bluuebunny/crossref_metadata_2025 huggingface dataset:
Do nitric oxide, carbon monoxide and hydrogen sulfide really qualify as ‘gasotransmitters’ in bacteria?
Authors: Wareham Lauren K. , Southam Hannah M. , Poole Robert K.
Published: September 2018

A gasotransmitter is defined as a small, generally reactive, gaseous molecule that, in solution, is generated endogenously in an organism and exerts important signalling roles. It is noteworthy that these molecules are also toxic and antimicrobial. We ask: is this definition of a gasotransmitter appropriate in the cases of nitric oxide, carbon monoxide and hydrogen sulfide (H2S) in microbes? Recent advances show that, not only do bacteria synthesise each of these gases, but the molecules also have important signalling or messenger roles in addition to their toxic effects. However, strict application of the criteria proposed for a gasotransmitter leads us to conclude that the term ‘small molecule signalling agent’, as proposed by Fukuto and others, is preferable terminology.
Recent advances in threshold-dependent gene drives for mosquitoes
Authors: Leftwich Philip T. , Edgington Matthew P. , Harvey-Samuel Tim , Carabajal Paladino Leonela Z. , Norman Victoria C. , Alphey Luke
Published: September 2018

Mosquito-borne diseases, such as malaria, dengue and chikungunya, cause morbidity and mortality around the world. Recent advances in gene drives have produced control methods that could theoretically modify all populations of a disease vector, from a single release, making whole species less able to transmit pathogens. This ability has caused both excitement, at the prospect of global eradication of mosquito-borne diseases, and concern around safeguards. Drive mechanisms that require individuals to be released at high frequency before genes will spread can therefore be desirable as they are potentially localised and reversible. These include underdominance-based strategies and use of the reproductive parasite Wolbachia. Here, we review recent advances in practical applications and mathematical analyses of these threshold-dependent gene drives with a focus on implementation in Aedes aegypti, highlighting their mechanisms and the role of fitness costs on introduction frequencies. Drawing on the parallels between these systems offers useful insights into practical, controlled application of localised drives, and allows us to assess the requirements needed for gene drive reversal.
Steady state analysis of a syntrophic model: the effect of a new input substrate concentration
Authors: Daoud Y. , Abdellatif N. , Sari T. , Harmand J.
Published: September 2018

In this work, we are interested in a reduced and simplified model of the anaerobic digestion process. We focus on the acetogenesis and hydrogenetrophic methanogenesis phases. The model describes a syntrophic relashionship between two microbial species (the acetogenic bacteria and the hydrogenetrophic methanogenic bacteria) with two input substrates (the fatty acids and the hydrogen) including both decay terms and inhibition of the acetogenic bacteria growth by an excess of hydrogen in the system. The existence and stability analysis of the steady states of the model points out the existence of a new equilibrium point which can be stable according to the operating parameters of the system. By means of operating diagrams, we show that, whatever the region of space considered, there exists only one locally exponentially stable steady state.
Modelling lymph flow in the lymphatic system: from 0D to 1D spatial resolution
Authors: Tretyakova Rufina M. , Lobov Gennady I. , Bocharov Gennady A.
Published: September 2018

In this study, we formulated a core mathematical model for describing the one-dimensional lymph flow in lymphatic vessels and branching network of lymphatic vessels. The 1D model was numerically implemented using the 1D haemodynamic modeling tools developed in T.M. Gamilov et al. and S. Simakov et al. [T.M. Gamilov et al., Transl. Med. 6 (2013) 5–13 and S. Simakov et al., Russian J. Numer. Anal. Math. Model. 28 (2013) 485–504]. The formulated model was calibrated using published data on lymph flow dynamics and other modelling studies of lymph flows. The comparison of 0D and 1D formulations of the lymph flow models is presented.
Mathematical study of a single leukocyte in microchannel flow
Authors: Boujena S. , Kafi O. , Sequeira A.
Published: September 2018

The recruitment of leukocytes and subsequent rolling, activation, adhesion and transmigration are essential stages of an inflammatory response. Chronic inflammation may entail atherosclerosis, one of the most devastating cardiovascular diseases. Understanding this mechanism is of crucial importance in immunology and in the development of anti-inflammatory drugs. Micropipette aspiration experiments show that leukocytes behave as viscoelastic drops during suction. The flow of non-Newtonian viscoelastic fluids can be described by differential, integral and rate-type constitutive equations. In this study, the rate-type Oldroyd-B model is used to capture the viscoelasticity of the leukocyte which is considered as a drop. Our main goal is to analyze a mathematical model describing the deformation and flow of an individual leukocyte in a microchannel flow. In this model we consider a coupled problem between a simplified Oldroyd-B system and a transport equation which describes the density considered as non constant in the Navier–Stokes equations. First we present the mathematical model and we prove the existence of solution, then we describe its numerical approximation using the level set method. Through the numerical simulations we analyze the hemodynamic effects of three inlet velocity values. We note that the hydrodynamic forces pushing the cell become higher with increasing inlet velocities.
Equilibrium and incentives for supervisor–postgraduate collaborations: A game-theoretic approach
Authors: Gou Qinglong , Wang Xinyu , Zhang Juzhi
Published: September 2018

