bluuebunny/crossref_metadata_2025 huggingface dataset:
Cysteine allows ovarian cancer cells to adapt to hypoxia and to escape from carboplatin cytotoxicity
Authors: Nunes Sofia C. , Ramos Cristiano , Lopes-Coelho Filipa , Sequeira Catarina O. , Silva Fernanda , Gouveia-Fernandes Sofia , Rodrigues Armanda , Guimarães António , Silveira Margarida , Abreu Sofia , Santo Vítor E. , Brito Catarina , Félix Ana , Pereira Sofia A. , Serpa Jacinta
Published: June 2018

Ovarian cancer is the second most common gynaecologic malignancy and the main cause of death from gynaecologic cancer, due to late diagnosis and chemoresistance. Studies have reported the role of cysteine in cancer, by contributing for hydrogen sulphide (H2S) generation and as a precursor of glutathione (GSH). However, the role of cysteine in the adaptation to hypoxia and therapy response remains unclear. We used several ovarian cancer cell lines, ES2, OVCAR3, OVCAR8, A2780 and A2780cisR, to clarify cysteine relevance in ovarian cancer cells survival upon hypoxia and carboplatin. Results show that ES2 and OVCAR8 cells presented a stronger dependence on cysteine availability upon hypoxia and carboplatin exposure than OVCAR3 cells. Interestingly, the A2780 cisR, but not A2780 parental cells, benefits from cysteine upon carboplatin exposure, showing that cysteine is crucial for chemoresistance. Moreover, GSH degradation and subsequent cysteine recycling pathway is associated with ovarian cancer as seen in peripheral blood serum from patients. Higher levels of total free cysteine (Cys) and homocysteine (HCys) were found in ovarian cancer patients in comparison with benign tumours and lower levels of GSH were found in ovarian neoplasms patients in comparison with healthy individuals. Importantly, the total and S-Homocysteinylated levels distinguished blood donors from patients with neoplasms as well as patients with benign from patients with malignant tumours. The levels of S-cysteinylated proteins distinguish blood donors from patients with neoplasms and the free levels of Cys in serum distinguish blood from patients with benign tumours from patients with malignant tumours. Herein we disclosed that cysteine contributes for a worse disease prognosis, allowing faster adaptation to hypoxia and protecting cells from carboplatin. The measurement of serum cysteine levels can be an effective tool for early diagnosis, for outcome prediction and follow up of disease progression.
Spatiotemporal disturbance characteristics determine functional stability and collapse risk of simulated microbial ecosystems
Authors: König Sara , Worrich Anja , Banitz Thomas , Centler Florian , Harms Hauke , Kästner Matthias , Miltner Anja , Wick Lukas Y. , Thullner Martin , Frank Karin
Published: June 2018

Terrestrial microbial ecosystems are exposed to many types of disturbances varying in their spatial and temporal characteristics. The ability to cope with these disturbances is crucial for maintaining microbial ecosystem functions, especially if disturbances recur regularly. Thus, understanding microbial ecosystem dynamics under recurrent disturbances and identifying drivers of functional stability and thresholds for functional collapse is important. Using a spatially explicit ecological model of bacterial growth, dispersal, and substrate consumption, we simulated spatially heterogeneous recurrent disturbances and investigated the dynamic response of pollutant biodegradation – exemplarily for an important ecosystem function. We found that thresholds for functional collapse are controlled by the combination of disturbance frequency and spatial configuration (spatiotemporal disturbance regime). For rare disturbances, the occurrence of functional collapse is promoted by low spatial disturbance fragmentation. For frequent disturbances, functional collapse is almost inevitable. Moreover, the relevance of bacterial growth and dispersal for functional stability also depends on the spatiotemporal disturbance regime. Under disturbance regimes with moderate severity, microbial properties can strongly affect functional stability and shift the threshold for functional collapse. Similarly, networks facilitating bacterial dispersal can delay functional collapse. Consequently, measures to enhance or sustain bacterial growth/dispersal are promising strategies to prevent functional collapses under moderate disturbance regimes.
A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
Authors: Jain Dharm Skandh , Gupte Sanket Rajan , Aduri Raviprasad
Published: June 2018

RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA. Here, we present a data-driven model for RPI prediction using a gradient boosting classifier. Amino acids and nucleotides are classified based on the high-resolution structural data of RNA protein complexes. The minimum structural unit consisting of five residues is used as the descriptor. Comparative analysis of existing methods shows the consistently higher performance of our method irrespective of the length of RNA present in the RPI. The method has been successfully applied to map RPI networks involving both long noncoding RNA as well as TERRA RNA. The method is also shown to successfully predict RNA and protein hubs present in RPI networks of four different organisms. The robustness of this method will provide a way for predicting RPI networks of yet unknown interactions for both long noncoding RNA and microRNA.
Nintedanib inhibits growth of human prostate carcinoma cells by modulating both cell cycle and angiogenesis regulators
Authors: da Silva Raquel Frenedoso , Dhar Deepanshi , Raina Komal , Kumar Dileep , Kant Rama , Cagnon Valeria Helena Alves , Agarwal Chapla , Agarwal Rajesh
Published: June 2018

