bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrostatic pressure-generated reactive oxygen species induce osteoarthritic conditions in cartilage pellet cultures
Authors: Rieder Bernhard , Weihs Anna M. , Weidinger Adelheid , Szwarc Dorota , Nürnberger Sylvia , Redl Heinz , Rünzler Dominik , Huber-Gries Carina , Teuschl Andreas H.
Published: November 2018

Osteoarthritis (OA) is one of the most common causes of disability and represents a major socio-economic burden. Despite intensive research, the molecular mechanisms responsible for the initiation and progression of OA remain inconclusive. In recent years experimental findings revealed elevated levels of reactive oxygen species (ROS) as a major factor contributing to the onset and progression of OA. Hence, we designed a hydrostatic pressure bioreactor system that is capable of stimulating cartilage cell cultures with elevated ROS levels. Increased ROS levels in the media did not only lead to an inhibition of glycosaminoglycans and collagen II formation but also to a reduction of already formed glycosaminoglycans and collagen II in chondrogenic mesenchymal stem cell pellet cultures. These effects were associated with the elevated activity of matrix metalloproteinases as well as the increased expression of several inflammatory cytokines. ROS activated different signaling pathways including PI3K/Akt and MAPK/ERK which are known to be involved in OA initiation and progression. Utilizing the presented bioreactor system, an OA in vitro model based on the generation of ROS was developed that enables the further investigation of ROS effects on cartilage degradation but can also be used as a versatile tool for anti-oxidative drug testing.
Properties of cell signaling pathways and gene expression systems operating far from steady-state
Authors: Di-Bella Juan Pablo , Colman-Lerner Alejandro , Ventura Alejandra C.
Published: November 2018

Ligand-receptor systems, covalent modification cycles, and transcriptional networks are basic units of signaling systems and their steady-state properties are well understood. However, the behavior of such systems before steady-state is poorly characterized. Here, we analyzed the properties of input-output curves for each of these systems as they approach steady-state. In ligand-receptor systems, the EC50 (concentration of the ligand that occupies 50% of the receptors) is higher before the system reaches steady-state. Based on this behavior, we have previously defined PRESS (for pre-equilibrium sensing and signaling), a general “systems level” mechanism cells may use to overcome input saturation. Originally, we showed that, given a step stimulation, PRESS operates when the kinetics of ligand-receptor binding are slower than the downstream signaling steps. Now, we show that, provided the input increases slowly, it is not essential for the ligand binding reaction itself to be slow. In addition, we demonstrate that covalent modification cycles and gene expression systems may also operate in PRESS mode. Thus, nearly all biochemical processes may operate in PRESS mode, suggesting that this mechanism may be ubiquitous in cell signaling systems.
Clinical management and prevention of dental caries in athletes: A four-year randomized controlled clinical trial
Authors: Frese C. , Wohlrab T. , Sheng L. , Kieser M. , Krisam J. , Frese F. , Wolff D.
Published: November 2018

The aims of this four-year randomized controlled clinical trial were to gain insights into management and prevention of dental caries and the effect of stannous fluoride products in athletes. Fifty-four participants were randomized into test and control groups. The test group used special stannous fluoride products. The primary endpoint dental caries was assessed by the ICDAS-II-System and analyzed both by a linear mixed model for repeated measures and a generalized linear mixed model. During the observation period an increase in caries-free surfaces from 64.91 ± 6.42 at baseline to 73.22 ± 4.43 was observed. In surfaces with caries superficialis and caries media, a decrease from 13.94 ± 5.70 and 2.96 ± 2.55 surfaces at baseline to 7.89 ± 3.18 and 0.46 ± 0.78 after 2.5 years was noted, respectively. The analysis showed no effect of stannous fluoride products, but a significant difference for the time of examination (p < 0.0001). In addition, it could be shown that at any time of examination, the odds of developing caries media on a new surface was significantly lower than at baseline (up to 25-times). Due to biannual dental examinations, professional tooth cleaning and restorative treatment the number of caries-free surfaces increased and the odds of a new surface to be afflicted with caries media decreased 25-fold.
Inactivation of NUPR1 promotes cell death by coupling ER-stress responses with necrosis
Authors: Santofimia-Castaño Patricia , Lan Wenjun , Bintz Jennifer , Gayet Odile , Carrier Alice , Lomberk Gwen , Neira José Luis , González Antonio , Urrutia Raul , Soubeyran Philippe , Iovanna Juan
Published: November 2018

