bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly specific blockade of CCR5 inhibits leukocyte trafficking and reduces mucosal inflammation in murine colitis
Authors: Mencarelli Andrea , Cipriani Sabrina , Francisci Daniela , Santucci Luca , Baldelli Franco , Distrutti Eleonora , Fiorucci Stefano
Published: August 2016

Targeted disruption of leukocyte trafficking to the gut represents a promising approach for the treatment of inflammatory bowel diseases (IBDs). CCR5, the shared receptor for MIP1α and β and RANTES, is expressed by multiple leukocytes. Here, we aimed to determine the role of CCR5 in mediating leukocyte trafficking in models of colitis and evaluate the therapeutic potential of maraviroc, an orally active CCR5 antagonist used in the treatment of CCR5-tropic HIV. Acute and chronic colitis were induced by administration of DSS or TNBS to wild-type and CCR5−/− mice or adoptive transfer of splenic naïve CD4+ T-cells from wild type or CCR5−/− mice into RAG-1−/−. CCR5 gene ablation reduced the mucosal recruitment and activation of CCR5-bearing CD4+ and CD11b+ leukocytes, resulting in profound attenuation of signs and symptoms of inflammation in the TNBS and transfer models of colitis. In the DSS/TNBS colitis and in the transfer model, maraviroc attenuated development of intestinal inflammation by selectively reducing the recruitment of CCR5 bearing leukocytes. In summary, CCR5 regulates recruitment of blood leukocytes into the colon indicating that targeting CCR5 may offer therapeutic options in IBDs.
Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles
Authors: Hu Shijia , Parker Joel , Divaris Kimon , Padilla Ricardo , Murrah Valerie , Wright John Timothy
Published: August 2016

Ameloblastoma is a locally invasive benign neoplasm derived from odontogenic epithelium and presents with diverse phenotypes yet to be characterized molecularly. High recurrence rates of 50–80% with conservative treatment in some sub-types warrants radical surgical resections resulting in high morbidity. The objective of the study was to characterize the transcriptome of ameloblastoma and identify relevant genes and molecular pathways using normal odontogenic tissue (human “dentome”) for comparison. Laser capture microdissection was used to obtain neoplastic epithelial tissue from 17 tumors which were examined using the Agilent 44 k whole genome microarray. Ameloblastoma separated into 2 distinct molecular clusters that were associated with pre-secretory ameloblast and odontoblast. Within the pre-secretory cluster, 9/10 of samples were of the follicular type while 6/7 of the samples in the odontoblast cluster were of the plexiform type (p < 0.05). Common pathways altered in both clusters included cell-cycle regulation, inflammatory and MAPkinase pathways, specifically known cancer-driving genes such as TP53 and members of the MAPkinase pathways. The pre-secretory ameloblast cluster exhibited higher activation of inflammatory pathways while the odontoblast cluster showed greater disturbances in transcription regulators. Our results are suggestive of underlying inter-tumor molecular heterogeneity of ameloblastoma sub-types and have implications for the use of tailored treatment.
Shape morphing Kirigami mechanical metamaterials
Authors: Neville Robin M. , Scarpa Fabrizio , Pirrera Alberto
Published: August 2016

Mechanical metamaterials exhibit unusual properties through the shape and movement of their engineered subunits. This work presents a new investigation of the Poisson’s ratios of a family of cellular metamaterials based on Kirigami design principles. Kirigami is the art of cutting and folding paper to obtain 3D shapes. This technique allows us to create cellular structures with engineered cuts and folds that produce large shape and volume changes and with extremely directional, tuneable mechanical properties. We demonstrate how to produce these structures from flat sheets of composite materials. By a combination of analytical models and numerical simulations we show how these Kirigami cellular metamaterials can change their deformation characteristics. We also demonstrate the potential of using these classes of mechanical metamaterials for shape change applications like morphing structures.
Simple Approach to Synthesize Amino-Functionalized Carbon Dots by Carbonization of Chitosan
Authors: Liu Xin , Pang Jinhui , Xu Feng , Zhang Xueming
Published: August 2016

Carbon dots (CDs) as a new series of fluorescent nanomaterials have drawn great attention in recent years owning to their unique properties. In this paper, a simple carbonization approach to synthesize amino-functionalized CDs was developed by using chitosan as the carbon precursor. The as-prepared CDs possessed desirable amino function group on their surface and exhibited bright luminescence with absolute quantum yield (QY) of 4.34%, excitation-, pH-dependent and up-conversion fluorescence behaviors. Furthermore, we have investigated the cytotoxicity and biocompatibility of the as-prepared CDs, which demonstrated that the as-prepared CDs have the potential applications in biosensing, cellular imaging and drug delivery.
A Novel Adhesion Index for Verifying the Extent of Adhesion for the Extensor Digitorum Communis in Patients with Metacarpal Fractures
Authors: Lai Ting-Yu , Chen Hsiao-I , Shih Cho-Chiang , Kuo Li-Chieh , Hsu Hsiu-Yun , Huang Chih-Chung
Published: August 2016