Prostate cancer (PCa) is the most common malignancy and second leading cause of cancer-related deaths in American men. Proliferating cells have higher need for nutrients and oxygen, triggering angiogenesis that plays a critical role in tumor growth, progression and metastasis. Consequently, immense focus has converged onto inhibitors of angiogenesis in cancer treatment, such as Nintedanib, which has shown exceptional antitumor activity via inhibiting cell proliferation and the resulting tumor growth, primarily due to its combined action on tumor cells, endothelial cells and pericytes. Accordingly, here we assessed both in vitro and in vivo efficacy of Nintedanib in PCa. The results showed that Nintedanib decreased cell viability in both androgen dependent- and -independent PCa cells, together with a decrease in cell motility and invasiveness. Nintedanib also reduced the expression of significant genes responsible for cell cycle progression. PCa PC3 xenograft-carrying nude mice treated with Nintedanib showed significantly decreased tumor volume and cell proliferation alongside diminished levels of pro-angiogenic molecules and blood vessel densities. In conclusion, we report that Nintedanib has strong efficacy against PCa in pre-clinical models via modulation of various pathways, and that it could be employed as a promising new strategy to manage PCa clinically.
Determination of the size distribution of non-spherical nanoparticles by electric birefringence-based methods
Authors: Arenas-Guerrero Paloma , Delgado Ángel V. , Donovan Kevin J. , Scott Kenneth , Bellini Tommaso , Mantegazza Francesco , Jiménez María L.
Published: June 2018

The in situ determination of the size distribution of dispersed non-spherical nanoparticles is an essential characterization tool for the investigation and use of colloidal suspensions. In this work, we test a size characterization method based on the measurement of the transient behaviour of the birefringence induced in the dispersions by pulsed electric fields. The specific shape of such relaxations depends on the distribution of the rotational diffusion coefficient of the suspended particles. We analyse the measured transient birefringence with three approaches: the stretched-exponential, Watson-Jennings, and multi-exponential methods. These are applied to six different types of rod-like and planar particles: PTFE rods, goethite needles, single- and double-walled carbon nanotubes, sodium montmorillonite particles and gibbsite platelets. The results are compared to electron microscopy and dynamic light scattering measurements. The methods here considered provide good or excellent results in all cases, proving that the analysis of the transient birefringence is a powerful tool to obtain complete size distributions of non-spherical particles in suspension.
Rapid recombinant protein expression in cell-free extracts from human blood
Authors: Burgenson David , Gurramkonda Chandrasekhar , Pilli Manohar , Ge Xudong , Andar Abhay , Kostov Yordan , Tolosa Leah , Rao Govind
Published: June 2018

Several groups have recently reported on the utility of cell-free expression systems to make therapeutic proteins, most of them employing CHO or E. coli cell-free extracts. Here, we propose an alternative that uses human blood derived leukocyte cell extracts for the expression of recombinant proteins. We demonstrate expression of nano luciferase (Nluc), Granulocyte-colony stimulating factor (G-CSF) and Erythropoietin (EPO) in cell-free leukocyte extracts within two hours. Human blood is readily available from donors and blood banks and leukocyte rich fractions are easy to obtain. The method described here demonstrates the ability to rapidly express recombinant proteins from human cell extracts that could provide the research community with a facile technology to make their target protein. Eventually, we envision that any recombinant protein can be produced from patient-supplied leukocytes, which can then be injected back into the patient. This approach could lead to an alternative model for personalized medicines and vaccines.
Precisely dating the Frasnian–Famennian boundary: implications for the cause of the Late Devonian mass extinction
Authors: Percival L. M. E. , Davies J. H. F. L. , Schaltegger U. , De Vleeschouwer D. , Da Silva A.-C. , Föllmi K. B.
Published: June 2018

The Frasnian–Famennian boundary records one of the most catastrophic mass extinctions of the Phanerozoic Eon. Several possible causes for this extinction have been suggested, including extra-terrestrial impacts and large-scale volcanism. However, linking the extinction with these potential causes is hindered by the lack of precise dating of either the extinction or volcanic/impact events. In this study, a bentonite layer in uppermost-Frasnian sediments from Steinbruch Schmidt (Germany) is re-analysed using CA-ID-TIMS U-Pb zircon geochronology in order to constrain the date of the Frasnian–Famennian extinction. A new age of 372.36 ± 0.053 Ma is determined for this bentonite, confirming a date no older than 372.4 Ma for the Frasnian–Famennian boundary, which can be further constrained to 371.93–371.78 Ma using a pre-existing Late Devonian age model. This age is consistent with previous dates, but is significantly more precise. When compared with published ages of the Siljan impact crater and basalts produced by large-scale volcanism, there is no apparent correlation between the extinction and either phenomenon, not clearly supporting them as a direct cause for the Frasnian–Famennian event. This result highlights an urgent need for further Late Devonian geochronological and chemostratigraphic work to better understand the cause(s) of this extinction.
GRAMD1B regulates cell migration in breast cancer cells through JAK/STAT and Akt signaling
Authors: Khanna Puja , Lee Joan Shuying , Sereemaspun Amornpun , Lee Haeryun , Baeg Gyeong Hun
Published: June 2018