In most universities, supervisors collaborate with their postgraduate students in writing papers. As a consequence, the relationship between supervisors and postgraduates in the collaborative work becomes the most important one among various relationships between them. In this paper, using a game model, we show that in the current educational system of China, there is a dilemma between supervisors and their postgraduates for their collaborative work – in most cases, either the supervisor or the students will not spend any effort in their joint work. After that, we also investigate whether the two common incentive strategies, i.e., (i) incentives to students, and (ii) incentives to faculties, can solve this dilemma. Our results show that a university can solve the problem by either (i) just using strong incentives to postgraduate students, or (ii) by using a combination of a normal incentive to students and a strong incentive to faculties. Also, we find that when the incentives to the students and to the faculties are below a certain level, all incentives will be just in vain – neither can they improve the serious relationship between supervisors and their postgraduates, nor can they improve the paper quality.
Closed form of the response function in FDH technologies: Theory, computation and application
Authors: Mostafaee Amin , Soleimani-Damaneh Majid
Published: September 2018

Response function (RF), which gives the value of maximum feasible outputs in response to changing the inputs, has a crucial role in performance analysis and scale elasticity measurement. In this paper, a polynomial-time algorithm is provided which is able to obtain the closed form of the RF under (nonconvex) FDH productions technologies. Finite convergence of the presented algorithm is proved; and it is established that the algorithm is polynomial-time from a complexity standpoint. Moreover, an application of the proposed procedure with real-world data accompanying some experiment-based computational discussions are given.
Domination integrity of some graph classes
Authors: Besirik Ayse , Kilic Elgin
Published: September 2018

The stability of a communication network has a great importance in network design. There are several vulnerability measures used to determine the resistance of network to the disruption in this sense. Domination theory provides a model to measure the vulnerability of a graph network. A new vulnerability measure of domination integrity was introduced by Sundareswaran in his Ph.D. thesis (Parameters of vulnerability in graphs (2010)) and defined as DI(G) = min{|S| + m(G − S):S ∈ V(G)} where m(G − S) denotes the order of a largest component of graph G − S and S is a dominating set of G. The domination integrity of an undirected connected graph is such a measure that works on the whole graph and also the remaining components of graph after any break down. Here we determine the domination integrity of wheel graph W1,n, Ladder graph Ln, Sm,n, Friendship graph Fn, Thorn graph of Pn and Cn which are commonly used graph models in network design.
The Role of Mangiferin in the Prevention of Experimentally Induced Iron Overload in an Animal Model
Authors: Estuningtyas Ari , Setiabudy Rianto , Wahidiyat Pustika , Freisleben Hans-Joachim
Published: September 2018

Background The leaves, fruit peels, and bark of mango trees (Mangifera indica L) contain mangiferin as an active compound with known anti-oxidative and iron chelating properties. This study aims to evaluate the benefits of mangiferin in the management of iron overload.

Methods Thirty rats were divided into five groups: normal control, rats with iron overload, and rats with iron overload treated with oral mangiferin doses of 50, 100, or 200 mg/kg BW, respectively. The iron overload in this rat model was induced by means of 15 mg intraperitoneal iron dextran, twice a week for 4 weeks. Plasma mangiferin was measured using high performance liquid chromatography, plasma ferritin by using enzyme linked immunosorbent assay, and iron contents of plasma, urine, and tissues by using atomic absorbance spectrophotometry.

Results Plasma mangiferin concentration at doses of 50, 100, or 200 mg/kg BW were 416.10±112.04, 310.55±134.18, and 450.11±165.99 ng/mL, respectively. At 50 mg/kg BW, mangiferin significantly decreased plasma ferritin levels (from 7051.14±1368.24 to 5543.80±1225.53 ng/mL, (p=0.037). Mangiferin also showed tendency to increase urinary iron excretion and to decrease cardiac and hepatic iron accumulation.

Conclusion In our model, oral administration of mangiferin showed non-linear pharmacokinetics and low bioavailability. At a dose of 50 mg/kg BW, mangiferin decreased plasma ferritin levels significantly. Mangiferin did not prevent the increase of plasma iron, although it exerted tendency to increase urinary iron excretion and to decrease iron accumulation in liver and heart.
Ask PCOS: Identifying Need to Inform Evidence-Based App Development for Polycystic Ovary Syndrome
Authors: Xu Rebecca , Gilbert Emily , Kuczynska-Burggraf Millicent , Tan Bryan , Teede Helena , Vincent Amanda , Gibson-Helm Melanie , Boyle Jacqueline
Published: September 2018

Background People are increasingly seeking health information and managing their health through electronic technologies. We aimed to determine if women with polycystic ovary syndrome (PCOS) identified a need for PCOS-related mobile health apps and to evaluate related apps currently available.