This study aims to determine if the relative displacement between the extensor digitorum communis (EDC) tendon and its surrounding tissues can be used as an adhesion index (AI) for assessing adhesion in metacarpal fractures by comparing two clinical measures, namely single-digit-force and extensor lag (i.e., the difference between passive extension and full active extension). The Fisher–Tippett block-matching method and a Kalman-filter algorithm were used to determine the relative displacements in 39 healthy subjects and 8 patients with metacarpal fractures. A goniometer was used to measure the extensor lag, and a force sensor was used to measure the single-digit-force. Measurements were obtained twice for each patient to evaluate the performance of the AI in assessing the progress of rehabilitation. The Pearson correlation coefficient was calculated to quantify the various correlations between the AI, extensor lag, and single-digit-force. The results showed strong correlations between the AI and the extensor lag, the AI and the single-digit-force, and the extensor lag and the single-digit-force (r = 0.718, −0.849, and −0.741; P = 0.002, P < 0.001, and P = 0.001, respectively). The AI in the patients gradually decreased after continuous rehabilitation, but remained higher than that of healthy participants.
Dual promoters of the major catalase (KatA) govern distinct survival strategies of Pseudomonas aeruginosa
Authors: Chung In-Young , Kim Bi-o , Jang Hye-Jeong , Cho You-Hee
Published: August 2016

KatA is the major catalase required for hydrogen peroxide (H2O2) resistance and acute virulence in Pseudomonas aeruginosa PA14, whose transcription is driven from the promoter (katAp1) located at 155 nucleotide (nt) upstream of the start codon. Here, we identified another promoter (katAp2), the +1 of which was mapped at the 51 nt upstream of the start codon, which was responsible for the basal transcription during the planktonic culture and down-regulated upon H2O2 treatment under the control by the master regulator of anaerobiosis, Anr. To dissect the roles of the dual promoters in conditions involving KatA, we created the promoter mutants for each -10 box (p1m, p2m, and p1p2m) and found that katAp1 is required for the function of KatA in the logarithmic growth phase during the planktonic culture as well as in acute virulence, whereas katAp2 is required for the function of KatA in the stationary phase as well as in the prolonged biofilm culture. This dismantling of the dual promoters of katA sheds light on the roles of KatA in stress resistance in both proliferative and growth-restrictive conditions and thus provides an insight into the regulatory impacts of the major catalase on the survival strategies of P. aeruginosa.
The Expression of Human Cytomegalovirus MicroRNA MiR-UL148D during Latent Infection in Primary Myeloid Cells Inhibits Activin A-triggered Secretion of IL-6
Authors: Lau Betty , Poole Emma , Krishna Benjamin , Montanuy Immaculada , Wills Mark R. , Murphy Eain , Sinclair John
Published: August 2016

The successful establishment and maintenance of human cytomegalovirus (HCMV) latency is dependent on the expression of a subset of viral genes. Whilst the exact spectrum and functions of these genes are far from clear, inroads have been made for protein-coding genes. In contrast, little is known about the expression of non-coding RNAs. Here we show that HCMV encoded miRNAs are expressed de novo during latent infection of primary myeloid cells. Furthermore, we demonstrate that miR-UL148D, one of the most highly expressed viral miRNAs during latent infection, directly targets the cellular receptor ACVR1B of the activin signalling axis. Consistent with this, we observed upregulation of ACVR1B expression during latent infection with a miR-UL148D deletion virus (ΔmiR-UL148D). Importantly, we observed that monocytes latently infected with ΔmiR-UL148D are more responsive to activin A stimulation, as demonstrated by their increased secretion of IL-6. Collectively, our data indicates miR-UL148D inhibits ACVR1B expression in latently infected cells to limit proinflammatory cytokine secretion, perhaps as an immune evasion strategy or to postpone cytokine-induced reactivation until conditions are more favourable. This is the first demonstration of an HCMV miRNA function during latency in primary myeloid cells, implicating that small RNA species may contribute significantly to latent infection.
Rapid detection of adulterated drugs in herbal dietary supplements by wooden-tip electrospray ionization mass spectrometry
Authors: Hu Bin , Huang Yingyan , Yin Guo , Zhang Gaofei , Zhang Liyang , Wang Tiejie , Yao Zhong-Ping
Published: August 2016

High-throughput wooden-tip electrospray ionization mass spectrometry for rapid detection of adulterated drugs in herbal dietary supplements.
Highly efficient sample stacking by enhanced field amplification on a simple paper device
Authors: Ma Biao , Song Yi-Zhen , Niu Ji-Cheng , Wu Zhi-Yong
Published: August 2016

Electrokinetic stacking based on field amplification was firstly introduced to a paper-based analytical device, and over 1000-fold signal improvement was achieved.
Three-dimensional graphene/Fe3O4-based magnetic solid phase extraction coupled with high performance liquid chromatography for determination of carvedilol in human blood plasma
Authors: Sereshti Hassan , Bakhtiari Sadjad
Published: August 2016

3D-graphene–Fe3O4-based magnetic SPE-HPLC for determination of carvedilol.
Multidimensional (3D/4D-QSAR) probability-guided pharmacophore mapping: investigation of activity profile for a series of drug absorption promoters
Authors: Bak A. , Kozik V. , Smolinski A. , Jampilek J.
Published: August 2016

A hybrid approach that combines 3D and 4D-QSAR methods based on grid and neural paradigms with automated IVE-PLS procedure was examined to identify the pharmacophore pattern for cholic acid derivatives as potential drug absorption promoters.
Single step incorporation of isatin to enaminone: a recyclable catalyst towards assembly of diverse four ring fused pyrrolo[2,3,4-kl]acridin-1-ones
Authors: Li Chunmei , Zhang Furen
Published: August 2016