Dysregulated JAK/STAT signaling has been implicated in breast cancer metastasis, which is associated with high relapse risks. However, mechanisms underlying JAK/STAT signaling-mediated breast tumorigenesis are poorly understood. Here, we showed that GRAMD1B expression is upregulated on IL-6 but downregulated upon treatment with the JAK2 inhibitor AG490 in the breast cancer MDA-MB-231 cells. Notably, Gramd1b knockdown caused morphological changes of the cells, characterized by the formation of membrane ruffling and protrusions, implicating its role in cell migration. Consistently, GRAMD1B inhibition significantly enhanced cell migration, with an increase in the levels of the Rho family of GTPases. We also found that Gramd1b knockdown-mediated pro-migratory phenotype is associated with JAK2/STAT3 and Akt activation, and that JAK2 or Akt inhibition efficiently suppresses the phenotype. Interestingly, AG490 dose-dependently increased p-Akt levels, and our epistasis analysis suggested that the effect of JAK/STAT inhibition on p-Akt is via the regulation of GRAMD1B expression. Taken together, our results suggest that GRAMD1B is a key signaling molecule that functions to inhibit cell migration in breast cancer by negating both JAK/STAT and Akt signaling, providing the foundation for its development as a novel biomarker in breast cancer.
Effect of Donor-Acceptor Vertical Composition Profile on Performance of Organic Bulk Heterojunction Solar Cells
Authors: Bi Sheng , Ouyang Zhongliang , Shaik Shoieb , Li Dawen
Published: June 2018

In organic bulk heterojunction solar cells (OSCs) donor-acceptor vertical composition profile is one of the crucial factors that affect power-conversion efficiency (PCE). In this simulation study, five different kinds of donor-acceptor vertical configurations, including sandwich type I and type II, charge transport favorable, charge transport unfavorable, and uniform vertical distribution, have been investigated for both regular and inverted OSC structures. OSCs with uniform and charge transport favorable vertical composition profiles demonstrate the highest efficiencies. High PCE from charge transport favorable configuration can be attributed to low recombination because of facilitated charge transport in active layer and collection at electrodes, while high PCE from uniform structure is due to sufficient interfaces for efficient exciton dissociation. OSCs with sandwich and charge transport unfavorable structures show much lower efficiencies. The physical mechanisms behind simulation results are explained based on energy band diagrams, dark current-voltage characteristics, and comparison of external quantum efficiency. In conclusion, experimental optimization of vertical composition profile should be directed to either uniform or charge transport favorable vertical configurations in order to achieve high-performance OSCs.
Highly-coherent stimulated phonon oscillations in a multi-core optical fiber
Authors: Diamandi H. Hagai , London Yosef , Bashan Gil , Bergman Arik , Zadok Avi
Published: June 2018

Opto-mechanical oscillators that generate coherent acoustic waves are drawing much interest, in both fundamental research and applications. Narrowband oscillations can be obtained through the introduction of feedback to the acoustic wave. Most previous realizations of this concept, sometimes referred to as “phonon lasers”, relied on radiation pressure and moving boundary effects in micro- or nano-structured media. Demonstrations in bulk crystals required cryogenic temperatures. In this work, stimulated emission of highly-coherent acoustic waves is achieved in a commercially-available multi-core fiber, at room temperature. The fiber is connected within an opto-electronic cavity loop. Pump light in one core is driving acoustic waves via electrostriction, whereas an optical probe wave at a different physical core undergoes photo-elastic modulation by the stimulated acoustic waves. Coupling between pump and probe is based entirely on inter-core, opto-mechanical cross-phase modulation: no direct optical feedback is provided. Single-frequency mechanical oscillations at hundreds of MHz frequencies are obtained, with side-mode suppression that is better than 55 dB. A sharp threshold and rapid collapse of the linewidth above threshold are observed. The linewidths of the acoustic oscillations are on the order of 100 Hz, orders of magnitude narrower than those of the pump and probe light sources. The relative Allan’s deviation of the frequency is between 0.1–1 ppm. The frequency may be switched among several values by propagating the pump or probe waves in different cores. The results may be used in sensing, metrology and microwave-photonic information processing applications.
Organic Solvent Nanofiltration for an Intensified Processing of Renewable Raw Materials
Authors: Werth K. , Skiborowski M.
Published: June 2018

Membrane separation processes promise significantly reduced energy requirements compared to classical thermal separation processes. The ability of organic solvent nanofiltration, a pressure-driven membrane process, to operate at mild temperatures makes it especially interesting for oleochemical processes. The membrane cut-off matches the molecular weight of most triglycerides and fatty acids, thus energy-efficient recovery of extraction solvents or selective recovery of fatty acids from waste oils is possible. This chapter presents the potential of organic solvent nanofiltration for important application fields in the oleochemical industry. Furthermore, the processing of non-edible oils and waste oils, which are promising feedstocks for more economic and ecological production processes, is discussed.
Process Intensification of Immobilized Enzyme Reactors
Authors: Shivaprasad Parimala , Carolina Emanuelsson Emma Anna
Published: June 2018

