bluuebunny/crossref_metadata_2025 huggingface dataset:
Downregulation of vimentin in macrophages infected with live Mycobacterium tuberculosis is mediated by Reactive Oxygen Species
Authors: Mahesh P. P. , Retnakumar R. J. , Mundayoor Sathish
Published: February 2016

Mycobacterium tuberculosis persists primarily in macrophages after infection and manipulates the host defence pathways in its favour. 2D gel electrophoresis results showed that vimentin, an intermediate filament protein, is downregulated in macrophages infected with live Mycobacterium tuberculosis H37Rv when compared to macrophages infected with heat- killed H37Rv. The downregulation was confirmed by Western blot and quantitative RT-PCR. Besides, the expression of vimentin in avirulent strain, Mycobacterium tuberculosis H37Ra- infected macrophages was similar to the expression in heat-killed H37Rv- infected macrophages. Increased expression of vimentin in H2O2- treated live H37Rv-infected macrophages and decreased expression of vimentin both in NAC and DPI- treated heat-killed H37Rv-infected macrophages showed that vimentin expression is positively regulated by ROS. Ectopic expression of ESAT-6 in macrophages decreased both the level of ROS and the expression of vimentin which implies that Mycobacterium tuberculosis-mediated downregulation of vimentin is at least in part due to the downregulation of ROS by the pathogen. Interestingly, the incubation of macrophages with anti-vimentin antibody increased the ROS production and decreased the survival of H37Rv. In addition, we also showed that the pattern of phosphorylation of vimentin in macrophages by PKA/PKC is different from monocytes, emphasizing a role for vimentin phosphorylation in macrophage differentiation.
Barrier crossing in small avian migrants: individual tracking reveals prolonged nocturnal flights into the day as a common migratory strategy
Authors: Adamík Peter , Emmenegger Tamara , Briedis Martins , Gustafsson Lars , Henshaw Ian , Krist Miloš , Laaksonen Toni , Liechti Felix , Procházka Petr , Salewski Volker , Hahn Steffen
Published: February 2016

Over decades it has been unclear how individual migratory songbirds cross large ecological barriers such as seas or deserts. By deploying light-level geolocators on four songbird species weighing only about 12 g, we found that these otherwise mainly nocturnal migrants seem to regularly extend their nocturnal flights into the day when crossing the Sahara Desert and the Mediterranean Sea. The proportion of the proposed diurnally flying birds gradually declined over the day with similar landing patterns in autumn and spring. The prolonged flights were slightly more frequent in spring than in autumn, suggesting tighter migratory schedules when returning to breeding sites. Often we found several patterns for barrier crossing for the same individual in autumn compared to the spring journey. As only a small proportion of the birds flew strictly during the night and even some individuals might have flown non-stop, we suggest that prolonged endurance flights are not an exception even in small migratory species. We emphasise an individual’s ability to perform both diurnal and nocturnal migration when facing the challenge of crossing a large ecological barrier to successfully complete a migratory journey.
Visualising the molecular alteration of the calcite (104) – water interface by sodium nitrate
Authors: Hofmann Sascha , Voïtchovsky Kislon , Spijker Peter , Schmidt Moritz , Stumpf Thorsten
Published: February 2016

The reactivity of calcite, one of the most abundant minerals in the earth’s crust, is determined by the molecular details of its interface with the contacting solution. Recently, it has been found that trace concentrations of NaNO3 severely affect calcite’s (104) surface and its reactivity. Here we combine molecular dynamics (MD) simulations, X-ray reflectivity (XR) and in situ atomic force microscopy (AFM) to probe the calcite (104) – water interface in the presence of NaNO3. Simulations reveal density profiles of different ions near calcite’s surface, with NO3− able to reach closer to the surface than CO32− and in higher concentrations. Reflectivity measurements show a structural destabilisation of the (104) surfaces’ topmost atomic layers in NaNO3 bearing solution, with distorted rotation angles of the carbonate groups and substantial displacement of the lattice ions. Nanoscale AFM results confirm the alteration of crystallographic characteristics, and the ability of dissolved NaNO3 to modify the structure of interfacial water was observed by AFM force spectroscopy. Our experiments and simulations consistently evidence a dramatic deterioration of the crystals’ surface, with potentially important implications for geological and industrial processes.
Paper-based analytical devices for environmental analysis
Authors: Meredith Nathan A. , Quinn Casey , Cate David M. , Reilly Thomas H. , Volckens John , Henry Charles S.
Published: February 2016

The field of paper-based microfluidics has experienced rapid growth over the past decade, in particular with new applications to environmental analysis.
Graphite paste electrode modified with Lewatit® FO36 nano-resin for simultaneous determination of ascorbic acid, acetaminophen and tryptophan
Authors: Rajabi Hossein , Noroozifar Meissam , Khorasani-Motlagh Mozhgan
Published: February 2016

TEM of surface of graphite paste electrode, modified with LFOR for simultaneous determination of ascorbic acid, acetaminophen and tryptophan.
Edge chlorination of hexa-peri-hexabenzocoronene investigated by density functional theory and vibrational spectroscopy
Authors: Maghsoumi Ali , Narita Akimitsu , Dong Renhao , Feng Xinliang , Castiglioni Chiara , Müllen Klaus , Tommasini Matteo
Published: February 2016