Single step synthesis of four ring fused pyrrolo[2,3,4-kl]acridin-1-ones using recoverable sulfonated carbonaceous material as heterogeneous catalyst.
SPIDER beam dump as diagnostic of the particle beam
Authors: Zaupa M. , Dalla Palma M. , Sartori E. , Brombin M. , Pasqualotto R.
Published: August 2016

The beam power produced by the negative ion source for the production of ion of deuterium extracted from RF plasma is mainly absorbed by the beam dump component which has been designed also for measuring the temperatures on the dumping panels for beam diagnostics. A finite element code has been developed to characterize, by thermo-hydraulic analysis, the sensitivity of the beam dump to the different beam parameters. The results prove the capability of diagnosing the beam divergence and the horizontal misalignment, while the entity of the halo fraction appears hardly detectable without considering the other foreseen diagnostics like tomography and beam emission spectroscopy.
A LIBS method for simultaneous monitoring of the impurities and the hydrogenic composition present in the wall of the TJ-II stellarator
Authors: López-Miranda B. , Zurro B. , Baciero A. , Martínez M.
Published: August 2016

The study of plasma-wall interactions and impurity transport in the plasma fusion devices is critical for the development of future fusion reactors. An experiment to perform laser induced breakdown spectroscopy, using minor modifications of our existing laser blow-off impurity injection system, has been set up thus making both experiments compatible. The radiation produced by the laser pulse focused at the TJ-II wall evaporates a surface layer of deposited impurities and the subsequent radiation produced by the laser-produced plasma is collected by two separate lens and fiber combinations into two spectrometers. The first spectrometer, with low spectral resolution, records a spectrum from 200 to 900 nm to give a survey of impurities present in the wall. The second one, with high resolution, is tuned to the wavelengths of the Hα and Dα lines in order to resolve them and quantify the hydrogen isotopic ratio present on the surface of the wall. The alignment, calibration, and spectral analysis method will be described in detail. First experimental results obtained with this setup will be shown and its relevance for the TJ-II experimental program discussed.
DMRG-CASPT2 study of the longitudinal static second hyperpolarizability of all-trans polyenes
Authors: Wouters Sebastian , Van Speybroeck Veronique , Van Neck Dimitri
Published: August 2016

We have implemented internally contracted complete active space second order perturbation theory (CASPT2) with the density matrix renormalization group (DMRG) as active space solver [Y. Kurashige and T. Yanai, J. Chem. Phys. 135, 094104 (2011)]. Internally contracted CASPT2 requires to contract the generalized Fock matrix with the 4-particle reduced density matrix (4-RDM) of the reference wavefunction. The required 4-RDM elements can be obtained from 3-particle reduced density matrices (3-RDM) of different wavefunctions, formed by symmetry-conserving single-particle excitations op top of the reference wavefunction. In our spin-adapted DMRG code chemps2 https://github.com/sebwouters/chemps2, we decompose these excited wavefunctions as spin-adapted matrix product states and calculate their 3-RDM in order to obtain the required contraction of the generalized Fock matrix with the 4-RDM of the reference wavefunction. In this work, we study the longitudinal static second hyperpolarizability of all-trans polyenes C2nH2n+2 [n = 4–12] in the cc-pVDZ basis set. DMRG-SCF and DMRG-CASPT2 yield substantially lower values and scaling with system size compared to RHF and MP2, respectively.
A novel method to recover DD fusion proton CR-39 data corrupted by fast ablator ions at OMEGA and the National Ignition Facility
Authors: Sutcliffe G. D. , Milanese L. M. , Orozco D. , Lahmann B. , Gatu Johnson M. , Séguin F. H. , Sio H. , Frenje J. A. , Li C. K. , Petrasso R. D. , Park H.-S. , Rygg J. R. , Casey D. T. , Bionta R. , Turnbull D. P. , Huntington C. M. , Ross J. S. , Zylstra A. B. , Rosenberg M. J. , Glebov V. Yu.
Published: August 2016

CR-39 detectors are used routinely in inertial confinement fusion (ICF) experiments as a part of nuclear diagnostics. CR-39 is filtered to stop fast ablator ions which have been accelerated from an ICF implosion due to electric fields caused by laser-plasma interactions. In some experiments, the filtering is insufficient to block these ions and the fusion-product signal tracks are lost in the large background of accelerated ion tracks. A technique for recovering signal in these scenarios has been developed, tested, and implemented successfully. The technique involves removing material from the surface of the CR-39 to a depth beyond the endpoint of the ablator ion tracks. The technique preserves signal magnitude (yield) as well as structure in radiograph images. The technique is effective when signal particle range is at least 10 μm deeper than the necessary bulk material removal.
High speed single- and dual-stage vertical positioners
Authors: Yong Yuen K. , Wadikhaye Sachin P. , Fleming Andrew J.
Published: August 2016

This article presents a high-speed single- and dual-stage vertical positioners for applications in optical systems. Each positioner employs a unique end-constraint method with orthogonal flexures to preload a piezoelectric stack actuator. This end-constraint method also significantly increases the first mechanical resonance frequency. The single-stage positioner has a displacement range of 7.6 μm and a first resonance frequency of 46.8 kHz. The dual-stage design consists of a long-range slow-stage and a short-range fast-stage. An inertial counterbalance technique was implemented on the fast-stage to cancel inertial forces resulting from high-speed motion. The dual-stage positioner has a combined travel range of approximately 10 μm and a first evident resonance frequency of 130 kHz.
Plasma mirrors for short pulse KrF lasers
Authors: Gilicze Barnabás , Barna Angéla , Kovács Zsolt , Szatmári Sándor , Földes István B.
Published: August 2016