The advantages of enzyme catalysis are high specificity and (enantio)selectivity, resulting in reactions with little or no by-products. The applications of enzymes in aqueous medium are well established and have been extended to organic synthesis more recently. The two limiting factors for large scale application of enzymes are continuous processing and process scale-up. Process intensification has the potential to overcome these challenges posed by conventional processing methods by incorporating a novel reactor design or by using alternate processing methods. Process intensified reactors like membrane reactors, microreactors, monolithic reactors and rotating disc reactors for enzyme catalyzed reactions will be discussed in this chapter. These reactors have shown an improved performance compared to the enzymatic reactors currently in use, and future opportunities include application for enzymatic catalysis on an industrial scale and advances in reactor design and process control.
Intensification of Functional Foods Production
Authors: Vaghari H. , Jafarizadeh-Malmiri H. , Harcourt N. , Sarabadani Z. , Anarjan N. , Berenjian A.
Published: June 2018

There is a need to produce more food with high health benefits and less environmental impact, known as sustainable intensification. Functional foods have beneficial effects on one or more functions of the human organism and are essential for the body to decrease the risk of developing disease. Among functional foods, some of them – such as essential oils and carotenoids – are hydrophobic components, and these have lower water solubility and, consequently, low bioavailability. Nanodispersions are very interesting due to their capability to extensively increase the solubility of lipophilic bioactive compounds, that is, neither soluble in water nor oil, and subsequently increase their bioavailability and stability. Extraction of lipophilic functional foods and production of their nanodispersions use large amounts of organic solvents and, hence, require a large amount of energy to remove the solvents from the final products. This chapter presents an overview on process intensification technologies used in functional foods for increasing the eco-efficiency of the process with the benefits of lower capital costs, substantial energy saving and decreased utilization of solvents. This work also focuses on experimental modelling related to process intensification of the preparation of functional nanosized lycopene from tomato processing wastes.
Highly efficient visible-light-induced photoactivity of the CdS–Mn/MoS2/CdTe/TiO2quaternary photocatalyst for label-free immunoassay of tris-(2,3-dibromopropyl) isocyanurate and enhanced solar hydrogen generation
Authors: Feng Hui , Zhang Songbai , Zhang Xiangyang , Liu Bo , Tang Niu
Published: June 2018

A novel visible-light-induced quaternary photocatalyst for TBC detection and solar hydrogen generation was successfully prepared.
Aβ under stress: the effects of acidosis, Cu2+-binding, and oxidation on amyloid β-peptide dimers
Authors: Liao Qinghua , Owen Michael C. , Bali Sofia , Barz Bogdan , Strodel Birgit
Published: June 2018

In light of the high affinity of Cu2+for Alzheimer's Aβ1–42and its ability to subsequently catalyze the formation of radicals, we examine the effects of Cu2+binding, Aβ oxidation, and an acidic environment on the conformational dynamics of the smallest Aβ1–42oligomer, the Aβ1–42dimer.
Cu(ii)–tBu–PHOX catalyzed enantioselective malonate addition onto 3-hydroxy 2-oxindoles: application in the synthesis of dimeric pyrroloindoline alkaloids
Authors: Babu K. Naresh , Kinthada Lakshmana K. , Pratim Das Partha , Bisai Alakesh
Published: June 2018

Cu(ii)–PHOX-catalyzed malonate addition onto 3-hydroxy 3-indolyl-2-oxindoles afforded products in >99% ee. A Cu(ii)-species has been identified as an active species based on detailed X-ray, NMR, CV and EPR experiments.
Growth of nanodroplets on a still microfiber under flow conditions
Authors: Yu Haitao , Rump Maaike , Maheshwari Shantanu , Bao Lei , Zhang Xuehua
Published: June 2018

Coupled effects from droplet formation and the local flow dramatically enhanced the droplet growth on a microfiber in flow.
Quantification and origin of cooperativity: insights from density functional reactivity theory
Authors: Rong Chunying , Zhao Dongbo , Yu Donghai , Liu Shubin
Published: June 2018

This work presents an approach to quantify cooperativity and appreciate its origin, whose effectiveness has been showcased by six examples.
Tailoring inorganic nanoadjuvants towards next-generation vaccines
Authors: Li Xia , Wang Xiupeng , Ito Atsuo
Published: June 2018

We comprehensively review the use of inorganic nanomaterials as vaccine adjuvants and provide an outlook on tailoring inorganic nanoadjuvants towards next-generation vaccines.
The role of nanoparticle shape in translocation across the pulmonary surfactant layer revealed by molecular dynamics simulations
Authors: Luo Zhen , Li Shixin , Xu Yan , Yan Zengshuai , Huang Fang , Yue Tongtao
Published: June 2018

We report using molecular dynamics simulations that the shape plays a dominant role in inhaled nanoparticle translocation through the pulmonary surfactant layer.
Selective synthesis of mono- and di-methylated amines using methanol and sodium azide as C1 and N1 sources
Authors: Chakrabarti Kaushik , Mishra Anju , Panja Dibyajyoti , Paul Bhaskar , Kundu Sabuj
Published: June 2018

The selective synthesis of various N,N-dimethylated and N-monomethylated amines from organic azides using methanol as a methylating agent is reported.
Engineering β-ketoenol structure functionality in hybrid silica as excellent adsorbent material for removal of heavy metals from water
Authors: Tighadouini Said , Radi Smaail , Anannaz Mohamed , Bacquet Maryse , Degoutin Stéphanie , Tillard Monique , Eddike Driss , Amhamdi Hassan , Garcia Yann
Published: June 2018