It was already described that genetic inhibition of NUPR1 induces tumor growth arrest. In this paper we studied the metabolism changes after NUPR1 downregulation in pancreatic cancer cells, which results in a significant decrease of OXPHOS activity with a concomitant lower ATP production which precedes the necrotic cell death. We demonstrated that NUPR1 downregulation induces a mitochondrial failure with a loss of the mitochondrial membrane potential, a strong increase in ROS production and a concomitant relocalization of mitochondria to the vicinity of the endoplasmic reticulum (ER). In addition, the transcriptomic analysis of NUPR1-deficient cells shows a decrease in the expression of some ER stress response-associated genes. Indeed, in ER stressors-treated cells with thapsigargin, brefeldin A or tunicamycin, a greater increase in necrosis and decrease of ATP content was observed in NUPR1-defficent cells. Finally, in vivo experiments, using acute pancreatitis which induces ER stress as well as NUPR1 activation, we observed that NUPR1 expression protects acinar cells from necrosis in mice. Importantly, we also report that the cell death observed after knocking-down NUPR1 expression is completely reversed by incubation with Necrostatin-1, but not by inhibiting caspase activity with Z-VAD-FMK. Altogether, these data enable us to describe a model in which inactivation of NUPR1 in pancreatic cancer cells results in an ER stress that induces a mitochondrial malfunction, a deficient ATP production and, as consequence, the cell death mediated by a programmed necrosis.
Toenail manganese as a potential biomarker for in utero and early childhood exposure studies
Authors: Cigan Shannon S. , McGovern Patricia M. , Choudhary Kriti , Miller Neely C. , Georgieff Michael , Rao Raghavendra , Stepanov Irina
Published: November 2018

Elevated in utero and early childhood exposure to manganese may have adverse effects on neurodevelopment. We conducted preliminary analyses to evaluate toenails as a matrix for investigating manganese exposure in infants. Infant and maternal toenail and hair samples were collected from 25 infants (7 months old) and their mothers. A subset of mothers was recruited in the third trimester of pregnancy and some also provided pre-natal toenail, hair, and blood samples, cord blood, and additional post-natal samples. Collected samples were analyzed by inductively coupled plasma mass-spectrometry. Toenail manganese levels in infants ranged from below the limit of detection (LOD) to 2.80 µg/g. Only 1 toenail sample and 4 hair samples contained levels of manganese below LOD. Associations between infant and maternal biomarkers were not statistically significant. Analysis of multiple post-natal toenail samples from a single infant-mother pair showed an increase in the infant’s toenail manganese and a decrease in maternal toenail manganese over the first year of the infant’s life. Overall, our findings suggest that toenails may serve as a valuable biological matrix for measuring manganese exposure in newborns and infants; however, additional studies are needed to determine the impact of the timing of toenail sample collection on its utility in assessing early life exposure and health outcomes.
Systematic Study of Ferromagnetism in CrxSb2−xTe3 Topological Insulator Thin Films using Electrical and Optical Techniques
Authors: Singh Angadjit , Kamboj Varun S. , Liu Jieyi , Llandro Justin , Duffy Liam B. , Senanayak Satyaprasad P. , Beere Harvey E. , Ionescu Adrian , Ritchie David A. , Hesjedal Thorsten , Barnes Crispin H. W.
Published: November 2018

Ferromagnetic ordering in a topological insulator can break time-reversal symmetry, realizing dissipationless electronic states in the absence of a magnetic field. The control of the magnetic state is of great importance for future device applications. We provide a detailed systematic study of the magnetic state in highly doped CrxSb2−xTe3 thin films using electrical transport, magneto-optic Kerr effect measurements and terahertz time domain spectroscopy, and also report an efficient electric gating of ferromagnetic order using the electrolyte ionic liquid [DEME][TFSI]. Upon increasing the Cr concentration from x = 0.15 to 0.76, the Curie temperature (Tc) was observed to increase by ~5 times to 176 K. In addition, it was possible to modify the magnetic moment by up to 50% with a gate bias variation of just ±3 V, which corresponds to an increase in carrier density by 50%. Further analysis on a sample with x = 0.76 exhibits a clear insulator-metal transition at Tc, indicating the consistency between the electrical and optical measurements. The direct correlation obtained between the carrier density and ferromagnetism - in both electrostatic and chemical doping - using optical and electrical means strongly suggests a carrier-mediated Ruderman-Kittel-Kasuya-Yoshida (RKKY) coupling scenario. Our low-voltage means of manipulating ferromagnetism, and consistency in optical and electrical measurements provides a way to realize exotic quantum states for spintronic and low energy magneto-electronic device applications.
Sequences encoding C2H2 zinc fingers inhibit polyadenylation and mRNA export in human cells
Authors: Russo Joseph , Jalkanen Aimee L. , Heck Adam M. , Schmidt Caleb M. , Wilusz Jeffrey , Wilusz Carol J.
Published: November 2018

The large C2H2-Zinc Finger (C2H2-ZNF) gene family has rapidly expanded in primates through gene duplication. There is consequently considerable sequence homology between family members at both the nucleotide and amino acid level, allowing for coordinated regulation and shared functions. Here we show that multiple C2H2-ZNF mRNAs experience differential polyadenylation resulting in populations with short and long poly(A) tails. Furthermore, a significant proportion of C2H2-ZNF mRNAs are retained in the nucleus. Intriguingly, both short poly(A) tails and nuclear retention can be specified by the repeated elements that encode zinc finger motifs. These Zinc finger Coding Regions (ZCRs) appear to restrict polyadenylation of nascent RNAs and at the same time impede their export. However, the polyadenylation process is not necessary for nuclear retention of ZNF mRNAs. We propose that inefficient polyadenylation and export may allow C2H2-ZNF mRNAs to moonlight as non-coding RNAs or to be stored for later use.
High Pressure Metamorphism Caused by Fluid Induced Weakening of Deep Continental Crust
Authors: Jamtveit Bjørn , Moulas Evangelos , Andersen Torgeir B. , Austrheim Håkon , Corfu Fernando , Petley-Ragan Arianne , Schmalholz Stefan M.
Published: November 2018