It is demonstrated for the first time that plasma mirrors can be successfully applied for KrF laser systems. High reflectivity up to 70% is achieved by optimization of the beam quality on the plasma mirror. The modest spectral shift and the good reflected beam quality allow its applicability for high power laser systems for which a new arrangement is suggested.
Chemical sputtering by H2+ and H3+ ions during silicon deposition
Authors: Landheer K. , Goedheer W. J. , Poulios I. , Schropp R. E. I. , Rath J. K.
Published: August 2016

We investigated chemical sputtering of silicon films by Hy+ ions (with y being 2 and 3) in an asymmetric VHF Plasma Enhanced Chemical Vapor Deposition (PECVD) discharge in detail. In experiments with discharges created with pure H2 inlet flows, we observed that more Si was etched from the powered than from the grounded electrode, and this resulted in a net deposition on the grounded electrode. With experimental input data from a power density series of discharges with pure H2 inlet flows, we were able to model this process with a chemical sputtering mechanism. The obtained chemical sputtering yields were (0.3–0.4) ± 0.1 Si atom per bombarding Hy+ ion at the grounded electrode and at the powered electrode the yield ranged from (0.4 to 0.65) ± 0.1. Subsequently, we investigated the role of chemical sputtering during PECVD deposition with a series of silane fractions SF (SF(%) = [SiH4]/[H2]*100) ranging from SF = 0% to 20%. We experimentally observed that the SiHy+ flux is not proportional to SF but decreasing from SF = 3.4% to 20%. This counterintuitive SiHy+ flux trend was partly explained by an increasing chemical sputtering rate with decreasing SF and partly by the reaction between H3+ and SiH4 that forms SiH3+.
MAcro-Electro-Mechanical Systems (MÆMS) based concept for microwave beam steering in reflectarray antennas
Authors: Momeni Hasan Abadi Seyed Mohamad Amin , Booske John H. , Behdad Nader
Published: August 2016

We present a new approach to perform beam steering in reflecting type apertures such as reflectarray antennas. The proposed technique exploits macro-scale mechanical movements of parts of the structure to achieve two-dimensional microwave beam steering without using any solid-state devices or phase shifters integrated within the aperture of the antenna. The principles of operation of this microwave beam steering technique are demonstrated in an aperture occupied by ground-plane-backed, sub-wavelength capacitive patches with identical dimensions. We demonstrate that by tilting the ground plane underneath the entire patch array layer, a phase shift gradient can be created over the aperture of the reflectarray that determines the direction of the radiated beam. Changing the direction and slope of this phase shift gradient on the aperture allows for performing beam steering in two dimensions using only one control parameter (i.e., tilt vector of the ground plane). A proof-of-concept prototype of the structure operating at X-band is designed, fabricated, and experimentally characterized. Experiments demonstrate that small mechanical movements of the ground plane (in the order of 0.05λ0) can be used to steer the beam direction in the ±10° in two dimensions. It is also demonstrated that this beam scanning range can be greatly enhanced to ±30° by applying this concept to the same structure when its ground plane is segmented.
Origin of a Raman scattering peak generated in single-walled carbon nanotubes by X-ray irradiation and subsequent thermal annealing
Authors: Murakami Toshiya , Matsuda Mitsuaki , Kisoda Kenji , Itoh Chihiro
Published: August 2016

We have found that a Raman scattering (RS) peak around 1870 cm−1 was produced by the annealing of the X-ray irradiated film of single-walled carbon nanotubes (SWNTs) at 450 oC. The intensity of 1870-cm−1 peak showed a maximum at the probe energy of 2.3 eV for the RS spectroscopy with various probe lasers. Both the peak position and the probe-energy dependence were almost identical to those of the one-dimensional carbon chains previously reported in multi-walled carbon nanotubes. Consequently, we concluded that the 1870-cm−1 peak found in the present study is attributed to carbon chains. The formation of carbon chains by the annealing at temperature lower than 500 oC is firstly reported by the present study. The carbon chains would be formed by aggregation of the interstitial carbons, which are formed as a counterpart of carbon vacancies by X-ray irradiation diffused on SWNT walls. The result indicates that the combination of X-ray irradiation and subsequent thermal annealing is a feasible tool for generating new nanostructures in SWNT.
Long-term measurement of body temperature in the southern hairy-nosed wombat (Lasiorhinus latifrons)
Authors: Descovich K. A. , Johnston S. , Lisle A. , Nicolson V. , Janssen T. , Brooks P. , Phillips C. J. C.
Published: August 2016