The molecular structure and vibrational properties of perchlorinated HBC and the parent HBC have been investigated by density functional theory calculations and vibrational spectroscopy.
A polyethylenimine functionalized porous/hollow nanoworm as a drug delivery system and a bioimaging agent
Authors: Sun Xiao , Cai Chuanjie , Wang Qian , Cai Dongqing , Qian Junchao , Chi Yu , Zheng Kang , Zhang Xin , Zhang Guilong , Zhong Kai , Wu Zhengyan
Published: February 2016

A porous/hollow PEI functionalized nanoworm was fabricated as a drug delivery system and a MR contrast agent.
A supramolecular ensemble of a PBI derivative and Cu2O NPs: potential photocatalysts for the Suzuki and Suzuki type coupling reactions
Authors: Singh Gurpreet , Kumar Manoj , Sharma Kamaldeep , Bhalla Vandana
Published: February 2016

The in situ generated supramolecular ensemble (2:Cu2O) of Cu2O NPs and aggregates of PBI derivative 2 exhibited excellent photocatalytic efficiency in the Suzuki–Miyaura and Suzuki type cross-coupling reactions under mild and eco-friendly conditions.
Soft implantable microelectrodes for future medicine: prosthetics, neural signal recording and neuromodulation
Authors: Lee Joong Hoon , Kim Hanseop , Kim Jeong Hun , Lee Sang-Hoon
Published: February 2016

Soft based implantable devices have provided various potential diagnostic options and therapeutic methods in diverse medical fields.
Environment friendly synthesis of polyvinylpyrrolidone nanofibers and their potential use as seed coats
Authors: Krishnamoorthy Vidya , Elumalai Gunasundari , Rajiv Sheeja
Published: February 2016

Incorporation of urea and cobalt nanoparticles into electrospun biocompatible PVP seed coats leads to controlled release of ammonia.
Facile synthesis of histidine functional poly(N-isopropylacrylamide): zwitterionic and temperature responsive materials
Authors: Brisson Emma R. L. , Xiao Zeyun , Levin Lucas , Franks George V. , Connal Luke A.
Published: February 2016

Reductive amination facilitates the protecting group free post-polymerization functionalisation of a temperature responsive, aldehyde-containing polymer with histidine.
Reprobing the mechanism of negative thermal expansion in siliceous faujasite
Authors: Attfield M. P. , Feygenson M. , Neuefeind J. C. , Proffen T. E. , Lucas T. C. A. , Hriljac J. A.
Published: February 2016

Combined Rietveld refinement and pair distribution function analysis of total neutron scattering data unveils the finer details of the negative thermal expansion mechanism of siliceous faujasite.
Reply to “Electrical properties analysis of materials with ferroic order”
Authors: Smari M. , Rahmouni H. , Elghoul N. , Walha I. , Dhahri E. , Khirouni K.
Published: February 2016

Real part of dielectric permittivity of the compound La0.5Ca0.2Ag0.3MnO3 as a function of temperature. The inset shows the plot of log(1/ε′ − 1/ε′m) as a function of log(T − Tm) measured at 1 kHz.
A trialkyl phosphine oxide functionalized task specific ionic liquid for actinide ion complexation: extraction and spectroscopic studies
Authors: Paramanik Minakshmi , Raut Dhaval R. , Sengupta Arijit , Ghosh Sunil K. , Mohapatra Prasanta K.
Published: February 2016

A trialkylphosphine oxide functionalized task specific ionic liquid (PO-TSIL) with a NTf2− counter anion was synthesized and evaluated for the extraction of actinide ions such as UO22+ and Pu4+ from acidic feed solutions.
Modulating the permeability of ferritin channels
Authors: Bernacchioni C. , Ghini V. , Theil E. C. , Turano P.
Published: February 2016

Electric field gradients across the C3 and C4 ferritin channels controls the directional Fe2+fluxes towards the catalytic ferroxidase center.
Violation of DNA neighbor exclusion principle in RNA recognition
Authors: Yousuf Muhammad , Youn Il Seung , Yun Jeonghun , Rasheed Lubna , Valero Rosendo , Shi Genggongwo , Kim Kwang S.
Published: February 2016

DNA intercalation has been very useful for engineering DNA-based functional materials.
Cyclic behaviors of amorphous shape memory polymers
Authors: Yu Kai , Li Hao , McClung Amber J. W. , Tandon Gyaneshwar P. , Baur Jeffery W. , Qi H. Jerry
Published: February 2016

Cyclic loading conditions are commonly encountered in the applications of shape memory polymers (SMPs), where the cyclic characteristics of the materials determine their performance during the service life, such as deformation resistance, shape recovery speed and shape recovery ratio.
Pseudopolymorphic seeding for the rational synthesis of hybrid membranes with a zeolitic imidazolate framework for enhanced molecular separation performance
Authors: Lo Yang , Kang Dun-Yen
Published: February 2016

This paper reports a novel methodology involving the use of pseudopolymorphic seeding for the rational synthesis of hydrogen-selective hybrid membranes with zeolitic imidazolate frameworks (ZIFs).
A facile preparation of CoFe2O4 nanoparticles on polyaniline-functionalised carbon nanotubes as enhanced catalysts for the oxygen evolution reaction
Authors: Liu Yang , Li Jing , Li Feng , Li Wenzhu , Yang Haidong , Zhang Xueyao , Liu Yansheng , Ma Jiantai
Published: February 2016