Design A national survey of women and a review of apps available on the iOS and Android platforms.

Setting Community recruitment in Australia in 2016 and review of mobile apps available in 2017.

Sample The survey received 264 responses. Sixteen apps related to PCOS were evaluated.

Main Outcome Measures Survey: Women's likeliness to use mobile health apps, specifically a PCOS-related app and preferred features of apps. App review: Mapping of available apps and evaluation using the Mobile Application Rating Scale (MARS).

Results Of 264 respondents, almost all women had a smartphone (98%), 72% had previously used an app to manage their health, and most (91%) would use a PCOS-specific app if available. The most important feature was the availability of current, evidence-based information. Current apps on PCOS lack provision of quality information.

Conclusion Women with PCOS would use a PCOS-specific app of good quality that responds to their needs and facilitates self-care; however, currently available apps are unlikely to meet their information needs.
Survey of Ventilation Practices in the Neonatal Intensive Care Units of the United States and Canada: Use of Volume-Targeted Ventilation and Barriers to Its Use
Authors: Gupta Ashish , Keszler Martin
Published: September 2018

Objective To provide current data on ventilation practices and use of volume-targeted ventilation (VTV) in neonatal intensive care units of the United States and Canada, to identify the perceived barriers to the implementation of VTV, and to assess the knowledge base of appropriate initial tidal volume (VT
) settings for different hypothetical clinical scenarios.

Study Design This was a cross-sectional online survey of individual neonatologists practicing in the United States and Canada.

Results We received 387 responses (estimated response rate: ∼20%). Use of VTV was much higher in Canada (81%) compared with 39% in the United States. In the United States, VTV use is highest in the Northwest at 77% and lowest in the Northeast at 32.5%. The chief barrier to use of VTV was lack of knowledge about VTV and lack of appropriate equipment. The five clinical scenarios revealed that the majority of responders failed to select appropriate evidence-based VT
for the specific scenario.

Conclusion Pressure-controlled ventilation remains the predominant approach to neonatal ventilation in the United States, while VTV is the preferred mode in Canada. Despite available data and important pathophysiological differences between patients, there is insufficient understanding of how to choose an appropriate VT
in a variety of common clinical scenarios among users of VTV.
Macrospin analysis of RF excitations within fully perpendicular magnetic tunnel junctions with second order easy-axis magnetic anisotropy contribution
Authors: Atitoaie Alexandru , Firastrau Ioana , Buda-Prejbeanu Liliana D. , Ebels Ursula , Volmer Marius
Published: September 2018

The conditions of field and voltage for inducing steady state excitations in fully perpendicular magnetic tunnel junctions (pMTJs), adapted for memory applications, were numerically investigated by the resolution of the Landau-Lifshitz-Gilbert equation in the macrospin approach. Both damping-like and the field-like spin transfer torque terms were taken into account in the simulations, as well as the contribution of the second order uniaxial anisotropy term (K2), which has been recently revealed in MgO-based pMTJs. An in-plane applied magnetic field balances the out of plane symmetry of the pMTJ and allows the signal detection. Using this model, we assessed the states of the free layer magnetization as a function of strength of K2 and polar θH angle of the applied field (varied from 90° to 60°). There are two stable states, with the magnetization in-plane or out of plane of the layer, and two dynamic states with self-sustained oscillations, called in-plane precession state (IPP) or out of plane precession state (OPP). The IPP mode, with oscillation frequencies up to 7 GHz, appears only for positive voltages if θH = 90°. However, it shows a more complex distribution when the field is slightly tilted out of plane. The OPP mode is excited only if K2 is considered and reaches a maximum oscillation frequency of 15 GHz. Large areas of dynamic states with high frequencies are obtained for strong values of the field-like torque and K2, when applying a slightly tilted external field toward the out of plane direction. The non-zero temperature does not modify the phase diagrams but reduces drastically the power spectral density peak amplitudes.
Axisymmetric rim instability of water droplet impact on a super-hydrophobic surface
Authors: Huang Xiao , Wan Kai-Tak , Taslim Mohammad E.
Published: September 2018

Fingering of an inviscid liquid droplet upon impact on a super-hydrophobic surface is revisited. Generation of coronal fingers is investigated here using a transverse rim instability analysis based on the toroidal curvature of rim, instead of the linear front assumption in the classical Rayleigh-Plateau (R-P) model. The governing equations are formulated from the first principles and solved numerically. For a droplet with a known volume and impact velocity, the model predicts the number of spires upon impact, k. Here k is found to be the largest wave number with a positive growth rate on the droplet rim and is shown to be in the order of (Weber)3/5. The theoretical model is consistent with our water droplet experiments for 60 < We < 160, superseding the R-P prediction.
The origin of the conductivity maximum vs. mixing ratio in pyridine/acetic acid and water/acetic acid
Authors: Aravindakshan Nikhil P. , Gemmell Kyle E. , Johnson Keith E. , East Allan L. L.
Published: September 2018