Studies of mineral equilibria in metamorphic rocks have given valuable insights into the tectonic processes operating at convergent plate margins during an orogeny. Geodynamic models simulating orogenesis and crustal thickening have been constrained by temperature and pressure estimates inferred from the mineral assemblages of the various lithologies involved along with age constrains from increasingly precise geochronological techniques. During such studies it is assumed that the pressure experienced by a given rock is uniquely related to its depth of burial. This assumption has been challenged by recent studies of high pressure (HP) and ultrahigh pressure (UHP) rocks. Here, we describe an example of Caledonian HP metamorphism from the Bergen Arcs in western Norway, and show that the associated formation of Caledonian eclogites at the expense of Proterozoic granulites was related to local pressure perturbations rather than burial, and that the HP metamorphism resulted from fluid-induced weakening of an initially dry and highly stressed lower crust when thrust upon the hyperextended margin of the Baltic shield.
Perioperative aspirin and long-term survival in patients undergoing coronary artery bypass graft
Authors: Ding Qian , Liu Hong , Zhang Zugui , Goldhammer Jordan , Yuen Eric , Li Zhongmin , Yao Linong , Young Nilas , Boyd Douglas , Weintraub William , Morris Rohinton , Sun Jianzhong
Published: November 2018

This study aimed to examine association between perioperative uses of aspirin and long-term survival in patients undergoing CABG. A retrospective cohort study was performed in 9,584 consecutive patients receiving cardiac surgery from three tertiary hospitals. Of all the patients, 4,132 patients undergoing CABG met inclusion criteria and were divided into four groups: with or without preoperative or postoperative aspirin respectively. 30-day postoperative and long-term mortality were compared with the use of propensity scores and inverse probability weighting adjustment to reduce the treatment-selection bias. The patients taking preoperative aspirin presented significantly more with comorbidities. However, the results of this study showed that preoperative aspirin (vs. no preoperative aspirin) was associated with significantly reduced the risk of 30-day mortality in the patients undergoing CABG. Further, the results of long-term mortality showed that the patients taking preoperative aspirin and postoperative aspirin (vs. not taking) were associated with significantly reduced the risk of 4-year mortality (14.8% vs. 18.1%, RR: 0.82, 95% CI: 0.75–0.89, P = 0.005; 10.7% vs. 16.2%, RR: 0.66, 95% CI: 0.50–0.82, P = 0.003). In conclusion, this cohort study showed that perioperative (before and after surgery) use of aspirin was associated with significant reduction in 30-day mortality without significant bleeding complications, also improved long-term survival in patients undergoing CABG.
Thidiazuron-induced somatic embryogenesis and changes of antioxidant properties in tissue cultures of half-high blueberry plants
Authors: Ghosh Amrita , Igamberdiev Abir U. , Debnath Samir C.
Published: November 2018

An efficient protocol of somatic embryogenesis (SE) has been developed for the first time in four half-high blueberry (Vaccinium corymbosumL. × V. angustifoliumAit.) cultivars. Thidiazuron (TDZ), a plant growth regulator with potential activities for shoot regeneration and shoot proliferation, was found most effective for somatic embryo formation when added to a nutrient medium at high concentration (9 µM). Although TDZ was also best for embryo germination at low concentration (2.3 µM), it was followed by zeatin at 4.6 µM for the same. Plantlets developed from SE were removed from the nutrient medium and transferred on a peat: perlite medium where 100% survival rate was acquired following the acclimatization process in a greenhouse. The concentrations of total phenolic and flavonoid contents were higher in greenhouse-grown conventionally cutting-propagated donor mother plants than those of respective SE plants for ‘St. Cloud’, ‘Patriot’ and ‘Northblue’ but not for ‘Chippewa’. The effect of propagation method and/or the older age of donor mother plants were clearly visible exclusively as the 15-year-old donor plants showed higher level of 2,2-diphenyl-1-picrylhydrazyl scavenging activity than the eight-weeks-old SE plants in all four cultivars.
An anti-clogging method for improving the performance and lifespan of blood plasma separation devices in real-time and continuous microfluidic systems
Authors: Kang Dong-Hyun , Kim Kyongtae , Kim Yong-Jun
Published: November 2018

On-chip blood plasma separators using microfluidic channels are typically developed as disposable devices for short-term use only because blood cells tend to clog the microchannels, limiting their application in real-time and continuous systems. In this study, we propose an anti-clogging method. We applied dielectrophoresis to prevent microchannel clogging in a plasma separator that can be used over long periods for real-time and continuous monitoring. Prior to applying the anti-clogging method, the blood plasma separator stopped working after 4 h. In contrast, by manipulating the separator with the new anti-clogging method at a voltage of 20 V, it continued working in a long-term experiment for 12 h without performance deterioration or an increase in cell loss. Two critical performance parameters of the manipulated separator, the purity efficiency and the plasma yield, were 97.23 ± 5.43% and 38.95 ± 9.34%, respectively, at 20 V after 15 min. Interestingly, the two performance parameters did not decrease during the long-term experiment. Hence, the blood plasma separator with the anti-clogging method is an interesting device for use in real-time and continuous blood plasma separation systems because of its consistent performance and improved lifespan.
Common solar wind drivers behind magnetic storm–magnetospheric substorm dependency
Authors: Runge Jakob , Balasis Georgios , Daglis Ioannis A. , Papadimitriou Constantinos , Donner Reik V.
Published: November 2018