A polyaniline-multiwalled carbon nanotube supported, high performance CoFe2O4 nanoparticle loaded electrocatalyst is synthesized through a novel and simple in situ process under mild conditions.
Flexible electrodes and supercapacitors for wearable energy storage: a review by category
Authors: Dong Liubing , Xu Chengjun , Li Yang , Huang Zheng-Hong , Kang Feiyu , Yang Quan-Hong , Zhao Xin
Published: February 2016

Currently-developed flexible electrodes/supercapacitors are summarized according a hierarchical and detailed classification strategy.
Microgels with tunable affinity-controlled protein release via desolvation of self-assembled peptide nanofibers
Authors: Fettis Margaret M. , Wei Yaohua , Restuccia Antonietta , Kurian Justin J. , Wallet Shannon M. , Hudalla Gregory A.
Published: February 2016

We demonstrate an approach to fabricate microgels from self-assembled peptide nanofibers via desolvation. Proteins can be co-desolvated with nanofibers to create protein-loaded microgels. Modifying nanofibers with a protein-binding ligand provides tunable affinity-controlled protein release.
Real-time evaluation of thin film drying kinetics using an advanced, multi-probe optical setup
Authors: Güldal Nusret S. , Kassar Thaer , Berlinghof Marvin , Ameri Tayebeh , Osvet Andres , Pacios Roberto , Li Destri Giovanni , Unruh Tobias , Brabec Christoph J.
Published: February 2016

A portable in situ drying chamber, equipped with white light reflectometry, photoluminescence and light scattering, is used to fully characterize the thermodynamic and kinetic changes of P3HT- and DPP-TT-T-based organic bulk-heterojunction thin films during drying.
Ultrabroad near-infrared photoluminescence from bismuth doped CsPbI3: polaronic defects vs. bismuth active centers
Authors: Zhou Yang , Zhou Dan-Dan , Liu Bo-Mei , Li Li-Na , Yong Zi-Jun , Xing Hao , Fang Yong-Zheng , Hou Jing-Shan , Sun Hong-Tao
Published: February 2016

We report on the observation of doping-induced luminescent polaronic defects in Bi activated CsPbI3.
MxMn8O16 (M = Ag or K) as promising cathode materials for secondary Mg based batteries: the role of the cation M
Authors: Huang Jianping , Poyraz Altug S. , Takeuchi Kenneth J. , Takeuchi Esther S. , Marschilok Amy C.
Published: February 2016

2 × 2 tunneled MxMn8O16 (M = Ag or K) materials delivered high initial capacities in Mg based electrolyte, and KxMn8O16 showed high cycle stability with a reversible capacity of >170 mA h g−1 after 20 cycles.
Rupture force of cell adhesion ligand tethers modulates biological activities of a cell-laden hydrogel
Authors: Lee Min Kyung , Park Jooyeon , Wang Xuefeng , Roein-Peikar Mehdi , Ko Eunkyung , Qin Ellen , Lee Jonghwi , Ha Taekjip , Kong Hyunjoon
Published: February 2016

Hydrogels coupled with integrin-binding deoxyribonucleic acid (DNA) tethers with pre-defined rupture forces can modulate phenotypic activities of stem cells.
Coordination networks incorporating halogen-bond donor sites and azobenzene groups
Authors: Fernandez-Palacio Francisco , Saccone Marco , Priimagi Arri , Terraneo Giancarlo , Pilati Tullio , Metrangolo Pierangelo , Resnati Giuseppe
Published: February 2016

A coordination network decorated with halogen-bond donor sites for specific guest binding.
Application of mild autohydrolysis to facilitate the dissolution of wood chips in direct-dissolution solvents
Authors: Deb Somdatta , Labafzadeh Sara R. , Liimatainen Unna , Parviainen Arno , Hauru Lauri K. J. , Azhar Shoaib , Lawoko Martin , Kulomaa Tuomas , Kakko Tia , Fiskari Juha , Borrega Marc , Sixta Herbert , Kilpeläinen Ilkka , King Alistair W. T.
Published: February 2016

Autohydrolysis, an economical pre-treatment, allows for dissolution and chemical modification of wood chips.
Metabolomics in diabetic complications
Authors: Filla Laura A. , Edwards James L.
Published: February 2016

In the past 15 years, the field of metabolomics has expanded the current understanding of the pathophysiology of diabetic complications far beyond oxidative stress and inflammation. Branched-chain amino acids, phospholipid metabolism, and the glutamine/glutamate cycle are just a few of the previously unknown pathways and biomarkers of diabetes which have come to light due to advancements in sensitivity, sample preparation, and data processing.
Alpha-synuclein: relating metals to structure, function and inhibition
Authors: McDowall J S , Brown D R
Published: February 2016