Explanations are provided for the first time for the historically known locations of electrical conductivity maxima versus mixing ratio (mole fraction of acid, xA) in mixtures of (i) acetic acid with water and (ii) acetic acid with pyridine. To resolve the question for the second system, density-functional-based molecular dynamic simulations were performed, at 1:1, 1:2, 1:3, 1:5, and 1:15 mixing ratios, to gain vital information about speciation. In a zeroth-order picture, the degree of ionization (and hence conductivity) would be maximal at xA = 0.5, but these two examples see this maximum shifted to the left (water/acetic acid, xAmax = 0.06), due to improved ion stability when the effective dielectric constant is high (i.e., water-rich mixtures), or right (pyridine/acetic acid xAmax = 0.83), due to improved acetate stability via “self-solvation” with acetic acid molecules (i.e., acid-rich mixtures) when the dielectric constant is low. A two-parameter equation, with theoretical justification, is shown to reproduce the entire 0 < xA < 1 range of data for electrical conductivity for both systems. Future work will pursue the applicability of these equations to other amine/carboxylic acid mixtures; preliminary fits to a third system (trimethylamine/acetic acid) give curious parameter values.
A study of irradiation effects in TiO2 using molecular dynamics simulation and complementary in situ transmission electron microscopy
Authors: Cowen Benjamin J. , El-Genk Mohamed S. , Hattar Khalid , Briggs Samuel A.
Published: September 2018

Understanding radiation damage in crystalline systems at the atomic scale is essential for the development of multi-scale predictive models for advancing nuclear science and engineering applications. State-of-the-art techniques used for investigating irradiation effects include molecular dynamics (MD) simulations, which can provide attosecond resolution of damage cascades over picosecond time scales, and in situ transmission electron microscopy (TEM), which can provide millisecond resolution in real-time. In this work, MD simulations and in situ TEM ion beam irradiation of crystalline TiO2 with 46 keV Ti1− ions are performed and results are compared. The MD results show that the ratio of the titanium to oxygen defects evolves during the radiation cascade. The vacancies are produced mostly in the core, while self-interstitials are concentrated at the periphery of the cascade. Cluster analysis of the MD results confirms the formation of a void (or a cluster of vacancies) that contains as much as ≈10 000 vacancies in the ballistic phase, compared to <1000 after annealing. The radial distribution functions and the simulated selected area electron diffraction patterns at the peak of the ballistic phase confirm the existence of a short-range order and medium-range order throughout the simulation. However, the long-range order reemerges after annealing of the cascade event in agreement with the in situ TEM ion beam irradiation experiments. The MD simulations and the experiments show no indication of amorphization.
Dense Kondo behavior in the low-temperature resistivity and specific heat for amorphous Ce50Al50 alloy
Authors: Ito Seiya , Seki Kazuho , Amakai Yusuke , Murayama Shigeyuki , Takano Hideaki , Momono Naoki , Kuwai Tomohiko
Published: September 2018

We measured the low-temperature specific heat Cp, resistivity ρ, and magnetoresistance Δρ(H)/ρ(0) for amorphous Ce50Al50 synthesized by a DC high-rate sputter method. The low-temperature Cp (T < 2 K) decreases rapidly toward 0 K and has no indication of phase transition. The value of γ0 which is extrapolated down to 0 K of the Cp/T is 117 mJ/molK2. The temperature dependence of ρ increases with decreasing temperature down to 0.6 K. We found that both a weak localization effect and a coherent Kondo state might be realized in the low-temperature region for the present alloy from the conductivity analysis. Furthermore, in the low-temperature ρ, a T2 term with a very large coefficient A was observed. The ratio of A/γ02 is 0.63 ×10-5 (μΩcm/K2)/(mJ/molK2)2 and is near the value of typical Ce-based heavy-fermion compounds. The magnetoresistances Δρ(H)/ρ(0) at 0.5 K and 2 K are almost constant in the magnetic field region of H < 10 kOe. We considered that the negative magnetoresistance effect is due to the weak localization and the positive magnetoresistance to the heavy-fermion state in the present alloy.
Multiplexed characterization of complex gas-phase mixtures combining chirped-pulse Fourier transform microwave spectroscopy and VUV photoionization time-of-flight mass spectrometry
Authors: Fritz Sean M. , Hays Brian M. , Hernandez-Castillo Alicia O. , Abeysekera Chamara , Zwier Timothy S.
Published: September 2018