The dynamical relationship between magnetic storms and magnetospheric substorms is one of the most controversial issues of contemporary space research. Here, we address this issue through a causal inference approach to two corresponding indices in conjunction with several relevant solar wind variables. We find that the vertical component of the interplanetary magnetic field is the strongest and common driver of both storms and substorms. Further, our results suggest, at least based on the analyzed indices, that there is no statistical evidence for a direct or indirect dependency between substorms and storms and their statistical association can be explained by the common solar drivers. Given the powerful statistical tests we performed (by simultaneously taking into account time series of indices and solar wind variables), a physical mechanism through which substorms directly or indirectly drive storms or vice versa is, therefore, unlikely.
Selective eye fixations on diagnostic face regions of dynamic emotional expressions: KDEF-dyn database
Authors: Calvo Manuel G. , Fernández-Martín Andrés , Gutiérrez-García Aida , Lundqvist Daniel
Published: November 2018

Prior research using static facial stimuli (photographs) has identified diagnostic face regions (i.e., functional for recognition) of emotional expressions. In the current study, we aimed to determine attentional orienting, engagement, and time course of fixation on diagnostic regions. To this end, we assessed the eye movements of observers inspecting dynamic expressions that changed from a neutral to an emotional face. A new stimulus set (KDEF-dyn) was developed, which comprises 240 video-clips of 40 human models portraying six basic emotions (happy, sad, angry, fearful, disgusted, and surprised). For validation purposes, 72 observers categorized the expressions while gaze behavior was measured (probability of first fixation, entry time, gaze duration, and number of fixations). Specific visual scanpath profiles characterized each emotional expression: The eye region was looked at earlier and longer for angry and sad faces; the mouth region, for happy faces; and the nose/cheek region, for disgusted faces; the eye and the mouth regions attracted attention in a more balanced manner for surprise and fear. These profiles reflected enhanced selective attention to expression-specific diagnostic face regions. The KDEF-dyn stimuli and the validation data will be available to the scientific community as a useful tool for research on emotional facial expression processing.
Conversion from environmental filtering to randomness as assembly rule of ground beetle assemblages along an urbanization gradient
Authors: Magura Tibor , Lövei Gábor L. , Tóthmérész Béla
Published: November 2018

Urbanization fragments, isolates or eliminates natural habitats, and changes the structure and composition of assemblages living in the remaining natural fragments. Knowing assembly rules is necessary to support and/or maintain biodiversity in urban habitats. We hypothesized that forest communities in rural sites are organized by environmental filtering, but this may be changed by urbanization, and in the suburban and urban forest fragments replaced by randomly organized assemblages, influenced by the colonization of species from the surrounding matrix. Evaluating simultaneously the functional and phylogenetic relationships of co-existing species, we showed that at the rural sites, co-existing ground beetle species were functionally and phylogenetically more similar than expected by chance, indicating that environmental filtering was the likely process structuring these communities. Contrary to this, in urban and suburban sites, the co-occurring species were functionally and phylogenetically not different from the null model, indicating randomly structured assemblages. According to our findings, changes in environmental and habitat characteristics accompanied by urbanization lead to assemblages of randomly colonized species from the surrounding matrix, threatening proper ecosystem functioning. To reassemble stochastically assembled species of urban and suburban fragments to structured, properly functioning communities, appropriate management strategies are needed which simultaneously consider recreational, economic and conservation criteria.
Electrical activation of degenerated photoreceptors in blind mouse retina elicited network-mediated responses in different types of ganglion cells
Authors: Haq Wadood , Dietter Johannes , Zrenner Eberhart
Published: November 2018

Electrical (e-) stimulation is explored in schemes to rescue the vision of blind people, e.g. those affected by Retinitis Pigmentosa (RP). We e-activated subretinally the surviving degenerated photoreceptors (d-Phrs) of the rd1 mouse (RP model) and evoked visual responses in the blind retina. The e-stimulation was applied with a single platinum/iridium electrode. The d-Phrs (calcium-imaging) and ganglion cells (GC) activity (MEA-recording) were recorded in simultaneous multilayer recordings. The findings of this study confirm that the d-Phrs responded to e-stimulation and modulated the retinal network-activity. The application of blockers revealed that the synaptic interactions were dependent on voltage-gated calcium channels and mediated by the transmitters glutamate and GABA. Moreover, the gap junctions coupled networks promoted the lateral-spread of the e-evoked activity in the outer (~60 µm) and inner (~120 µm) retina. The activated GCs were identified as subtypes of the ON, OFF and ON-OFF classes. In conclusion, d-Phrs are the ideal interface partners for implants to elicit enhanced visual responses at higher temporal and spatial resolution. Furthermore, the retina’s intact circuity at the onset of complete blindness makes it a tempting target when considering the implantation of implants into young patients to provide a seamless transition from blinding to chip-aided vision.
Comparative genomic and functional analyses of four sequenced Bacillus cereus genomes reveal conservation of genes relevant to plant-growth-promoting traits
Authors: Zeng Qingchao , Xie Jianbo , Li Yan , Gao Tantan , Xu Cheng , Wang Qi
Published: November 2018