Alpha-synuclein has long been studied due to its involvement in the progression of Parkinson’s disease (PD), a common neurodegenerative disorder, although a consensus on the exact function of this protein is elusive. This protein shows remarkable structural plasticity and this property is important for both correct cellular function and pathological progression of PD. Formation of intracellular oligomeric species within the substantia nigra correlates with disease progression and it has been proposed that formation of a partially folded intermediate is key to the initiation of the fibrillisation process. Many factors can influence changes in the structure of alpha-synuclein such as disease mutations and interaction with metals and neurotransmitters. High concentrations of both dopamine and metals are present in the substantia nigra making this an ideal location for both the structural alteration of alpha-synuclein and the production of toxic oxygen species. The recent proposal that alpha-synuclein is a ferrireductase is important as it can possibly catalyse the formation of such reactive species and as a result exacerbate neurodegeneration.
Synthesis of amphiphilic nanoparticles and multi-block hydrophilic copolymers by a facile and effective “living” radical polymerization in water
Authors: Wu Juanjuan , Jiang Hongjuan , Zhang Lifen , Cheng Zhenping , Zhu Xiulin
Published: February 2016

A convenient and robust approach using MANDC-COOH as the initiator and oxidatively stable Cu(OAc)2as the catalyst to synthesize amphiphilic nanoparticles and hydrophilic multi-block copolymers was successfully developed in water.
Dynamic switching of ionic conductivity by cooperative interaction of polyviologen and liquid crystals for efficient charge storage
Authors: Sato Kan , Yamasaki Takaaki , Mizuma Takahiro , Oyaizu Kenichi , Nishide Hiroyuki
Published: February 2016

The ionic conductivity of a liquid crystal electrolyte was switched along with redox reactions of polyviologen.
Effects of pyridyl group orientations on the optoelectronic properties of regio-isomeric diketopyrrolopyrrole based π-conjugated polymers
Authors: Yue Jing , Sun Sheng , Liang Junfei , Zhong Wenkai , Lan Linfeng , Ying Lei , Huang Fei , Yang Wei , Cao Yong
Published: February 2016

The orientation of the N-atom in the pyridyl groups shows pronounced effects on the molecular geometry and charge transport properties.
Robustness analysis of locomotion controllers for mechanical rectifier systems in natural oscillation
Authors: Mei Chengcai , Zhu Lijun , Chen Zhiyong
Published: February 2016

A class of feedback controllers has been proposed to achieve a desired locomotion behaviour for mechanical rectifier systems in recent work. It is inspired by a biological neuron circuit called central pattern generator and is expected to exhibit robust and adaptive abilities against system parameter uncertainties and external disturbances. The controller was originally designed in an ideal situation that system parameters such as friction coefficients were precisely known, and measurement channels and actuation circuits were noiseless. In this study, the authors conduct specific robustness analysis for the locomotion controller with respect to system parameter variations and measurement and actuation noises. The numerical study shows that the locomotion controller is able to maintain a reasonable performance under these circumstances.
Extraction of informative regions of a face for facial expression recognition
Authors: Kumar Sunil , Bhuyan M.K. , Chakraborty Biplab Ketan
Published: February 2016

The aim of facial expression recognition (FER) algorithms is to extract discriminative features of a face. However, discriminative features for FER can only be obtained from the informative regions of a face. Also, each of the facial subregions have different impacts on different facial expressions. Local binary pattern (LBP) based FER techniques extract texture features from all the regions of a face, and subsequently the features are stacked sequentially. This process generates the correlated features among different expressions, and hence affects the accuracy. This research moves toward addressing these issues. The authors' approach entails extracting discriminative features from the informative regions of a face. In this view, they propose an informative region extraction model, which models the importance of facial regions based on the projection of the expressive face images onto the neural face images. However, in practical scenarios, neutral images may not be available, and therefore the authors propose to estimate a common reference image using Procrustes analysis. Subsequently, weighted‐projection‐based LBP feature is derived from the informative regions of the face and their associated weights. This feature extraction method reduces miss‐classification among different classes of expressions. Experimental results on standard datasets show the efficacy of the proposed method.
Bag‐of‐features for image memorability evaluation
Authors: Lahrache Souad , El Ouazzani Rajae , El Qadi Abderrahim
Published: February 2016

Image memorability represents the degree to which images are remembered or forgotten after a period of time. Studying image memorability in computer vision is the task of finding special characteristics in memorable images, in order to develop a representative model of this type of images. Several approaches have been realised to examine features that can affect image memorability. In this study, the authors use bag‐of‐features as another kind of visual feature descriptor to assess image memorability. The authors’ method based on bag‐of‐visual‐words (BoVWs) technique involves four main steps. First, the authors extract local image features from regions/points of interest which are automatically detected. Then, they encode these local features by mapping them to a created visual vocabulary. Later, the authors apply features pooling and normalisation techniques to obtain image BoVW representation. Finally, the authors use this representation to examine image memorability as a problem of classification. They present different implementation choices for each step and compare reached results. The authors’ method performs best significant results in comparison with other approaches found in literature.
Characterisation of high‐frequency modulator response via measurements of optical modulation sidebands
Authors: Ng W. , Sarkissian R. , Mahalingam H.
Published: February 2016