We report details of the design and operation of a single apparatus that combines Chirped-Pulse Fourier Transform Microwave (CP-FTMW) spectroscopy with vacuum ultraviolet (VUV) photoionization Time-of-Flight Mass Spectrometry (TOFMS). The supersonic expansion used for cooling samples is interrogated first by passing through the region between two microwave horns capable of broadband excitation and detection in the 2-18 GHz frequency region of the microwave. After passing through this region, the expansion is skimmed to form a molecular beam, before being probed with 118 nm (10.5 eV) single-photon VUV photoionization in a linear time-of-flight mass spectrometer. The two detection schemes are powerfully complementary to one another. CP-FTMW detects all components with significant permanent dipole moments. Rotational transitions provide high-resolution structural data. VUV TOFMS provides a gentle and general method for ionizing all components of a gas phase mixture with ionization thresholds below 10.5 eV, providing their molecular formulae. The advantages, complementarity, and limitations of the combined methods are illustrated through results on two gas-phase mixtures made up of (i) three furanic compounds, two of which are structural isomers of one another, and (ii) the effluent from a flash pyrolysis source with o-guaiacol as the precursor.
Exploring the preferences of a culturally congruent, peer-based HIV prevention intervention for black men who have sex with men
Authors: Dangerfield II Derek T. , Harawa Nina T. , McWells Charles , Hilliard Charles , Bluthenthal Ricky N.
Published: September 2018

Background
HIV testing, treatment initiation and treatment adherence have been emphasised for Black men who have sex with men (BMSM). However, many BMSM do not get tested, obtain HIV treatment or adhere to treatment. It is essential to highlight barriers to HIV testing, treatment adherence and the ideal components for an intervention: peer mentors, socioeconomic resources and participant incentives. Methods: Five focus groups (n = 24) were conducted among HIV-negative and HIV-positive BMSM aged ≥18 years in Los Angeles, California, USA to explore motivations and barriers to testing and treatment and the components of an ideal, culturally competent HIV testing intervention for BMSM. Results: Barriers to HIV testing included fear and stigma associated with discovering a HIV-positive status and drug use. Motivations for testing included experiencing symptoms, beginning new relationships, perceptions of risk and peer mentors. Conclusions: Future HIV prevention and treatment efforts should consider these components to improve health outcomes among BMSM.
Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways
Authors: Xu Fangda , Bandara Asanga , Akiyama Hisashi , Eshaghi Behnaz , Stelter David , Keyes Tom , Straub John E. , Gummuluru Suryaram , Reinhard Björn M.
Published: September 2018

Significance

Membrane-wrapped noble metal nanoparticles provide a synthetic platform to investigate lipid-mediated, glycoprotein-independent virus–cell interactions. Different from membrane-wrapped virus-like particles (VLPs), these artificial virus nanoparticles (AVNs) are not derived from cellular systems and can contain organic or inorganic cores optimized for imaging or delivery purposes. A particular advantage is the rational control over the AVN membrane composition, which can be complex or undefined in VLP. This work shows that monosialodihexosylganglioside-presenting AVNs accumulate in virus-containing compartments (VCCs) that represent assembly sites for HIV-1. VCCs provide evasion for HIV-1 from the immune system as well as antiviral therapeutics. The ability to target VCCs with AVNs provides opportunities for eradicating a putative reservoir of HIV-1 persistence.
Metal–insulator-transition engineering by modulation tilt-control in perovskite nickelates for room temperature optical switching
Authors: Liao Zhaoliang , Gauquelin Nicolas , Green Robert J. , Müller-Caspary Knut , Lobato Ivan , Li Lin , Van Aert Sandra , Verbeeck Johan , Huijben Mark , Grisolia Mathieu N. , Rouco Victor , El Hage Ralph , Villegas Javier E. , Mercy Alain , Bibes Manuel , Ghosez Philippe , Sawatzky George A. , Rijnders Guus , Koster Gertjan
Published: September 2018

Significance

Correlated transition metal oxide perovskites receive a lot of attention due to their unique physical properties, which are largely driven by distortion of the BO
6
octahedral network. In bulk, the control of the octahedral network is normally obtained by cation substitutions in a random alloy. Similar to the charge donors in semiconductors, cation substitutions will introduce scattering and disorder. The development of artificial heterostructures offers unprecedented opportunities to lattice engineering to achieve desired properties. In this work, we demonstrated a structural analogue of modulation doping in nickelate heterostructures through the interfacial transfer of tilt patterns. Modulation tilt control was used to remotely control the Ni–O bonds in the compound SmNiO
3
and thereby its critical temperature for optimal optical switching application.
Dante: genotyping of known complex and expanded short tandem repeats
Authors: Budiš Jaroslav , Kucharík Marcel , Ďuriš František , Gazdarica Juraj , Zrubcová Michaela , Ficek Andrej , Szemes Tomáš , Brejová Broňa , Radvanszky Jan
Published: September 2018

Motivation

Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2–6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays.

Results

We propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated datasets and on datasets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these datasets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases.

Availability and implementation

Dante is open source software, freely available for download at https://github.com/jbudis/dante.