SomeBacillusstrains function as predominant plant-growth-promoting rhizobacteria.Bacillus cereus905 is a rod-shaped Gram-positive bacterium isolated from wheat rhizosphere and is a rhizobacterium that exhibits significant plant-growth-promoting effects. Species belonging to the genusBacillusare observed in numerous different habitats. Several papers onB.cereusare related to pathogens that causes food-borne illness and industrial applications. However, genomic analysis of plant-associatedB.cereushas yet to be reported. Here, we conducted a genomic analysis comparing strain 905 with three otherB.cereusstrains and investigate the genomic characteristics and evolution traits of the species in different niches. The genome sizes of fourB.cereusstrains range from 5.38 M to 6.40 M, and the number of protein-coding genes varies in the four strains. Comparisons of the fourB.cereusstrains reveal 3,998 core genes. The function of strain-specific genes are related to carbohydrate, amino acid and coenzyme metabolism and transcription. Analysis of single nucleotide polymorphisms (SNPs) indicates local diversification of the four strains. SNPs are unevenly distributed throughout the four genomes, and function interpretation of regions with high SNP density coincides with the function of strain-specific genes. Detailed analysis indicates that certain SNPs contribute to the formation of strain-specific genes. By contrast, genes related to plant-growth-promoting traits are highly conserved. This study shows the genomic differences between four strains from different niches and provides an in-depth understanding of the genome architecture of these species, thus facilitating genetic engineering and agricultural applications in the future.
Effects of spatial consistency and individual difference on touch-induced visual suppression effect
Authors: Hidaka Souta , Suzuishi Yosuke , Ide Masakazu , Wada Makoto
Published: November 2018

Crossmodal studies have reported not only facilitatory but also inhibitory perceptual interactions. For instance, tactile stimulation to the index finger of a hand leads to the degradation of visual discrimination performance (touch-induced visual suppression, TIVS). It has been suggested that the magnitude of TIVS depends on the spatial congruency of visuo-tactile stimuli and on individual differences in task performance. We performed a detailed investigation of the effects of spatial consistency and individual differences on the occurrence of TIVS. The visual target and tactile stimulus were presented at co-localized, ipsilateral but not co-localized, or contralateral positions. The degree of autistic traits has been reported to be well variable among the general population and to reflect differences in sensory processing. Therefore, we assessed the magnitude of autistic traits using the autism-spectrum quotient (AQ) as an index of individual differences. TIVS occurred particularly at the ipsilateral but not co-localized position. In contrast, the magnitude of the TIVS was positively correlated with the AQ score when the stimuli were presented at the co-localized position. These findings suggest that the occurrence of TIVS can be modulated both by the spatial relationship between the visual and tactile stimuli and by individual differences in autistic traits.
Individual variability in diving, movement and activity patterns of adult bearded seals in Svalbard, Norway
Authors: Hamilton Charmain D. , Kovacs Kit M. , Lydersen Christian
Published: November 2018

Bearded seals are one of the least studied Arctic marine mammals, despite their circumpolar distribution and importance as a resource to Inuit communities. In this study, adult bearded seals (Erignathus barbatus) were equipped with GPS-Argos-CTD-SRDLs in Svalbard, Norway (2011–2012, n = 7) to document their diving, activity and movement patterns in a region where their habitat is changing rapidly. Five seals transmitted for > 8 months, sending 21,738 GPS-positions and 17,866 dives between July and April. The seals spent little time hauled out (≤ 5%). Diving, which occupied 74 ± 3% of their time, was generally shallow (24 ± 7 m, max: 391 m) and of short duration (6.6 ± 1.5 min, max: 24 min) with deeper, longer dives in winter/spring compared to summer. All seals occupied shallow, coastal areas and relatively small 50% home ranges (10–32 km2). However, individuals exhibited high degrees of specialization in their habitat use and diving behaviour, differing markedly with respect to proportions of benthic vs pelagic dives (range: 51–95% benthic dives), distance to glacier fronts (range: 3–22 km) and in the time spent at the bottom of dives (range: 43–77%). Having specialized strategies within a generalist population may help bearded seals adapt in a rapidly changing Arctic ecosystem.
Obesity shows preserved plasma proteome in large independent clinical cohorts
Authors: Cominetti Ornella , Núñez Galindo Antonio , Corthésy John , Valsesia Armand , Irincheeva Irina , Kussmann Martin , Saris Wim H. M. , Astrup Arne , McPherson Ruth , Harper Mary-Ellen , Dent Robert , Hager Jörg , Dayon Loïc
Published: November 2018