The southern hairy-nosed wombat (Lasiorhinus latifrons) is a nocturnal, fossorial marsupial that has evolved a range of physiological and behavioural adaptations to its semiarid environment. This study describes long-term core body temperature (Tb) of L. latifrons in a population with opportunities for behavioural thermoregulation through burrow use. Tb was measured hourly in 12 captive L. latifrons using implanted dataloggers over a 9-month period from late winter to late autumn. Data were examined for daily patterns, seasonal changes, sex differences and the relationship with environmental conditions (ambient temperature, den temperature and relative humidity). Tb ranged from 30.9 to 38.8°C, and had a distinct nychthemeral rhythm, with peak temperatures occurring at night in line with nocturnal activity. Females had a higher mean Tb (34.9°C) than males (34.4°C). The relationship between external ambient temperature and body temperature was negative, with body temperature decreasing as ambient temperature increased. This study is an important step towards a comprehensive picture of thermoregulation in L. latifrons, which may become vulnerable in the future if environmental temperatures rise and water availability decreases.
Difficulties identifying Australian sea lions (Neophoca cinerea) in the wild using whisker spot patterns
Authors: Osterrieder Sylvia K. , Parnum Iain M. , Kent Chandra P. Salgado , Robinson Randall W.
Published: August 2016

Individual identification is a beneficial tool in behavioural and ecological research. In mark–recapture studies, for example, it can improve abundance, residency and site fidelity estimates. Two non-invasive, photo-identification approaches, using whisker spot patterns, were tested to identify wild individual Australian sea lions (Neophoca cinerea). The Chamfer distance transform algorithm has shown promising results when applied to captive individuals. An alternative matching method using row/column locations of whisker spots, previously applied to lions (Panthera leo) was also tested. Resighting wild N. cinerea in this study proved unfeasible with both methods. Excessive variation between photographs of the same individual was found when applying the Chamfer distance transform, and similarity between photograph-pairs appeared to decrease with increasing time between photographs. Insufficient variation among N. cinerea row/column pattern was detected to successfully discriminate among individuals, averaging 39 mystacial spots (range 30–46, n = 20) in seven rows and 9–10 columns. Additionally, different observers marking the same photographs introduced considerable variation. Colour difference (red, green and blue colour levels) between the whisker spots and surrounding fur affected marking spot locations significantly, increasing uncertainty when contrast decreased. While other pattern-matching algorithms may improve performance, accurate identification of spot locations was the current limitation.
Fire exclusion and soil texture interact to influence temperate grassland flora in south-eastern Australia
Authors: Moxham Claire , Dorrough Josh , Bramwell Mick , Farmilo Brad J.
Published: August 2016

Fire has a major influence on the structure and composition of temperate grasslands and woodlands. We investigated whether the impacts of fire exclusion on a temperate grassland plant community varied according to the scale of investigation and soil texture. Ten sites with known fire histories were selected along a soil texture gradient in south-eastern Australia. Floristics and ground layer attributes were investigated at small (0.25 m2) and large (100 m2) spatial scales in regularly burnt and unburnt grasslands. Fire exclusion over a 10 year period led to declines in native species diversity, richness and cover at both spatial scales and in most cases effects were consistent regardless of soil texture. However, the richness of native plant species at small scales and the cover of native plants at large scales were most negatively influenced by fire exclusion on fine textured soils. Conversely, at large scales, exotic plant richness and cover were only weakly increased by fire exclusion. Responses of eight common species were modelled and in seven of these, fire exclusion was a strong predictor of occurrence, although both positive and negative responses were observed. These results reiterate the importance of frequent fire as a management tool in temperate grasslands, but also shed light on how sites may require specific fire management regimes depending on the underlying soil texture.
Newly arrived refugee children with Helicobacter pylori are thinner than their non-infected counterparts
Authors: Benson Jill , Rahim Razlyn Abdul , Agrawal Rishi
Published: August 2016

The hypothesis of this study was that those refugee children with Helicobacter pylori are thinner than their non-infected counterparts. This cross-sectional study investigated the height and weight of newly arrived refugee children up to age 19 years, who were screened for H. pylori using a stool antigen test at the Migrant Health Service in Adelaide between August 2010 and October 2013. Of 460 children, 21% were infected with H. pylori. After adjusting for vitamin B12 and iron levels, ethnicity, age and sex, the odds of being thin in the 10- to 19-year-old age group was 4.28-fold higher (95% CI 1.48–12.4) if they were H. pylori positive compared with those who were H. pylori negative. The difference between the two groups is statistically significant (P=0.01). Screening and treatment for H. pylori in the general population in developed countries is not recommended unless there are symptoms such as dyspepsia or risk of peptic ulcer, duodenal ulcer or gastric cancer. Given the findings of this study, a recommendation could be made that newly arrived refugee children who are thin should be tested for H. pylori. Thinness in children may influence their cognitive ability, school performance, physical endurance and hence their ability to successfully settle into their new country.
Waltzing route toward double-helix formation in cholesteric shells
Authors: Darmon Alexandre , Benzaquen Michael , Seč David , Čopar Simon , Dauchot Olivier , Lopez-Leon Teresa
Published: August 2016

Significance

Droplets of chiral liquid crystals, or cholesterics, typically exhibit an intriguing radial defect which results from frustrations in the molecular order. This configuration shows a fascinating analogy to the Dirac monopole, a hypothetical magnetic charge, and plays a crucial role in the droplet optical properties, recently exploited to produce microlasers. Despite its evident interest, the nature of this disclination remains uncertain. We experimentally show, by studying spherical cholesteric shells, that it is composed of two line defects that wrap around each other on a double-helix structure. By tuning the system chirality, we can make this configuration dissociate into two independent stacks of disclination rings. The transition between configurations is reversible and entails an unexpected defect waltz dynamics.
Carbohydrate-binding domain of the POMGnT1 stem region modulates
O
-mannosylation sites of α-dystroglycan
Authors: Kuwabara Naoyuki , Manya Hiroshi , Yamada Takeyuki , Tateno Hiroaki , Kanagawa Motoi , Kobayashi Kazuhiro , Akasaka-Manya Keiko , Hirose Yuriko , Mizuno Mamoru , Ikeguchi Mitsunori , Toda Tatsushi , Hirabayashi Jun , Senda Toshiya , Endo Tamao , Kato Ryuichi
Published: August 2016