Supplementary information

Supplementary data are available at Bioinformatics online.
CATANA: a tool for generating comprehensive annotations of alternative transcript events
Authors: Shiau Cheng-Kai , Huang Jia-Hsin , Tsai Huai-Kuang
Published: September 2018

In higher eukaryotes, the generation of transcript isoforms from a single gene through alternative splicing (AS) and alternative transcription (AT) mechanisms increases functional and regulatory diversities. Annotating these alternative transcript events is essential for genomic studies. However, there are no existing tools that generate comprehensive annotations of all these alternative transcript events including both AS and AT events. In the present study, we develop CATANA, with the encoded exon usage patterns based on the flattened gene model, to identify ten types of AS and AT events. We demonstrate the power and versatility of CATANA by showing greater depth of annotations of alternative transcript events according to either genome annotation or RNA-seq data.

Availability and implementation

CATANA is available on https://github.com/shiauck/CATANA.

Supplementary information

Supplementary data are available at Bioinformatics online.
The metagenome of the female upper reproductive tract
Authors: Li Fei , Chen Chen , Wei Weixia , Wang Zirong , Dai Juanjuan , Hao Lilan , Song Liju , Zhang Xiaowei , Zeng Liping , Du Hui , Tang Huiru , Liu Na , Yang Huanming , Wang Jian , Madsen Lise , Brix Susanne , Kristiansen Karsten , Xu Xun , Li Junhua , Wu Ruifang , Jia Huijue
Published: September 2018

Background

The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.

Results

We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale.

Conclusions

We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.
Metabolomics investigation of dietary effects on flesh quality in grass carp (Ctenopharyngodon idellus)
Authors: Zhao Honghao , Chong Jasmine , Tang Rong , Li Li , Xia Jianguo , Li Dapeng
Published: September 2018

Background

The ultrahigh density intensive farming model of grass carp (Ctenopharyngodon idellus) may elicit growth inhibition, decrease flesh quality, and increase disease susceptibility of fish. The degradation in quality and excessive fat accumulation in cultured C. idellus have long been attributed to possible alterations in the lipid metabolism of fish muscle tissues as a result of overnutrition from artificial diets. To investigate the effects of different diets on fish muscle quality, a large-scale metabolomics study was performed on 250 tails of C. idellus.

Findings

The experimental fish were divided into four groups based on sex and diet—female artificial feed (FAF), female grass feed, male artificial feed (MAF), and male grass feed (MGF). After a 113-day rearing period, the artificial feed (AF) group showed a significantly higher total mass of muscle fat (P < 0.01), with the FAF group being the highest. Metabolomics profiling based on liquid chromatography-mass spectrometry revealed distinctive patterns of clustering according to the four groups. Overall, artificial feeding was associated with higher concentrations of docosapentaenoic acid, dihomo-gamma-linolenic acid, and arachidonic acid, whereas grass feeding was associated with elevated n-3 unsaturated fatty acids (UFAs) such as eicosapentaenoic acid, alpha-linolenic acid, and gamma-linolenic acid. Artificial feeding also resulted in significant increased docosahexaenoic acid in MAF muscle than in MGF fish, whereas there was no significance in the comparison of female samples. Metabolic pathway analyses using both targeted and untargeted approaches consistently revealed that arachidonic acid metabolism and steroid hormone biosynthesis pathways were significantly different between AF and grass fed groups.

Conclusions

Our results suggest that grass is a better source of dietary fatty acid and protein when compared to artificial feed. Grass feeding could effectively lower triglycerides in serum, reduce fat accumulation, and alter lipid compositions in fish muscle by increasing the concentrations of n-3 UFAs, leading to better nutrition and health.
Temporal partitioning and the effects of climate change on two ecologically similar desert bats
Authors: Lambert Connor T , Hall Lucas K , Larsen Randy T , Knight Robert N , McMillan Brock R
Published: September 2018

Climate change is predicted to create increasingly arid deserts with fewer and smaller water sources. Because free water is already limiting for arid-adapted animals, reductions in water likely will impact desert species and how they compete for this limited resource. Our objective was to examine how the size of water sources influenced competition between 2 ecologically similar bats, Parastrellus hesperus and Myotis californicus, in the American Southwest. Bats are a highly successful taxon in deserts, although many rely upon access to free water. We examined bat activity observationally over 35 different-sized water sources throughout the Mojave Desert in southwestern Utah, United States, and experimentally reduced the surface area of 2 water sources. Parastrellus hesperus and M. californicus typically occurred at the same water sources, but both species temporally partitioned their use of shared water sources regardless of the surface area of the water. Experimentally reducing surface area of water sources negatively affected drinking behaviors of both species and resulted in higher overall activity, but temporal partitioning still occurred. While loss of water may influence some competitive interactions, mechanisms such as temporal partitioning can potentially allow continued co-use of limited resources by competing species.
Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque
Authors: Caparosa Ellen M , Sedgewick Andrew J , Zenonos Georgios , Zhao Yin , Carlisle Diane L , Stefaneanu Lucia , Jankowitz Brian T , Gardner Paul , Chang Yue-Fang , Lariviere William R , LaFramboise William A , Benos Panayiotis V , Friedlander Robert M
Published: September 2018

BACKGROUND

Many studies have explored molecular markers of carotid plaque development and vulnerability to rupture, usually having examined whole carotid plaques. However, there are regional differences in plaque morphology and known shear-related mechanisms in areas surrounding the lipid core.