The authors report an approach to characterise the radiofrequency (RF)‐response and bandwidth of photonic modulators by measuring their modulation sidebands in the optical domain. After taking into account the RF‐response measured independently for photodetectors, they demonstrated excellent agreement with swept‐frequency measurements over a broad frequency range of ∼6 to 40 GHz. They also evaluated the dynamic half‐wave voltage (Vπ) of a Mach–Zehnder (MZ) LiNbO3 modulator by modelling and measuring the asymmetry of its RF‐drive on the two MZ arms. Since there are no RF‐bandwidth constraints in the authors’ reported approach, the technique can be extended to measure the RF‐response of optical modulators at frequencies beyond those supported by microwave instrumentation such as network analysers.
Non‐linear feedback control of the p 53 protein–mdm 2 inhibitor system using the derivative‐free non‐linear Kalman filter
Authors: Rigatos Gerasimos G.
Published: February 2016

It is proven that the model of the p 53–mdm 2 protein synthesis loop is a differentially flat one and using a diffeomorphism (change of state variables) that is proposed by differential flatness theory it is shown that the protein synthesis model can be transformed into the canonical (Brunovsky) form. This enables the design of a feedback control law that maintains the concentration of the p 53 protein at the desirable levels. To estimate the non‐measurable elements of the state vector describing the p 53–mdm 2 system dynamics, the derivative‐free non‐linear Kalman filter is used. Moreover, to compensate for modelling uncertainties and external disturbances that affect the p 53–mdm 2 system, the derivative‐free non‐linear Kalman filter is re‐designed as a disturbance observer. The derivative‐free non‐linear Kalman filter consists of the Kalman filter recursion applied on the linearised equivalent of the protein synthesis model together with an inverse transformation based on differential flatness theory that enables to retrieve estimates for the state variables of the initial non‐linear model. The proposed non‐linear feedback control and perturbations compensation method for the p 53–mdm 2 system can result in more efficient chemotherapy schemes where the infusion of medication will be better administered.
Effect of bath temperature and concentration of buffer salt on the optoelectronic characteristics of CdS thin films synthesised by chemical bath deposition method
Authors: Kakhaki Zahra Makhdoumi , Youzbashi Amirali , Sangpour Parvaneh , Naderi Nima , Kazemzadeh Asghar
Published: February 2016

CdS thin films were deposited onto glass substrate by the chemical bath deposition method, using cadmium chloride (CdCl2) as a source of cadmium, thiourea (CS(NH2)2) as a source of sulphur, ammonium nitrate (NH4NO3) as buffer salt and ammonia as pH controller and complexing agent. The effects of the deposition temperature and the concentration of ammonium nitrate on the structural, compositional, optical and optoelectrical properties of CdS thin films were investigated. The optimised sample was utilised for fabrication of photodetectors. A high photosensitivity and a short response time was reported for the photodetectors based on the sample with the bath temperature of 65°C and concentration of ammonium nitrate of 1.5 M compare with the other samples.
Effect of the Cu and Ni content on the crystallization temperature and crystallization mechanism of La–Al–Cu(Ni) metallic glasses
Authors: Li Peiyou
Published: February 2016

The effect of the Cu and Ni content on the crystallization mechanism and the crystallization temperatures of La–Al–Cu(Ni) metallic glasses (MGs) was studied by differential scanning calorimetry (DSC). The experimental results have shown that the DSC curves obtained for the La–Al–Cu and La–Al–Ni MGs exhibit two and three crystallization temperatures, respectively. The crystallization temperatures of the La–Al–Cu and La–Al–Ni MGs result from the merging and splitting of thermal events related to the corresponding eutectic atomic pairs in the La72Cu28 and La81.6Al18.4 MGs, and La72Ni28 and La81.6Al18.4 MGs, respectively. In addition, Al- and Ni-containing clusters with weak or strong atomic interaction in the Al–Ni atomic pairs strongly affect the crystallization mechanism and thus the crystallization temperature of La–Al–Ni MGs. This study provides a novel understanding of the relation between the crystallization temperature and the underlying crystallization mechanisms in La–Al–Cu(Ni) MGs.
The laboratory diagnosis of Strongyloides stercoralis
Authors: Watts Matthew R , Robertson Gemma , Bradbury Richard
Published: February 2016

It is estimated that over 30million people worldwide are infected by the nematode, Strongyloides stercoralis1. It is endemic in sub-tropical and tropical parts of Australia, with high rates of infection documented in some indigenous communities2. Due to the potential for chronic autoinfection, that may persist for decades, migration leads to the presence of the infection in non-endemic areas1. Transmission to humans is generally through the penetration of larvae through the skin, following contact with faecally contaminated soil1. Disease severity ranges from asymptomatic chronic carriage to an overwhelming illness, where large numbers spread throughout the body, usually triggered by immunosuppression1.
Protozoa PCR: boon or bane
Authors: Pham Colin , Sheorey Harsha
Published: February 2016

Parasite detection in faeces has traditionally been performed by microscopy, a procedure that is labour-intensive and highly specialised. In addition, identification by microscopy based on morphological features alone is subjective and prone to wide variability. Although enzyme immunoassays (EIA) of high sensitivity have been developed1 they can detect only a limited range of pathogens. Given these factors the introduction of Polymerase Chain Reaction (PCR) into the routine diagnostic laboratory has improved parasite detection rates2. The ability to multiplex has enabled the detection of multiple targets from a single sample and provides an objective alternative to identification by morphology.
Malaria: global challenges for malaria eradication
Authors: Brown Graham , Rogerson Stephen
Published: February 2016