Significance

Congenital muscular dystrophy (CMD) is caused by hypoglycosylation of α-dystroglycan (α-DG). In some CMD patients, mutations in the gene encoding protein
O
-linked mannose β1,2-
N
-acetylglucosaminyltransferase 1,
POMGnT1
, are responsible for such hypoglycosylation. Many CMD-related genes are thought to be involved in the glycosylation of core M3, a specific
O
-mannose–type structure in α-DG. Although POMGnT1 has long been known to be associated with CMD, its role in the glycosylation of core M3 remains unclear. Our results reveal that the stem domain of POMGnT1 modulates
O
-mannosylation of α-DG via its carbohydrate-binding activity. These findings explain how POMGnT1 attaches β-GlcNAc to clustered
O
-mannose sites and influences postphosphoryl modification of core M3. Our study provides important insight into how disease-associated mutations cause CMD pathogenesis.
Basin‐Scale Variation in the Spatial Pattern of Fall Movement of Juvenile Coho Salmon in the West Fork Smith River, Oregon
Authors: Hance Dalton J. , Ganio Lisa M. , Burnett Kelly M. , Ebersole Joseph L.
Published: August 2016

For several species of salmonids, Oncorhynchus and Salvelinus spp., inhabiting Pacific coastal temperate streams, juvenile fish have been recorded moving between main‐stem and tributary habitats during the transition from the summer dry season to the winter wet season. Movement connecting summer and winter habitats may be particularly important for Coho Salmon O. kisutch because availability of overwintering habitat can limit freshwater survival for this species. Here, we describe basin‐scale variability in movement between main‐stem and tributary habitat for juvenile Coho Salmon tagged in the summer with PIT tags and detected in the fall at four stationary detection sites at tributary–main‐stem confluences of the West Fork Smith River, Oregon. We used odds ratios to evaluate spatial patterns in tributary–main‐stem movement across tributary junctions at upper‐river, midriver, and lower‐river locations. Three types of movement were assessed: (1) emigration out of tributaries into the main stem, (2) immigration into a tributary from the main stem downstream from the tributary junction, and (3) immigration from the main stem upstream from the tributary junction. The likelihood of emigration had a distinct spatial pattern. Only at the two upper‐river detection sites were juvenile Coho Salmon more likely to emigrate than immigrate. Fish immigrating into a midriver tributary were more likely to originate from the main stem downstream from the confluence, whereas fish immigrating into two lower‐river tributaries were more likely to originate from the main stem upstream from the confluence. This basin‐scale variation in patterns of immigration and emigration demonstrates complexity in the connectivity of juvenile Coho Salmon seasonal habitats within a stream network. We conclude that effective restoration planning and watershed management should account for the spatial pattern of connectivity of summer‐rearing and overwintering habitat throughout a stream network and consider the full diversity of movement patterns that may be required for fish to access seasonal habitats.

Received December 30, 2015; accepted May 4, 2016 Published online August 5, 2016
Investigation of idiomorphic ferrite and allotriomorphic ferrite using electron backscatter diffraction technique
Authors: Chi Y. T. , Tsai Y. T. , Huang B. M. , Yang J. R.
Published: August 2016

A heat treatment for a vanadium-containing steel involving high-temperature austenitisation followed by two-stage isothermal holding was deliberately conducted to produce allotriomorphic ferrite (ALF), idiomorphic ferrite (IDF) and martensite. The resulting microstructures and crystallographic relationships with respect to the parent austenite grains were examined using the electron backscatter diffraction technique. Results indicated that IDF grains did not possess a specific orientation relationship (OR) with respect to the surrounding austenite matrix. The detailed substructures of IDF were also examined. In contrast, the ALF grains had an approximate Kurdjumov–Sachs OR with respect to one or both of the adjacent austenite grains; the latter case was termed a dual OR and was analysed in detail.
Examining the Durability of Incidentally Learned Trust from Gaze Cues
Authors: Strachan James W. A. , Tipper Steven P.
Published: August 2016

In everyday interactions we find our attention follows the eye gaze of faces around us. As this cueing is so powerful and difficult to inhibit, gaze can therefore be used to facilitate or disrupt visual processing of the environment, and when we experience this we infer information about the trustworthiness of the cueing face. However, to date no studies have investigated how long these impressions last. To explore this we used a gaze-cueing paradigm where faces consistently demonstrated either valid or invalid cueing behaviours. Previous experiments show that valid faces are subsequently rated as more trustworthy than invalid faces. We replicate this effect (Experiment 1) and then include a brief interference task in Experiment 2 between gaze cueing and trustworthiness rating, which weakens but does not completely eliminate the effect. In Experiment 3, we explore whether greater familiarity with the faces improves the durability of trust learning and find that the effect is more resilient with familiar faces. Finally, in Experiment 4, we push this further and show that evidence of trust learning can be seen up to an hour after cueing has ended. Taken together, our results suggest that incidentally learned trust can be durable, especially for faces that deceive.
Endotoxin‐ and Mechanical Stress–Induced Epigenetic Changes in the Regulation of the Nicotinamide Phosphoribosyltransferase Promoter
Authors: Elangovan Venkateswaran Ramamoorthi , Camp Sara M. , Kelly Gabriel T. , Desai Ankit A. , Adyshev Djanybek , Sun Xiaoguang , Black Stephen M. , Wang Ting , Garcia Joe G. N.
Published: August 2016