OBJECTIVE

To determine whether there are regional differences in protein expression along the long axis of the carotid plaque and how that might produce gaps in our understanding of the carotid plaque molecular signature.

METHODS

Levels of 7 inflammatory cytokines (IL-1β, IL-6, IL-8, IL-10, IL-12 p70, IFN-γ, and TNF-α) and caspase-3 were analyzed in prebifurcation, bifurcation, and postbifurcation segments of internal carotid plaques surgically removed from symptomatic and asymptomatic patients. Expression profiles of miRNAs and mRNAs were determined with microarrays for the rupture-prone postbifurcation segment for comparison with published whole plaque results.

RESULTS

Expression levels of all proteins examined, except IL-10, were lowest in the prebifurcation segment and significantly higher in the postbifurcation segment. Patient group differences in protein expression were observed for the prebifurcation segment; however, no significant differences were observed in the postbifurcation segment between symptomatic and asymptomatic patients. Expression profiles from postbifurcation carotid plaques identified 4 novel high priority miRNAs differentially expressed between patient groups (miR-214, miR-484, miR-942, and miR-1287) and 3 high-confidence miRNA:mRNA targets, including miR-214:APOD, miR-484:DACH1, and miR-942:GPR56.

CONCLUSION

The results demonstrate regional differences in protein expression for the first time and show that focus on the rupture-prone postbifurcation region leads to prioritization for further study of novel miRNA gene regulation mechanisms.
A STUDY OF A DOSE CONSTRAINT FOR OCCUPATIONALLY EXPOSED WORKERS IN THE US NUCLEAR POWER PLANTS
Authors: Kong Tae Young , Akabani Gamal , Poston John W
Published: September 2018

One of the most important issues in the nuclear power industry is the implementation of the 2007 Recommendations of the International Commission on Radiological Protection (ICRP) published in ICRP Publication 103. These recommendations include the implementation of the concept of dose constraints for occupationally exposed workers at nuclear power plants (NPPs). When considering these changes from a cost–benefit standpoint, the implementation of dose constraints is still highly controversial. This study analysed annual occupational dose distributions to determine whether a dose constraint is needed for occupationally exposed workers at the US NPPs. Results of the analysis showed that the use of dose constraints had no positive impact on radiation safety of workers at NPPs in the USA. In fact, it appears that the implementation of dose constraints will impose an unnecessary regulatory burden on licensees. Based on these results, implementation of dose constraints is not recommended.
Turning fibroblasts into cardiomyocytes: technological review of cardiac transdifferentiation strategies
Authors: Klose Kristin , Gossen Manfred , Stamm Christof
Published: September 2018

To date, no viable therapeutic options exist for the effective and sustained reversal of cardiac failure, other than heart transplantation and mechanical circulatory assist devices. Therefore, divergent strategies aiming at the de novo formation of contractile tissue, as a prerequisite for the restoration of cardiac pump function, are currently being pursued. Clinical trials involving the transplantation of somatic progenitor cells failed. The search for alternative cell‐based strategies to combat the consequences of ischemic injury has sparked widespread interest in the genetic and pharmacologic reprogramming of fibroblasts into cardiomyocytes, harnessing the abundant in vivo pool of cardiac fibroblasts. Here, we provide a comprehensive overview of in vitro and in vivo cardiac reprogramming studies identified in an extensive literature search. We systematically review and evaluate feasibility, efficiency, and reproducibility of the different technologies currently being explored. Finally, we discuss potential safety issues deduced from preclinical studies and identify obstacles that must be overcome before clinical translation.—Klose, K., Gossen, M., Stamm, C. Turning fibroblasts into cardiomyocytes: technological review of cardiac transdifferentiation strategies. FASEB J. 33, 49–70 (2019). www.fasebj.org
New Drugs 2018, part 3
Authors: Hussar Daniel A.
Published: September 2018

This article discusses eight drugs recently approved by the FDA, including their indications and contraindications, precautions, dosage, and nursing considerations. The article also includes summary charts on 14 recently approved antineoplastic drugs and four drugs approved for rare disorders.
Hearing and Auditory Processing Abilities in Primary School Children with Learning Difficulties
Authors: Choi Seong Min Robyn , Kei Joseph , Wilson Wayne J.
Published: September 2018

Objectives:

This study aimed to investigate hearing and auditory processing ability in primary school children with learning difficulties (LD).