The enormous decline in the annual morbidity and mortality from malaria is the spectacular global public health success of the past decade. This achievement results largely from increased finance for investment in measures known to prevent malaria: bednets treated with long-lasting insecticides, chemoprophylaxis, and rapid access to effective treatment. Such has been the success of these measures that plans are being put in place to achieve the vision of a malaria-free world within the next three decades. Large financial and political commitments and ongoing research will be required to maintain the gains, overcome known and unknown challenges such as drug and insecticide resistance, and to achieve those goals. Effective vaccines or methods for reducing mosquito vectorial capacity would add enormously to the chance of achieving this goal. The aim of this article is to summarise the current status of malaria control, the recent research successes, the challenges being addressed, and the plan for progress to elimination of malaria in the longer term.
American eel (Anguilla rostrata) substrate selection for daytime refuge and winter thermal sanctuary
Authors: Tomie J. P. N. , Cairns D. K. , Hobbs R. S. , Desjardins M. , Fletcher G. L. , Courtenay S. C.
Published: February 2016

We addressed hypotheses that anguillid eels use mud as a substrate refuge only in the absence of substrate cavities, and that the winter distribution of eels in coastal bay and estuarine habitat is limited to waters warmer than the freezing point of fish tissue (~–0.7°C). In the seasonally ice-covered southern Gulf of St Lawrence, Canada, locations of summer fyke and winter spear fisheries indicate that American eels (Anguilla rostrata) are widely distributed in both summer and winter in shallow soft-bottomed bay and estuarine habitat. Captive eels in fresh water preferred mud substrates during summer, during pre-winter cooling and during post-winter warming periods, but in winter chose mud and cobble substrates at approximately equal frequencies. Plasma antifreeze was not detected in blood sampled from eels speared in mud under winter ice. Winter bottom water temperatures in an eel wintering site were below the approximate freezing point of fish tissue 29.9% of the time. Mud of eel wintering grounds is warmer than overlying water and appears to serve as a thermal sanctuary that allows eels to safely overwinter under ice-covered waters. American eels in the southern Gulf of St Lawrence spend ~67% of their annual cycle within the substrate.
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
Authors: Wong Alan S. L. , Choi Gigi C. G. , Cui Cheryl H. , Pregernig Gabriela , Milani Pamela , Adam Miriam , Perli Samuel D. , Kazer Samuel W. , Gaillard Aleth , Hermann Mario , Shalek Alex K. , Fraenkel Ernest , Lu Timothy K.
Published: February 2016

Significance

The systematic discovery of new gene and drug combinations that modulate complex biological phenotypes and human diseases requires scalable and multiplexed screening technologies. We leverage the programmability of the CRISPR-Cas9 system for multiplexed targeting of specific genomic loci and the versatility of the combinatorial genetics en masse (CombiGEM) technology to rapidly assemble barcoded combinatorial genetic perturbation libraries that can be tracked with high-throughput sequencing. CombiGEM-CRISPR enables simple, massively parallel screening of barcoded combinatorial gene perturbations in human cells, and the translation of these hits into effective drug combinations. This approach is broadly applicable for performing pooled combinatorial genetic perturbations to map out how the orchestrated action of genes controls complex phenotypes and to translate these findings into novel drug combinations.
Lowering the threshold for online learning with Facebook
Authors: Fourie Christine
Published: February 2016

Students’ understanding of their own learning needs can improve, if they can be made more aware of their own learning processes by supporting their metacognitive development. Research has shown that membership of online communities can positively contribute to the social acculturation process of first year students (Wohn, Ellison, Khan, Fewins-Bliss, & Gray, 2013). Moreover, these social networking sites could meet specific learning needs. A group of South African first year medical students doing a second language communication course were invited to become members of a closed Facebook group with the purpose of lowering the threshold of online learning. These students reported that their metacognitive awareness about their own learning processes was raised, which made it possible for them to progress towards and access the online learning experience. Data collected during the course were analysed following the grounded theory method and a framework for raising metacognitive awareness was created.
Weak hand holds in two sign languages and two genres
Authors: Sáfár Anna , Kimmelman Vadim
Published: February 2016

In this paper, we provide a quantitative analysis of weak hand holds based on corpus data. We include both a cross-linguistic analysis of these holds in narrative data from Russian Sign Language (RSL) and Sign Language of the Netherlands (NGT), and a language-internal, cross-genre analysis comparing NGT narrative and conversational data. We classified the functions of all holds found in two corpora of RSL and NGT, and analyzed their formal characteristics. We found that holds in RSL and NGT have similar functions. However, holds are significantly more frequent in RSL than in NGT. In addition, we found that the distribution of holds across different functions varies between different genres in NGT. The similarities between RSL and NGT in the domain of holds may be attributed to modality effects. The differences in frequency of holds ask for a language-specific explanation, and we discuss several possible scenarios.
Indirect object markers in Georgian Sign Language
Authors: Makharoblidze Tamar
Published: February 2016

