jeroen R. , Nagtegaal Iris D. , Tol Jolien , van Cleef Patricia H. J. , Span Paul N. , Bult Peter
Published: August 2019

Breast cancer treatment depends on human epidermal growth factor receptor-2 (HER2) status, which is often determined using dual probe fluorescence in situ hybridisation (FISH). Hereby, also loss and gain of the centromere of chromosome 17 (CEP17) can be observed (HER2 is located on chromosome 17). CEP17 gain can lead to difficulty in interpretation of HER2 status, since this might represent true polysomy. With this study we investigated whether isolated polysomy is present and how this effects HER2 status in six breast cancer cell lines and 97 breast cancer cases, using HER2 FISH and immunohistochemistry, DNA ploidy assessment and multiplex ligation dependent probe amplification. We observed no isolated polysomy of chromosome 17 in any cell line. However, FISH analysis did show CEP17 gain in five of six cell lines, which reflected gains of the whole chromosome in metaphase spreads and aneuploidy with gain of multiple chromosomes in all these cases. In patients’ samples, gain of CEP17 indeed correlated with aneuploidy of the tumour (91.1%; p < 0.001). Our results indicate that CEP17 gain is not due to isolated polysomy, but rather due to widespread aneuploidy with gain of multiple chromosomes. As aneuploidy is associated with poor clinical outcome, irrespective of tumour grade, this could improve future therapeutic decision making.
Subwavelength acoustic monopole source emission enhancement through dual gratings
Authors: Mei Jun , Wu Ying
Published: August 2019

Acoustic source emission rate is generally low at low frequencies. In this work, we propose a simple design of ‘LEGO’-type acoustic metamaterial that can significantly enhance the low frequency emission rate of an acoustic monopole source. Such enhancement is resulted from the coupling between resonances of a cavity and a dual grating comprised of two concentric layers of periodically distributed narrow slits. We develop an effective medium model to characterize the enhancement. Because of its simple structure, the metamaterial is easy to fabricate and thus facilitates the applications in various domains such as oil exploration.