A chelating adsorbent based on the chemical modification of silica by an efficient host able to capture toxic metals, is presented.
Enhanced photocatalytic performance and stability of visible-light-driven Z-scheme CdS/Ag/g-C3N4 nanosheets photocatalyst
Authors: Qin Yingying , Li Hong , Dong Hongjun , Ma Changchang , Li Xiuying , Liu Xinlin , Liu Yang , Li Chunxiang , Yan Yongsheng
Published: June 2018

A novel Z-scheme CdS/Ag/g-C3N4 nanosheets photocatalyst was synthesized by combining the hydrothermal and photo-deposition techniques, where Ag nanoparticles as carrier transport channels significantly improve the separation efficiency of electron–hole pairs.
Resistance of water transport in carbon nanotube membranes
Authors: Zhang Xin , Zhou Wei , Xu Fang , Wei Mingjie , Wang Yong
Published: June 2018

Identifying the sources of interfacial resistance and depressing it by using an hourglass-shaped pore mouth.
Light-mediated one-pot synthesis of an ABC triblock copolymer in aqueous solution via RAFT and the effect of pH on copolymer self-assembly
Authors: Guragain Sudhina , Perez-Mercader Juan
Published: June 2018

We present the triblock copolymer self-assembly resulting into different morphologies that occurred during the polymerization of a hydrophobic third block in aqueous solution.
Noble-gas-infused neoprene closed-cell foams achieving ultra-low thermal conductivity fabrics
Authors: Moran Jeffrey L. , Cottrill Anton L. , Benck Jesse D. , Liu Pingwei , Yuan Zhe , Strano Michael S. , Buongiorno Jacopo
Published: June 2018

Herein, we develop, demonstrate, and model a repeatable process for synthesizing ultra-low-thermal-conductivity closed-cell neoprene garments by infusing high-molecular-weight noble gases.
Concentrated electrolytes stabilize bismuth–potassium batteries
Authors: Zhang Ruding , Bao Jingze , Wang YuHuang , Sun Chuan-Fu
Published: June 2018

A 5 molar concentrated electrolyte effectively stabilizes bismuth–potassium batteries due to its elevated resistance to electrochemical reduction.
Gradient flow approach to an exponential thin film equation: global existence and latent singularity
Authors: Gao Yuan , Liu Jian-Guo , Lu Xin Yang
Published: June 2018

In this work, we study a fourth order exponential equation,ut= Δe−Δuderived from thin film growth on crystal surface in multiple space dimensions. We use the gradient flow method in metric space to characterize the latent singularity in global strong solution, which is intrinsic due to high degeneration. We define a suitable functional, which reveals where the singularity happens, and then prove the variational inequality solution under very weak assumptions for initial data. Moreover, the existence of global strong solution is established with regular initial data.
Subependymomas – Characteristics of a “Leave me Alone” Lesion
Authors: Kammerer Sara , Mueller-Eschner Monika , Lauer Arne , Luger Anna-Luisa , Quick-Weller Johanna , Franz Kea , Harter Patrick , Berkefeld Joachim , Wagner Marlies
Published: June 2018

Purpose Intracranial subependymomas are rare, mostly asymptomatic tumours, which are often found incidentally and therefore did not receive much attention in previous literature. By being classified as benign grade I in the WHO classification of tumours of the central nervous system, they are given a special status compared to the other ependymal tumours. Tumor recurrences are a rarity, spinal “drop metastases” do not occur. While etiological, pathological and therapeutic characteristics have been subject of several publications over the last few decades and have meanwhile been well studied, the imaging characteristics are much less well received.

Material and method Retrospective analysis of our relatively large group of 33 patients with subependymoma, including 4 patients with a mixture of subependymomas with ependymal cell fractions in terms of imaging and clinical aspects and with reference to a current literature review.

Results Subependymomas have typical image morphologic characteristics that differentiate them from tumors of other entities, however, the rare subgroup of histopathological mixtures of subependymomas with ependymal cell fractions has no distinctly different imaging properties.

Conclusions Knowing the imaging characteristics of subpendymoma and their differential diagnoses is of particular importance in order to be able to decide between the necessity of follow-up controls, an early invasive diagnosis or, depending on the entity, tumor resection.

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Citation Format
Antimicrobial and Efflux Inhibitor Activity of Usnic Acid Against Mycobacterium abscessus
Authors: Ramis Ivy , Vianna Júlia , Reis Ana , von Groll Andrea , Ramos Daniela , Viveiros Miguel , da Silva Pedro
Published: June 2018

New drugs are needed to treat infections with antimicrobial-resistant Mycobacterium abscessus; therefore, we evaluated usnic acid as an antimicrobial agent and efflux inhibitor (EI) against M. abscessus. Usnic acid showed antimicrobial activity, and synergistically, the EI verapamil increased this activity. In addition, when we evaluated the interaction of antimicrobials with usnic acid, the increase of their activity was observed. Finally, usnic acid showed an efflux inhibitory effect between the classical EIs verapamil and carbonyl cyanide m-chlorophenylhydrazine. In conclusion, usnic acid showed both antimicrobial and EI activity, indicating that this natural compound may be a promising scaffold for new drugs against this difficult-to-treat microorganism.
Recommendations for the Use of Testosterone in Male Transgender
Authors: Costa Laura Bregieiro Fernandes , Rosa-e-Silva Ana Carolina Japur de Sá , Medeiros Sebastião Freitas de , Nacul Andrea Prestes , Carvalho Bruno Ramalho de , Benetti-Pinto Cristina Laguna , Yela Daniela Angerame , Maciel Gustavo Arantes Rosa , Soares Júnior José Maria , Maranhão Técia Maria de Oliveira
Published: June 2018