Holistic human proteome maps are expected to complement comprehensive profile assessment of health and disease phenotypes. However, methodologies to analyze proteomes in human tissue or body fluid samples at relevant scale and performance are still limited in clinical research. Their deployment and demonstration in large enough human populations are even sparser. In the present study, we have characterized and compared the plasma proteomes of two large independent cohorts of obese and overweight individuals using shotgun mass spectrometry (MS)-based proteomics. Herein, we showed, in both populations from different continents of about 500 individuals each, the concordance of plasma protein MS measurements in terms of variability, gender-specificity, and age-relationship. Additionally, we replicated several known and new associations between proteins, clinical and molecular variables, such as insulin and glucose concentrations. In conclusion, our MS-based analyses of plasma samples from independent human cohorts proved the practical feasibility and efficiency of a large and unified discovery/replication approach in proteomics, which was also recently coined “rectangular” design.
Robustness of elastic properties in polymer nanocomposite films examined over the full volume fraction range
Authors: Alonso-Redondo E. , Belliard L. , Rolle K. , Graczykowski B. , Tremel W. , Djafari-Rouhani B. , Fytas G.
Published: November 2018

Polymers with nanoparticle inclusions are attractive materials because physical properties can be tuned by varying size and volume fraction range. However, elastic behavior can degrade at higher inclusion fractions when particle-particle contacts become important, and sophisticated measurement techniques are required to study this crossover. Here, we report on the mechanical properties of materials with BaTiO3 nanoparticles (diameters < 10 nm) in a polymer (poly(methyl methacrylate)) matrix, deposited as films in different thickness ranges. Two well-known techniques, time and frequency domain Brillouin light scattering, were employed to probe the composition dependence of their elastic modulus. The time domain experiment revealed the biphasic state of the system at the highest particle volume fraction, whereas frequency domain Brillouin scattering provided comprehensive information on ancillary variables such as refractive index and directionality. Both techniques prove complementary, and can in particular be used to probe the susceptibility of elastic properties in polymer nanocomposites to aging.
Spent embryo culture medium metabolites are related to the in vitro attachment ability of blastocysts
Authors: D’Souza Fiona , Uppangala Shubhashree , Asampille Gitanjali , Salian Sujith Raj , Kalthur Guruprasad , Talevi Riccardo , Atreya Hanudatta S. , Adiga Satish Kumar
Published: November 2018

The metabolomic profile of an embryo culture medium can aid in the advanced prediction of embryonic developmental potential and genetic integrity. But it is not known if this technology can be used to determine the in vitro potential of inner cell mass (ICM) in adherence and proliferation. Here, we investigated the developmental potential of mouse 2-cell embryos carrying cisplatin-induced DNA lesions (IDL), beyond blastocyst stage using ICM outgrowth assay. The genetic integrity of ICM cells was determined by comet assay. The metabolic signatures of spent medium were recorded 84 hours post injection of hCG (hpi-hCG), and after 96 hours of extended in vitro culture (Ex 96) by NMR spectroscopy. We observed that blastocysts that lack the ability to adhere in vitro had an increased requirement of pyruvate (p < 0.01), lactate (p < 0.01), and were accompanied by a significant reduction of pyruvate-alanine ratio in the culture medium. We propose that the aforementioned metabolites from 84 hpi-hCG spent medium be further explored using appropriate experimental models, to prove their potential as biomarkers in the prediction of implantation ability of in vitro derived human embryos in clinical settings.
Temperature Sensing of Deep Abdominal Region in Mice by Using Over-1000 nm Near-Infrared Luminescence of Rare-Earth-Doped NaYF4 Nanothermometer
Authors: Sekiyama Shota , Umezawa Masakazu , Kuraoka Shuhei , Ube Takuji , Kamimura Masao , Soga Kohei
Published: November 2018

Luminescence nanothermometry has attracted much attention as a non-contact thermal sensing technique. However, it is not widely explored for in vivo applications owing to the low transparency of tissues for the light to be used. In this study, we performed biological temperature sensing in deep tissues using β-NaYF4 nanoparticles co-doped with Yb3+, Ho3+, and Er3+ (NaYF4: Yb3+, Ho3+, Er3+ NPs), which displayed two emission peaks at 1150 nm (Ho3+) and 1550 nm (Er3+) in the >1000 nm near-infrared wavelength region, where the scattering and absorption of light by biological tissues are at the minimum. The change in the luminescence intensity ratio of the emission peaks of Ho3+ and Er3+ (IHo/IEr) in the NaYF4: Yb3+, Ho3+, Er3+ nanothermometer differs corresponding to the thickness of the tissue. Therefore, the relationship between IHo/IEr ratio and temperature needs to be calibrated by the depth of the nanothermometer. The temperature-dependent change in the IHo/IEr was evident at the peritoneal cavity level, which is deeper than the subcutaneous tissue level. The designed experimental system for temperature imaging will open the window to novel luminescent nanothermometers for in vivo deep tissue temperature sensing.
The characterization of flavored hookahs aroma profile and in response to heating as analyzed via headspace solid-phase microextraction (SPME) and chemometrics
Authors: Farag Mohamed A. , Elmassry Moamen M. , El-Ahmady Sherweit H.
Published: November 2018