Mechanical ventilation, a lifesaving intervention for patients with acute respiratory distress syndrome (ARDS), also unfortunately contributes to excessive mechanical stress and impaired lung physiological and structural integrity. We have elsewhere established the pivotal role of increased nicotinamide phosphoribosyltransferase (NAMPT) transcription and secretion as well as its direct binding to the toll‐like receptor 4 (TLR4) in the progression of this devastating syndrome; however, regulation of this critical gene in ventilator‐induced lung injury (VILI) is not well characterized. On the basis of an emerging role for epigenetics in enrichment of VILI and CpG sites within the NAMPT promoter and 5′UTR, we hypothesized that NAMPT expression and downstream transcriptional events are influenced by epigenetic mechanisms. Concomitantly, excessive mechanical stress of human pulmonary artery endothelial cells or lipopolysaccharide (LPS) treatment led to both reduced DNA methylation levels in the NAMPT promoter and increased gene transcription. Histone deacetylase inhibition by trichostatin A or Sirt‐1–silencing RNA attenuates LPS‐induced NAMPT expression. Furthermore, recombinant NAMPT administration induced TLR4‐dependent global H3K9 hypoacetylation. These studies suggest a complex epigenetic regulatory network of NAMPT in VILI and ARDS and open novel strategies for combating VILI and ARDS.
Notes on endpoint estimates for multilinear fractional integral operators
Authors: Komori-Furuya Yasuo
Published: August 2016

We prove the strong type estimates for the multilinear fractional integral operators of Kenig and Stein type at critical indices. Our results are optimal.
PcircRNA_finder: a software for circRNA prediction in plants
Authors: Chen Li , Yu Yongyi , Zhang Xinchen , Liu Chen , Ye Chuyu , Fan Longjiang
Published: August 2016

Motivation: Recent studies reveal an important role of non-coding circular RNA (circRNA) in the control of cellular processes. Because of differences in the organization of plant and mammal genomes, the sensitivity and accuracy of circRNA prediction programs using algorithms developed for animals and humans perform poorly for plants.

Results: A circRNA prediction software for plants (termed PcircRNA_finder) was developed that is more sensitive in detecting circRNAs than other frequently used programs (such as find_circ and CIRCexplorer), Based on analysis of simulated and real rRNA-/RNAase R RNA-Seq data from Arabidopsis thaliana and rice PcircRNA_finder provides a more comprehensive sensitive, precise prediction method for plants circRNAs.

Availability and Implementation:  http://ibi.zju.edu.cn/bioinplant/tools/manual.htm.

Contact:  fanlj@zju.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
FARAO: the flexible all-round annotation organizer
Authors: Hammarén Rickard , Pal Chandan , Bengtsson-Palme Johan
Published: August 2016

Summary: With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets.

Availability and Implementation: FARAO is implemented in Perl and is supported under Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download under the MIT License from http://microbiology.se/software/farao/.

Contact:  johan.bengtsson-palme@microbiology.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evolution trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper
Authors: Yin Wei , Wang Zong-ji , Li Qi-ye , Lian Jin-ming , Zhou Yang , Lu Bing-zheng , Jin Li-jun , Qiu Peng-xin , Zhang Pei , Zhu Wen-bo , Wen Bo , Huang Yi-jun , Lin Zhi-long , Qiu Bi-tao , Su Xing-wen , Yang Huan-ming , Zhang Guo-jie , Yan Guang-mei , Zhou Qi
Published: August 2016

Snake’s numerous fascinating features distinctive from other tetrapods necessitate a rich history of genome evolution that is still obscure. To address this, we report the first high-quality genome of a viper,Deinagkistrodon acutusand comparative analyses using other species from major snake and lizard lineages. We map the evolution trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion. And in the viper many TEs may have been rewired into the regulatory network of brain genes, as shown by their associated expression with nearby genes in the brain but not in other tissues. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes, and also functional degeneration of genes associated with vision and hearing. ManyHoxandTbxlimb-patterning genes show evidence of relaxed selective constraints, and such genes’ phylogenetic distribution supports fossil evidence for a successive loss of forelimbs then hindlimbs during the snake evolution. Finally, we infer that the Z and W sex chromosomes had undergone at least three recombination suppression events at the ancestor of advanced snakes, with the W chromosomes showing a gradient of degeneration from basal to advanced snakes. These results, together with all the genes identified as undergoing adaptive or degenerative evolution episodes at respective snake lineages forge a framework for our deep understanding into snakes’ molecular evolution history.
Ultraslow water-mediated transmembrane interactions regulate the activation of A2Aadenosine receptor
Authors: Lee Yoonji , Kim Songmi , Choi Sun , Hyeon Changbong
Published: August 2016