This paper presents one of the first studies on Georgian Sign Language (gesl), a sign language that has not previously been taken into consideration in typological research on sign languages. We focus on three types of indirect object markers, that is, auxiliary-like elements that introduce an additional argument. We discuss four markers in total. Interestingly, three of these markers do not only introduce an argument but also come with additional semantics, namely respect, disrespect, and causation. It will further be shown that the presence of an indirect object marker frees the word order in the sentence.
New Purcell Documents from the Court of King's Bench
Authors: Duncan Cheryll
Published: February 2016

Two legal documents recently discovered among The National Archives at Kew in London provide new information about Henry Purcell's final years. The only known instances of the composer's involvement with the law, these rare archival finds shed light on his familial relations and financial circumstances at that point in his career when he was turning his attention to the London stage. The first case involves Purcell's sister-in-law Amy Howlett, who owed him £40; and the second concerns his unpaid bill at an exclusive West End retailer's. The new material confirms beyond doubt the identity of Purcell's in-laws, and shows that he was not just short of money in the 1690s, but that he was actually in debt at the time of his death. Other areas of enquiry include the élite social milieu in which the Purcells increasingly moved, and their possible place of residence in 1691–3. These aspects are discussed in relation to Purcell's enhanced public profile at that time, and within the wider context of the culture of consumption and credit in late seventeenth-century England. The two lawsuits are transcribed and translated in full, and their legal implications explicated.
Cross-cultural differences and similarities underlying other-race effects for facial identity and expression
Authors: Yan Xiaoqian , Andrews Timothy J. , Jenkins Rob , Young Andrew W.
Published: February 2016

Perceptual advantages for own-race compared to other-race faces have been demonstrated for the recognition of facial identity and expression. However, these effects have not been investigated in the same study with measures that can determine the extent of cross-cultural agreement as well as differences. To address this issue, we used a photo sorting task in which Chinese and Caucasian participants were asked to sort photographs of Chinese or Caucasian faces by identity or by expression. This paradigm matched the task demands of identity and expression recognition and avoided constrained forced-choice or verbal labelling requirements. Other-race effects of comparable magnitude were found across the identity and expression tasks. Caucasian participants made more confusion errors for the identities and expressions of Chinese than Caucasian faces, while Chinese participants made more confusion errors for the identities and expressions of Caucasian than Chinese faces. However, analyses of the patterns of responses across groups of participants revealed a considerable amount of underlying cross-cultural agreement. These findings suggest that widely repeated claims that members of other cultures “all look the same” overstate the cultural differences.
Microbial sphingomyelinase induces RhoA-mediated reorganization of the apical brush border membrane and is protective against invasion
Authors: Saslowsky David E. , Thiagarajah Jay R. , McCormick Beth A. , Lee Jean C. , Lencer Wayne I.
Published: February 2016

The apical brush border membrane (BBM) of intestinal epithelial cells forms a highly structured and dynamic environmental interface that serves to regulate cellular physiology and block invasion by intestinal microbes and their products. How the BBM dynamically responds to pathogenic and commensal bacterial signals can define intestinal homeostasis and immune function. We previously found that in model intestinal epithelium, the conversion of apical membrane sphingomyelin to ceramide by exogenous bacterial sphingomyelinase (SMase) protected against the endocytosis and toxicity of cholera toxin. Here we elucidate a mechanism of action by showing that SMase induces a dramatic, reversible, RhoA-dependent alteration of the apical cortical F-actin network. Accumulation of apical membrane ceramide is necessary and sufficient to induce the actin phenotype, and this coincides with altered membrane structure and augmented innate immune function as evidenced by resistance to invasion by Salmonella.
FastLSU: a more practical approach for the Benjamini–Hochberg FDR controlling procedure for huge-scale testing problems
Authors: Madar Vered , Batista Sandra
Published: February 2016

Motivation: We address a common problem in large-scale data analysis, and especially the field of genetics, the huge-scale testing problem, where millions to billions of hypotheses are tested together creating a computational challenge to control the inflation of the false discovery rate. As a solution we propose an alternative algorithm for the famous Linear Step Up procedure of Benjamini and Hochberg.

Results: Our algorithm requires linear time and does not require any P-value ordering. It permits separating huge-scale testing problems arbitrarily into computationally feasible sets or chunks. Results from the chunks are combined by our algorithm to produce the same results as the controlling procedure on the entire set of tests, thus controlling the global false discovery rate even when P-values are arbitrarily divided. The practical memory usage may also be determined arbitrarily by the size of available memory.

Availability and implementation: R code is provided in the supplementary material.

Contact:  sbatista@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures
Authors: Wright Erik S. , Vetsigian Kalin H.
Published: February 2016

Summary: For numerous experimental applications, PCR primers must be designed to efficiently amplify a set of homologous DNA sequences while giving rise to amplicons with maximally diverse signatures. We developed DesignSignatures to automate the process of designing primers for high-resolution melting (HRM), fragment length polymorphism (FLP) and sequencing experiments. The program also finds the best restriction enzyme to further diversify HRM or FLP signatures. This enables efficient comparison across many experimental designs in order to maximize signature diversity.

Availability and implementation: DesignSignatures is accessible as a web tool at www.DECIPHER.cee.wisc.edu, or as part of the DECIPHER open source software package for R available from BioConductor.