Design:

A nonrandomized, cross-sectional single measure research design was used. A total of 486 children, aged 7.7 to 10.8 years and attending years 3 and 4 in six primary schools, were classified as having an LD (n = 67) or being typically developing (TD, n = 419). This classification was based on a Learning Score generated from their school report results and National Assessment Program – Literacy and Numeracy scores. All children attempted a conventional hearing assessment (CHA) involving pure-tone audiometry, tympanometry, acoustic reflexes (AR), and otoacoustic emissions (OAEs). Children returning pure-tone audiometry results within normal limits also attempted an auditory processing assessment (APA) including dichotic digits (DD) and low-pass filtered speech (LPFS) tests.

Results:

In children with LD, 21/67 (31.4%) failed the CHA, 20/58 (34.5%) failed the APA, and 32/58 (55.2%) failed the overall hearing assessment (OHA) if they failed either or both CHA and APA. In comparison, in TD children, 55/413 (13.3%) failed the CHA, 52/314 (16.6%) failed the APA, and 86/313 (27.5%) failed the OHA. Proportionally, children with LD were 2.4 times more likely than TD children to fail the CHA, 2.1 times more likely to fail the APA, and 2.0 times more likely to fail the OHA. In children who had completed the OHA, multiple linear regressions showed average AR thresholds, DD scores, and LPFS scores explained 13 to 18% of the variance in the Learning Score.

Conclusion:

The potential for hearing impairment should be investigated in children with LD. These investigations should begin with CHA, and for children returning normal-hearing thresholds, should continue with measures of AR, DD, and LPFS, to ensure these children receive the appropriate auditory support needed to enhance their learning.
Evolving Use of Biomarkers in the Management of Heart Failure
Authors: Paul Sara , Harshaw-Ellis Karol
Published: September 2018

Objective, noninvasive, clinical assessment of patients with heart failure can be made using biomarker measurements, including natriuretic peptides, cardiac troponins, soluble suppression of tumorigenicity 2, and galectin-3. The aim of this review is to provide clinicians with guidance on the use of heart failure biomarkers in clinical practice. The authors provide a didactic narrative based on current literature, an exemplary case study, and their clinical experience.
Liposomal Bupivacaine Transversus Abdominis Plane Block Versus Epidural Analgesia in a Colon and Rectal Surgery Enhanced Recovery Pathway: A Randomized Clinical Trial
Authors: Felling Daniel R. , Jackson Miles W. , Ferraro Jane , Battaglia Michael A. , Albright Jeremy J. , Wu Juan , Genord Cheryl K. , Brockhaus Kara K. , Bhave Rohit A. , McClure Amanda M. , Shanker Beth-Ann , Cleary Robert K.
Published: September 2018

BACKGROUND:

Multimodal pain management is an integral part of enhanced recovery pathways. The most effective pain management strategies have not been determined.

OBJECTIVE:

The purpose of this study was to compare liposomal bupivacaine transversus abdominis plane block with epidural analgesia in patients undergoing colorectal surgery.

DESIGN:

This is a single-institution, open-label randomized (1:1) trial.

SETTING:

This study compared liposomal bupivacaine transversus abdominis plane block with epidural analgesia in patients undergoing elective open and minimally invasive colorectal surgery in an enhanced recovery pathway.

PATIENTS:

Two hundred were enrolled. Following randomization, allocation, and follow-up, there were 92 patients with transversus abdominis plane block and 87 patients with epidural analgesia available for analysis.

INTERVENTIONS:

The interventions comprised liposomal bupivacaine transversus abdominis plane block versus epidural analgesia.

MAIN OUTCOME MEASURES:

The primary outcomes measured were numeric pain scores and the overall benefit of analgesia scores.

RESULTS:

There were no significant differences in the Numeric Pain Scale and Overall Benefit of Analgesia Score between groups. Time trend analysis revealed that patients with transversus abdominis plane block had higher numeric pain scores on the day of surgery, but that the relationship was reversed later in the postoperative period. Opioid use was significantly less in the transversus abdominis plane block group (206.84 mg vs 98.29 mg, p < 0.001). There were no significant differences in time to GI recovery, hospital length of stay, and postoperative complications. Cost was considerably more for the epidural analgesia group.

LIMITATIONS:

This study was conducted at a single institution.

CONCLUSIONS:

This randomized trial shows that perioperative pain management with liposomal bupivacaine transversus abdominis plane block is as effective as epidural analgesia and is associated with less opioid use and less cost. These data and the more favorable risk profile suggest that liposomal bupivacaine transversus abdominis plane block is a viable multimodal perioperative pain management option for this patient population in an established enhanced recovery pathway. Clinical Trial Registration: http://www.clinicaltrials.gov (NCT02591407). See Video Abstract at http://links.lww.com/DCR/A737.