Water molecules inside G-protein coupled receptor have recently been spotlighted in a series of crystal structures. To decipher the dynamics and functional roles of internal waters in GPCR activity, we studied A2Aadenosine receptor usingμsec-molecular dynamics simulations. Our study finds that the amount of water flux across the transmembrane (TM) domain varies depending on the receptor state, and that the water molecules of the TM channel in the active state flow three times slower than those in the inactive state. Depending on the location in solvent-protein interface as well as the receptor state, the average residence time of water in each residue varies frompsec tonsec. Especially, water molecules, exhibiting ultraslow relaxation (nsec) in the active state, are found around the microswitch residues that are considered activity hotspots for GPCR function. A continuous allosteric network spanning the TM domain, arising from water-mediated contacts, is unique in the active state, underscoring the importance of slow waters in the GPCR activation.
Genetic Diversity, Population Structure and Species Delimitation ofTrialeurodes vaporariorum(greenhouse whitefly)
Authors: Wainaina J. M. , De Barro P. , Kubatko L. , Kehoe M. A. , Harvey J. , Karanja D. , Boykin L. M.
Published: August 2016

Genetic diversity withinTrialeurodes vaporariorum(Westwood, 1856) remains largely unexplored, particularly within regions of Sub-Saharan Africa. In this study,T. vaporariorumsamples were obtained from three locations in Kenya: Katumani, Kiambu and Kajiado counties. DNA extraction, PCR and Sanger sequencing were carried out on ~750 bp fragment of the mitochondria cytochrome c oxidase I (COI) gene from individual whiteflies. In addition, global populations were assessed and 19 haplotypes were identified, with three main haplotypes (Hp_19, Hp_10, Hp_011) circulating within Kenya. Measures of genetic diversity amongT. vaporariorumpopulations resulted in haplotype diversity of 0.411, nucleotide diversity 0.00096, and Tajima’s D -0. 30315, (P>0.10). Analysis of population structure across global sequences using Structurama indicated one population globally, with posterior probability of 0.72. Bayesian and maximum likelihood phylogenetic analysis gave support for two clades (Clade I = an admixed global population and Clade II = subset of Kenyan and 1 Greek sequence). Species delimitation between the two clades was assessed by four parameters; posterior probability, Kimura’s two parameter (K2P), Rodrigo’s P (Randomly distinct) and Rosenberg’s reciprocal monophyly (P(AB). The two clades within the phylogenetic tree showed evidence of distinctness based on; Kimura two parameters (K2P) (p = -1.21E-01), Rodrigo’s P (RD) (p =0.05) and Rosenberg’s P(AB) (p = 2.3E -13). Overall, low genetic diversity within the Kenyan samples is a likely indicator of recent population expansion and colonization with this region and plausible signs of species complex formation in Sub-Saharan Africa.
Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls
Authors: Rost Fabian , Albors Aida Rodrigo , Mazurov Vladimir , Brusch Lutz , Deutsch Andreas , Tanaka Elly M. , Chara Osvaldo
Published: August 2016

Axolotls are unique in their ability to regenerate the spinal cord. However, the mechanisms that underlie this phenomenon remain poorly understood. Previously, we showed that resting stem cells in the axolotl spinal cord revert to a molecular state resembling embryonic neuroepithelial cells and functionally acquire rapid proliferative divisions during regeneration. Here we refine in space and time this increase in cell proliferation during regeneration, and identify a dynamic high-proliferation zone in the regenerating spinal cord. By tracking sparsely-labeled cells, we quantify cell influx into the regenerate. Taking a mathematical modelling approach, we integrate these quantitative biological datasets across cellular and tissue level to provide a mechanistic and quantitative understanding of regenerative spinal cord outgrowth. We find that the acceleration of the cell cycle is necessary and sufficient to drive the outgrowth of the regenerating spinal cord in axolotls.
BayesFM: a software program to fine-map multiple causative variants in GWAS identified risk loci
Authors: Fang Ming , Georges Michel
Published: August 2016

Absract

We herein describe a new method to fine-map GWAS-identified risk loci based on the Bayesian Least Absolute Shrinkage Selection Operator (LASSO) combined with a Monte Carlo Markov Chain (MCMC) approach, and corresponding software package (BayesFM). We characterize the performances of BayesFM using simulated data, showing that it outperforms standard forward selection both in terms of sensitivity and specificity. We apply the method to theNOD2locus, a well-established risk locus for Crohn’s disease, in which we identify 13 putative independent signals.
An RNA-binding tropomyosin recruits kinesin-1 dynamically tooskarmRNPs
Authors: Gáspár Imre , Sysoev Vasily , Komissarov Artem , Ephrussi Anne
Published: August 2016

Localization and local translation ofoskarmRNA at the posterior pole of theDrosophilaoocyte directs abdominal patterning and germline formation in the embryo. The process requires recruitment and precise regulation of motor proteins to form transport-competent mRNPs. We show that the posterior-targeting kinesin-1 is loaded upon nuclear export ofoskarmRNPs, prior to their dynein-dependent transport from the nurse cells into the oocyte. We demonstrate that kinesin-1 recruitment requires theDmTropomyosin1-I/C isoform, an atypical RNA-binding tropomyosin that binds directly to dimerizingoskar3’UTRs. Finally, we show that a small but dynamically changing subset ofoskarmRNPs gets loaded with inactive kinesin-1 and that the motor is activated during mid-oogenesis by the functionalized splicedoskarRNA localization element. This inefficient, dynamic recruitment of Khc decoupled from cargo-dependent motor activation constitutes an optmized, coordinated mechanism of mRNP transport, by minimizing interference with other cargo-transport processes and between the cargo associated dynein and kinesin-1.