Flavors profiling in flavored hookah tobacco is an issue of increasing scrutiny for the health sector owing to its adverse effects on humans, especially being heated to produce smoke. This study aims at tackling the components involved in the flavored hookah tobacco from a chemical and biological point of view. Detecting individual flavor compounds, within a complex hookah tobacco matrix was accomplished using headspace solid phase microextraction (SPME). A total of 114 volatiles were identified in 13 flavored hookah tobacco products, with esters amounting for the major component up to 40%. Whereas oxygenated monoterpenes presented another major volatile class, contributing up to 23%, including (E)-anethole. Superheating flavored hookah tobacco at 190 °C resulted in the release of a mixture of phenol derivatives and polycyclic aromatic compounds that are indicative of coal tar, a major component produced during hookah tobacco usage with potential health hazards. This study provides the first comprehensive volatile profile of hookah tobacco products from different origins identifying chemical components involved in flavors. It is expected to serve as informative grounds for the better understanding of hookah tobacco production and usage. The information presented is also expected to raise awareness on the health risks of hookah tobacco smoking.
Quantitative Gadolinium-Free Cardiac Fibrosis Imaging in End Stage Renal Disease Patients Reveals A Longitudinal Correlation with Structural and Functional Decline
Authors: Stromp Tori A. , Spear Tyler J. , Holtkamp Rebecca M. , Andres Kristin N. , Kaine Joshua C. , Alghuraibawi Wissam H. , Leung Steve W. , Fornwalt Brandon K. , Vandsburger Moriel H.
Published: November 2018

Patients with end stage renal disease (ESRD) suffer high mortality from arrhythmias linked to fibrosis, but are contraindicated to late gadolinium enhancement magnetic resonance imaging (MRI). We present a quantitative method for gadolinium-free cardiac fibrosis imaging using magnetization transfer (MT) weighted MRI, and probe correlations with widely used surrogate markers including cardiac structure and contractile function in patients with ESRD. In a sub-group of patients who returned for follow-up imaging after one year, we examine the correlation between changes in fibrosis and ventricular structure/function. Quantification of changes in MT revealed significantly greater fibrotic burden in patients with ESRD compared to a healthy age matched control cohort. Ventricular mechanics, including circumferential strain and diastolic strain rate were unchanged in patients with ESRD. No correlation was observed between fibrotic burden and concomitant measures of either circumferential or longitudinal strains or strain rates. However, among patients who returned for follow up examination a strong correlation existed between initial fibrotic burden and subsequent loss of contractile function. Gadolinium-free myocardial fibrosis imaging in patients with ESRD revealed a complex and longitudinal, not contemporary, association between fibrosis and ventricular contractile function.
Similar recovery time of microbial functions from fungicide stress across biogeographical regions
Authors: Schreiner Verena C. , Feckler Alexander , Fernández Diego , Frisch Katharina , Muñoz Katherine , Szöcs Eduard , Zubrod Jochen P. , Bundschuh Mirco , Rasmussen Jes J. , Kefford Ben J. , Axelsen Josepha , Cedergreen Nina , Schäfer Ralf B.
Published: November 2018

Determining whether the structural and functional stress responses of communities are similar across space and time is paramount for forecasting and extrapolating the consequences of anthropogenic pressures on ecosystems and their services. Stream ecosystems are under high anthropogenic pressure; however, studies have only examined the response of stream communities across large scales over multiple generations. We studied the responses of leaf-associated microbial communities in streams within three European biogeographical regions to chemical stress in a microcosm experiment with multiple cycles of fungicide pollution and resource colonisation. Fungal community composition and the ecosystem function leaf decomposition were measured as response variables. Microbial leaf decomposition showed similar recovery times under environmental levels of fungicide exposure across regions. Initially, the decomposition declined (between 19 and 53%) under fungicide stress and recovered to control levels during the third cycle of pollution and colonisation. Although community composition and its stress response varied between regions, this suggests similar functional community adaptation towards fungicide stress over time. Genetic, epigenetic and physiological adaptations, as well as species turnover, may have contributed to community adaptation but further studies are required to determine if and to which extent these mechanisms are operating. Overall, our findings provide the first evidence of a similar functional response of microbial leaf decomposition to chemical stress across space and time.
Employing fingerprinting of medicinal plants by means of LC-MS and machine learning for species identification task
Authors: Kharyuk Pavel , Nazarenko Dmitry , Oseledets Ivan , Rodin Igor , Shpigun Oleg , Tsitsilin Andrey , Lavrentyev Mikhail
Published: November 2018

A dataset of liquid chromatography-mass spectrometry measurements of medicinal plant extracts from 74 species was generated and used for training and validating plant species identification algorithms. Various strategies for data handling and feature space extraction were tested. Constrained Tucker decomposition, large-scale (more than 1500 variables) discrete Bayesian Networks and autoencoder based dimensionality reduction coupled with continuous Bayes classifier and logistic regression were optimized to achieve the best accuracy. Even with elimination of all retention time values accuracies of up to around 85% were achieved on validation set for plant species and plant organ identification. Benefits and drawbacks of used algortihms were discussed. Preliminary test showed that developed approaches exhibit tolerance to changes in data created by using different extraction methods and/or equipment. Dataset with more than 2200 chromatograms was published in an open repository.
Black carbon yields highest nutrient and lowest arsenic release when using rice residuals in paddy soils
Authors: Schaller Jörg , Wang Jiajia , Islam Md. Rafiqul , Planer-Friedrich Britta
Published: November 2018