Gender incongruence is defined as a condition in which an individual self-identifies and desires to have physical characteristics and social roles that connote the opposite biological sex. Gender dysphoria is when an individual displays the anxiety and/or depression disorders that result from the incongruity between the gender identity and the biological sex. The gender affirmation process must be performed by a multidisciplinary team. The main goal of the hormone treatment is to start the development of male physical characteristics by means of testosterone administration that may be offered to transgender men who are 18 years old or over. The use of testosterone is usually well tolerated and improves the quality of life. However, there is still lack of evidence regarding the effects and risks of the long-term use of this hormone. Many different pharmacological formulations have been used in the transsexualization process. The most commonly used formulation is the intramuscular testosterone esters in a short-term release injection, followed by testosterone cypionate or testosterone enanthate. In the majority of testosterone therapy protocols, the male physical characteristics can be seen in almost all users after 6 months of therapy, and the maximum virilization effects are usually achieved after 3 to 5 years of regular use of the hormone. To minimize risks, plasmatic testosterone levels should be kept within male physiological ranges (300 to 1,000 ng/dl) during hormonal treatment. It is recommended that transgender men under androgen therapy be monitored every 3 months during the 1st year of treatment and then, every 6 to 12 months.
Nanoparticles confined to a spherical surface in the presence of an external field: Interaction forces and induced microstructure
Authors: Quintana C. , González-Mozuelos P.
Published: June 2018

The structural response of a set of charged nanoparticles confined to move on a spherical surface under the influence of an external field is studied by Brownian Dynamics (BD) simulations and by an integral equation approach (IEA). Considering an identical nanoparticle as the source of the external field, we analyze the force exerted by the N confined particles on the external one, as well as the corresponding potential energy, focusing on their dependence on the distance of the external particle to the center of the sphere r0. The connection of the force and potential to the equilibrium local distribution of the adsorbed particles, that is, the microstructure within the spherical monolayer induced by the external nanoparticle, which is also dependent on r0, is elucidated by this analysis. It is found that the external particle needs to surmount a considerable potential barrier when moving toward the spherical surface, although much smaller than the one generated by a uniform surface distribution with an equivalent amount of charge. This is understood in terms of the correlation hole within the confined monolayer induced by the external particle. Another interesting conclusion is that the IEA provides an accurate, almost quantitative, description of the main features observed in the BD results, yet it is much less computationally demanding. The connection of these results with the overall chemical equilibrium of charged surfactant nanoparticles in the context of Pickering emulsions is also briefly discussed.
Kinematical lie algebras in 2 + 1 dimensions
Authors: Andrzejewski Tomasz , Figueroa-O’Farrill José Miguel
Published: June 2018

We classify kinematical Lie algebras in dimension 2 + 1. This is approached via the classification of deformations of the static kinematical Lie algebra. In addition, we determine which kinematical Lie algebras admit invariant symmetric inner products.
Spectral concentration of thermal conductivity in GaN—A first-principles study
Authors: Garg Jivtesh , Luo Tengfei , Chen Gang
Published: June 2018

We find using first-principles analysis of thermal conductivity (k) in isotopically pure Gallium nitride (GaN) that almost 60% of the heat is conducted by phonons in a very narrow frequency range of 5–7 THz (spanning only 9% of the frequencies in GaN). This spectral focusing of thermal conductivity is found to be due to a combination of two effects—a large increase in lifetimes of phonons through suppression of anharmonic scattering in the 5–7 THz frequency range coupled with a large phonon density of states at the same frequencies. Understanding of the effect is provided by solving the phonon Boltzmann transport equation in the single mode relaxation time approximation along with the use of harmonic and anharmonic force constants derived from density functional theory. The results can have important implications for engineering the thermal performance of devices based on GaN.
Tunneling splittings from path-integral molecular dynamics using a Langevin thermostat
Authors: Vaillant C. L. , Wales D. J. , Althorpe S. C.
Published: June 2018

We report an improved method for the calculation of tunneling splittings between degenerate configurations in molecules and clusters using path-integral molecular dynamics (PIMD). Starting from an expression involving a ratio of thermodynamic density matrices at the bottom of the symmetric wells, we use thermodynamic integration with molecular dynamics simulations and a Langevin thermostat to compute the splittings stochastically. The thermodynamic integration is performed by sampling along the semiclassical instanton path, which provides an efficient reaction coordinate as well as being physically well-motivated. This approach allows us to carry out PIMD calculations of the multi-well tunneling splitting pattern in the water dimer and to refine previous PIMD calculations for one-dimensional models and malonaldehyde. The large (acceptor) splitting in the water dimer agrees to within 20% of benchmark variational results, and the smaller splittings agree to within 10%.
Aspects of nucleation on curved and flat surfaces
Authors: Horsley Eric M. , Lavrentovich Maxim O. , Kamien Randall D.
Published: June 2018