Contact:  kalin@discovery.wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Characterization of clinical signs in the human interactome
Authors: Chagoyen Monica , Pazos Florencio
Published: February 2016

Motivation: Many diseases are related by shared associated molecules and pathways, exhibiting comorbidities and common phenotypes, an indication of the continuous nature of the human pathological landscape. Although it is continuous, this landscape is always partitioned into discrete diseases when studied at the molecular level. Clinical signs are also important phenotypic descriptors that can reveal the molecular mechanisms that underlie pathological states, but have seldom been the subject of systemic research. Here, we quantify the modular nature of the clinical signs associated with genetic diseases in the human interactome.

Results: We found that clinical signs are reflected as modules at the molecular network level, to at least to the same extent as diseases. They can thus serve as a valid complementary partition of the human pathological landscape, with implications for etiology research, diagnosis and treatment.

Contact:  monica.chagoyen@cnb.csic.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data
Authors: Chen Jinyu , Zhang Shihua
Published: February 2016

Motivation: The underlying relationship between genomic factors and the response of diverse cancer drugs still remains unclear. A number of studies showed that the heterogeneous responses to anticancer treatments of patients were partly associated with their specific changes in gene expression and somatic alterations. The emerging large-scale pharmacogenomic data provide us valuable opportunities to improve existing therapies or to guide early-phase clinical trials of compounds under development. However, how to identify the underlying combinatorial patterns among pharmacogenomics data are still a challenging issue.

Results: In this study, we adopted a sparse network-regularized partial least square (SNPLS) method to identify joint modular patterns using large-scale pairwise gene-expression and drug-response data. We incorporated a molecular network to the (sparse) partial least square model to improve the module accuracy via a network-based penalty. We first demonstrated the effectiveness of SNPLS using a set of simulation data and compared it with two typical methods. Further, we applied it to gene expression profiles for 13 321 genes and pharmacological profiles for 98 anticancer drugs across 641 cancer cell lines consisting of diverse types of human cancers. We identified 20 gene-drug co-modules, each of which consists of 30 cell lines, 137 genes and 2 drugs on average. The majority of identified co-modules have significantly functional implications and coordinated gene-drug associations. The modular analysis here provided us new insights into the molecular mechanisms of how drugs act and suggested new drug targets for therapy of certain types of cancers.

Availability and implementation: A matlab package of SNPLS is available at http://page.amss.ac.cn/shihua.zhang/

Contact: zsh@amss.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cosmopolitanism and Music in the Nineteenth Century
Authors: Magaldi Cristina
Published: February 2016

This essay explores cosmopolitanism during the nineteenth century, not merely as a concept intertwined with the nation-state, but rather as an experience shaped by shared perceptions of the world and shared views of modernity. It discusses the potential of the concept of a cosmopolitan cultural network during the nineteenth century, within and beyond Europe, to steer music historiography and critique away from a focus on issues of national identity and nationalistic music aesthetics. It argues that cosmopolitans from the margins of Europe expanded on European musics’ many aesthetic possibilities, while they problematized boundaries between local and universal, between originals and copies, between margins and centers, and ultimately between the European and the non-European.
Patterns of Food Consumption in Early Modern Iran
Authors: Matthee Rudolph
Published: February 2016

This article examines patterns of food consumption in early modern Iran from a historical perspective and in a global context. The discussion focuses on the period of the Safavid and the Qajar dynasties, or the early sixteenth to early twentieth centuries. The article first considers Iran’s cultural linkage to the world between the seventh-century Arab invasion and the advent of modern communications in relatively recent times. It then looks at the origins and movement of food in Iran before analyzing the diet of Iranians, especially fresh fruit and vegetables. It also explores regional variations in food consumption patterns in Iran and concludes with an overview of the changes that have occurred in food consumption patterns in the country since the 1960s.
The Mock Academic Faculty Position Competition: A Pilot Professional and Career Development Opportunity for Postdoctoral Fellows
Authors: Henderson Rita Isabel , Syed Naweed
Published: February 2016

Problem

Medical educators face a dilemma in countries like Canada, where policy makers and strategic planners have prioritized highly qualified personnel and expanded recruitment of advanced trainees at a time when early-career specialists face prolonged job insecurity as they transition to professional employment. The University of Calgary Cumming School of Medicine hatched the Mock Academic Faculty Position competition to test the school’s existing capacity to address the pressing career development needs of highly trained graduates.

Approach

The competition was piloted in May–June 2014. Approximately 180 postdoctoral fellows were invited to compete; 34 submitted portfolios. The Postdoctoral Program Office established a longlist of 12 applicants. Through reviews, a selection committee identified 3 finalists to participate in a daylong event consisting of a research presentation and committee interview. The event was followed by approximately 70 audience members at any given time who were invited to complete anonymous evaluation forms and/or exit interviews.

Outcomes

The selection committee deduced a vast majority of applicants did not sell their skills effectively or demonstrate research programs independent from supervisors. Exit interviews conducted with 40 audience members indicated 36 (90%) picked the same finalist as the selection committee, 34 (85%) found the process “nerve racking,” and 28 (70%) had no previous idea of what goes on inside an academic committee interview.

Next Steps

A key recommendation for future iterations is early attention to systematizing feedback to ensure more direct impact for nonfinalists. Alternative initiatives for those gearing up for industry or public-sector work are being prepared.