Rice straw increasingly remains on the fields for nutrient supply to the next generation of crop plants. It can be applied either fresh or after burning to black carbon or ash. A central concern during rice cultivation is accumulation of carcinogenic arsenic and the question arises how much rice straw application contributes to nutrient versus arsenic supply in paddy fields. Laboratory incubation experiments were performed to assess the effect of rice straw, black carbon and ash on element mobilization. Our experiments showed initially higher silicon and phosphorus release from black carbon compared to fresh straw amendments. However, more re-sorption to soil lead to finally slightly lower pore water concentrations for black carbon versus fresh straw amendments. Highest arsenic, iron, manganese and dissolved organic carbon concentrations were observed after fresh rice straw application. Black carbon and ash application lead to only minor increases of arsenic compared to controls without amendments. Overall, for silicon and phosphorus the soil acts as sink while for iron and arsenic it was the main source. In summary, burning of rice straw to black carbon prior to application seems to yield a high increase in desired nutrient and a decrease in undesired arsenic mobilization in paddy soils.
Graphene platelets from shungite rock modulate electropolymerization and charge storage mechanisms of soft-template synthetized polypyrrole-based nanocomposites
Authors: Politi Sara , Carcione Rocco , Tamburri Emanuela , Matassa Roberto , Lavecchia Teresa , Angjellari Mariglen , Terranova Maria Letizia
Published: November 2018

We report here on soft-template electropolymerizations of polypyrrole (Ppy)-based nanocomposites triggered by graphene platelets (GP) from shungite (SH) rocks. A properly designed procedure for an efficient extraction of graphene platelets from SH powders is established to produce remarkable graphene materials in a low oxidation state and with a high electrical conductivity (1490 S cm−1). By using positively and negatively charged templating surfactants the role played by the graphene units on the electropolymerization reactions is pointed out by SEM, EDX, TEM, SAED, XPS and Raman spectroscopy. The morphological/structural characterizations highlight that GP from SH have a surface chemistry suitable for selective and mutual interactions with the growing Ppy chains. CV and galvanostatic charge/discharge measurements evidence that GP improve the transport of both electrons and ions within the bulk material by means of a synergistic action with the polymer phase. This cooperative behavior induces an enhancement of the specific capacitance up to 250 F g−1 at 2 A g−1. The Ppy-GP materials produced following the settled protocols result to be appropriate for fabricating multifunctional charge transport and storage electroactive systems.
A Fréchet tree distance measure to compare phylogeographic spread paths across trees
Authors: Reimering Susanne , Muñoz Sebastian , McHardy Alice C.
Published: November 2018

Phylogeographic methods reconstruct the origin and spread of taxa by inferring locations for internal nodes of the phylogenetic tree from sampling locations of genetic sequences. This is commonly applied to study pathogen outbreaks and spread. To evaluate such reconstructions, the inferred spread paths from root to leaf nodes should be compared to other methods or references. Usually, ancestral state reconstructions are evaluated by node-wise comparisons, therefore requiring the same tree topology, which is usually unknown. Here, we present a method for comparing phylogeographies across different trees inferred from the same taxa. We compare paths of locations by calculating discrete Fréchet distances. By correcting the distances by the number of paths going through a node, we define the Fréchet tree distance as a distance measure between phylogeographies. As an application, we compare phylogeographic spread patterns on trees inferred with different methods from hemagglutinin sequences of H5N1 influenza viruses, finding that both tree inference and ancestral reconstruction cause variation in phylogeographic spread that is not directly reflected by topological differences. The method is suitable for comparing phylogeographies inferred with different tree or phylogeographic inference methods to each other or to a known ground truth, thus enabling a quality assessment of such techniques.
Three-dimensional structure of the orbicularis retaining ligament: an anatomical study using micro-computed tomography
Authors: O Jehoon , Kwon Hyun-Jin , Choi You-Jin , Cho Tae-Hyeon , Yang Hun-Mu
Published: November 2018

The orbicularis retaining ligament (ORL) is an important structure for maintaining the eyelid and cheek skin and contouring the characteristic facial appearance. However, the ORL is a delicate structure that is easily damaged in manual dissection. This study aimed to comprehensively investigate the ORL using a micro-computed tomography (mCT) with phosphotungstic acid (PTA) preparation for the acquisition of its three-dimensional information non-destructively. Twenty-two specimens were obtained from non-embalmed human cadaver (mean age 73.7 years). Multidirectional images of the mCT showed that the ORL consisted of continuous tiny plates with a multilayered plexiform shape. The modified Verhoeff Van Gieson staining and immunofluorescence revealed a ligamentous tissue consisting of multiple fibroelastic bundles. The preorbicularis fibres of the ORL had more layers and a more intricate arrangement than its retro-orbicularis fibres. The number, complexity and ambiguity of the ORL fibres increased in the lateral area and their density and extent increased near the dermis. Its dermal anchorage was shown as a confluence of its fibroelastic tissue into the dermis. The ORL comprises a multilayered meshwork of very thin continuous fibroelastic plates and its related cutaneous deformities might be a complicated outcome of subcutaneous tissue shrinkage, lipid accumulation and ORL retention.