We investigate the energetics of droplets sourced by the thermal fluctuations in a system undergoing a first-order transition. In particular, we confine our studies to two dimensions with explicit calculations in the plane and on the sphere. Using an isoperimetric inequality from the differential geometry literature and a theorem on the inequality’s saturation, we show how geometry informs the critical droplet size and shape. This inequality establishes a “mean field” result for nucleated droplets. We then study the effects of fluctuations on the interfaces of droplets in two dimensions, treating the droplet interface as a fluctuating line. We emphasize that care is needed in deriving the line curvature energy from the Landau-Ginzburg energy functional and in interpreting the scalings of the nucleation rate with the size of the droplet. We end with a comparison of nucleation in the plane and on a sphere.
Extended integral wall-model for large-eddy simulations of compressible wall-bounded turbulent flows
Authors: Catchirayer M. , Boussuge J.-F. , Sagaut P. , Montagnac M. , Papadogiannis D. , Garnaud X.
Published: June 2018

Wall-modeling is required to make large-eddy simulations of high-Reynolds number wall-bounded turbulent flows feasible in terms of computational cost. Here, an extension of the integral wall-model for large-eddy simulations (iWMLESs) for incompressible flows developed by Yang et al. [“Integral wall model for large eddy simulations of wall-bounded turbulent flows,” Phys. Fluids 27(2), 025112 (2015)] to compressible and isothermal flows is proposed and assessed. The iWMLES approach is analogous to the von Kármán-Pohlhausen integral method for laminar flows: the velocity profile is parameterized, and unknown coefficients are determined by matching boundary conditions obeying the integral boundary layer momentum equation. It allows non-equilibrium effects such as pressure gradient and convection to be included at a computing cost similar to analytical wall-models. To take into account density variations and temperature gradients, the temperature profile is also parameterized and the integral compressible boundary layer energy equation is considered. Parameterized profiles are based on the usual logarithmic wall functions with corrective terms to extend their range of validity. Instead of solving a set of differential equations as wall-models based on the thin boundary layer equation approach, a simple linear system is solved. The proposed wall-model is implemented in a finite-volume cell-centered structured grid solver and assessed on adiabatic and isothermal plane channel flows at several friction Reynolds and Mach numbers. For low Mach number cases, mean profiles, wall fluxes, and turbulent fluctuations are in agreement with those of Direct Numerical Simulation (DNS). For supersonic flows, the results are in good agreement with the DNS data, especially the mean velocity quantities and the wall friction, while standard analytical wall-models show their limits.
Ultrathin acoustic metasurfaces for reflective wave focusing
Authors: Qi Shuibao , Assouar Badreddine
Published: June 2018

An advanced concept of reflective acoustic focusing based on an ultrathin metasurface is numerically and analytically investigated. We propose a designed reflective metasurface with a thickness of λ/15, with λ being wavelength, composed of locally resonant Helmholtz-like elements which discretely realize the 2π phase shift. The theoretical design based on the generalized Snell's law is numerically achieved by the proposed ultrathin metasurface. Numerical simulations and theoretical analysis have converged to a good consensus and validated the ultrathin reflective metasurface concept for acoustic focusing. Furthermore, another reflective metasurface with sub-wavelength thickness (λ/8) and based on the coiling-up-space concept constructed by three-dimensional (3D) labyrinthine elements is investigated and compared to the ultrathin one. Despite both metasurfaces illustrating equivalent good performances for acoustic focusing, the ultrathin one demonstrates its superiority with thinner thickness, simpler design, and easier fabrication, which would greatly facilitate its real implementation in relevant applications.
Single antiferromagnetic skyrmion transistor based on strain manipulation
Authors: Zhao Xiaofeng , Ren Ruizhi , Xie Gang , Liu Yan
Published: June 2018

Magnetic skyrmions are envisioned as ideal candidates as information carriers for future spintronic devices, which have attracted a great deal of attention in recent years. In this paper, we design a spintronic device based on antiferromagnetic skyrmions, which is a single antiferromagnetic skyrmion transistor. The transistor consists of a source, a skyrmion island, a barrier region, and a drain. The barrier region is controlled by strains. We demonstrate the feasibility of the transistor by micromagnetic simulations. We find that the number of skyrmions that can pass the barrier region can be controlled by adjusting the strength of strain in the barrier region and the current density. In an appropriate current-strain region, skyrmions can flow from the skyrmion island to the drain one by one. This mechanism offers a promising route for designing tunable skyrmionic-mechanic devices.
Atomic-scale strain manipulation of a charge density wave
Authors: Gao Shang , Flicker Felix , Sankar Raman , Zhao He , Ren Zheng , Rachmilowitz Bryan , Balachandar Sidhika , Chou Fangcheng , Burch Kenneth S. , Wang Ziqiang , van Wezel Jasper , Zeljkovic Ilija
Published: June 2018

Significance

Charge density waves (CDWs) are simple periodic reorganizations of charge in a crystal, and yet they are still poorly understood and continue to bear surprises. External perturbations, such as strain or pressure, can in principle push a CDW phase into a different ordering geometry. However, engineering this type of quantum criticality has been experimentally challenging. Here, we implement a simple method for straining bulk materials. By applying it to
2H
-NbSe
2
, a prototypical CDW system studied for decades, we discover two dramatic strain-induced CDW phase transitions. Our atomic-scale spectroscopic imaging measurements, combined with theory, reveal the distinct roles of electrons and phonons in forming these emergent states, thus opening a window into the rich phenomenology of CDWs.
Methane in groundwater before, during, and after hydraulic fracturing of the Marcellus Shale
Authors: Barth-Naftilan E. , Sohng J. , Saiers J. E.
Published: June 2018

Significance

This study incorporates time series sampling of groundwater before, during, and after drilling, hydraulic fracturing, and initiation of shale gas production. Using monitoring wells installed next to gas well pads and above gas well laterals, previously undocumented responses to drilling and a gas well casing breach were observed, although groundwater impacts arising from the process of hydraulic fracturing were not detected. We discover considerable temporal variability in methane concentrations in deeper horizons of freshwater aquifers and attribute this to persistent shifts in aquifer recharge that influence mixing between shallow freshwater and comparatively saline and methane-rich deep groundwater. These results have implications for attribution of groundwater contamination to specific stages of shale gas development or natural processes and improving regulatory monitoring.
A versatile nanobody-based toolkit to analyze retrograde transport from the cell surface
Authors: Buser Dominik P. , Schleicher Kai D. , Prescianotto-Baschong Cristina , Spiess Martin
Published: June 2018

Significance

Retrograde transport from the cell surface to intracellular compartments is essential for homeostasis and cell physiology. We developed derivatized nanobodies to follow proteins from the cell surface to endosomes and the
trans
-Golgi network. Nanobodies are an emerging class of protein binders with many advantages over conventional antibodies: they are small and noncross-linking, and can be produced in bacteria. Using a nanobody against GFP, our tool is widely applicable to any GFP-tagged protein of interest. It allows the quantitative analysis of endocytic and retrograde transport biochemically, by fixed- and live-cell imaging and by electron microscopy. As proof-of-principle, we applied them to determine the contribution of adaptor protein-1/clathrin in retrograde transport of the mannose-6-phosphate receptors to the
trans
-Golgi.
Commensal pathogen competition impacts host viability
Authors: Fast David , Kostiuk Benjamin , Foley Edan , Pukatzki Stefan
Published: June 2018

Significance

Enteric pathogens including the causative agent of cholera,
Vibrio cholerae
, use the type-six secretion system (T6SS) to kill commensal microbes in the host intestine. Eradicating competing microbes allows pathogens to improve colonization. However, it is not known whether commensal destruction has additional consequences on host viability. We used the
Drosophila
model of cholera to determine the impacts of T6SS on fly health and longevity. We found that T6SS-dependent competition with the symbiotic
Acetobacter pasteurianus
intensified disease symptoms, and accelerated host death. Gnotobiotic flies without
A. pasteurianus
abolished T6SS-dependent death, and reintroduction of
A. pasteurianus
alone was sufficient to restore accelerated death. These observations implicate T6SS-dependent interactions with commensal bacteria as a factor for the progression of cholera.
Accelerating pathway evolution by increasing the gene dosage of chromosomal segments
Authors: Tumen-Velasquez Melissa , Johnson Christopher W. , Ahmed Alaa , Dominick Graham , Fulk Emily M. , Khanna Payal , Lee Sarah A. , Schmidt Alicia L. , Linger Jeffrey G. , Eiteman Mark A. , Beckham Gregg T. , Neidle Ellen L.
Published: June 2018

Significance

Gene duplication and divergence are cornerstones of evolution. Genetic redundancy resulting from repeated DNA provides flexibility for transient changes in copy number that may confer selective benefit under new or changing environmental conditions. This work describes a method for creating tandem arrays of specific DNA segments in a bacterium,Acinetobacter baylyi, to accelerate experimental evolution. The induced chromosomal gene amplification mimics a natural process that would otherwise occur more slowly and stochastically. The success of this approach for the evolution of novel protein function was demonstrated with studies of an enzyme that has bioenergy applications in lignin valorization. A protein variant, which emerged from Evolution by Amplification and Synthetic biology, is beneficial in a different bacterium, indicating the broad utility of the method.
mRNA-binding protein tristetraprolin is essential for cardiac response to iron deficiency by regulating mitochondrial function
Authors: Sato Tatsuya , Chang Hsiang-Chun , Bayeva Marina , Shapiro Jason S. , Ramos-Alonso Lucia , Kouzu Hidemichi , Jiang Xinghang , Liu Ting , Yar Sumeyye , Sawicki Konrad T. , Chen Chunlei , Martínez-Pastor María Teresa , Stumpo Deborah J. , Schumacker Paul T. , Blackshear Perry J. , Ben-Sahra Issam , Puig Sergi , Ardehali Hossein
Published: June 2018

Significance

Iron deficiency is the most common nutrient deficiency, yet cardiomyopathy rarely develops in these patients. We solved this paradox and identified a protective mechanism involving the mRNA-binding protein tristetraprolin (TTP), which adjusts mitochondrial function in response to iron deficiency. Mice lacking TTP in their hearts were phenotypically normal at baseline but developed spontaneous cardiomyopathy under iron deficiency and exhibited increased reactive oxygen species (ROS)-mediated damage in their hearts. We further demonstrate that down-regulation of specific iron-containing mitochondrial complexes by TTP is the mechanism preventing the formation of dysfunctional mitochondria, subsequent ROS production, and cellular damage. In summary, we show that activation of TTP is part of a required pathway protecting critical organ function when iron becomes scarce.