bluuebunny/crossref_metadata_2025 huggingface dataset:
Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection
Authors: Stettler Karin , Beltramello Martina , Espinosa Diego A. , Graham Victoria , Cassotta Antonino , Bianchi Siro , Vanzetta Fabrizia , Minola Andrea , Jaconi Stefano , Mele Federico , Foglierini Mathilde , Pedotti Mattia , Simonelli Luca , Dowall Stuart , Atkinson Barry , Percivalle Elena , Simmons Cameron P. , Varani Luca , Blum Johannes , Baldanti Fausto , Cameroni Elisabetta , Hewson Roger , Harris Eva , Lanzavecchia Antonio , Sallusto Federica , Corti Davide
Published: July 2016

Characterizing the Zika virus antibody response

Given the public health emergency that Zika virus poses, scientists are seeking to understand the Zika-specific immune response. Stettler
et al.
analyzed 119 monoclonal antibodies isolated from four donors that were infected with Zika virus during the present epidemic, including two individuals that had previously been infected with dengue virus, another member of the flavivirus family. Neutralizing antibodies primarily recognized the envelope protein domain III (EDIII) or quaternary epitopes on the intact virus, and an EDIII-targeted antibody protected mice against lethal infection. Some EDI/II-targeting antibodies cross-reacted with dengue virus in vitro and could enhance disease in dengue-infected mice. Whether dengue and Zika virus antibodies cross-react in humans remains to be tested.

Science
, this issue p.
823
An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation
Authors: Schur Florian K. M. , Obr Martin , Hagen Wim J. H. , Wan William , Jakobi Arjen J. , Kirkpatrick Joanna M. , Sachse Carsten , Kräusslich Hans-Georg , Briggs John A. G.
Published: July 2016

Maturation and inhibition of HIV-1

HIV-1 undergoes a two-step assembly process controlled largely by a single region of its Gag protein. Schur
et al.
determined a complete atomic model for this region within an assembled Gag protein lattice using cryo-electron tomography together with subtomogram averaging. Amino acids from different parts of multiple Gag molecules come together to form an intricate network of interactions that drive HIV-1 assembly. The final step of maturation into the infectious HIV-1 virus is controlled by structural changes in Gag that alter the accessibility of the final cleavage site to the viral protease.

Science
, this issue p.
506
Draft Genome Sequences of Two
Aspergillus fumigatus
Strains, Isolated from the International Space Station
Authors: Singh Nitin Kumar , Blachowicz Adriana , Checinska Aleksandra , Wang Clay , Venkateswaran Kasthuri
Published: July 2016

Draft genome sequences of
Aspergillus fumigatus
strains (ISSFT-021 and IF1SW-F4), opportunistic pathogens isolated from the International Space Station (ISS), were assembled to facilitate investigations of the nature of the virulence characteristics of the ISS strains to other clinical strains isolated on Earth.
Draft Genome Sequence of
Salmonella enterica
subsp.
enterica
Serovar Lille Strain CRJJGF_000101 (Phylum
Gammaproteobacteria
)
Authors: Gupta Sushim K. , McMillan Elizabeth A. , Jackson Charlene R. , Desai Prerak T. , Porwollik Steffen , McClelland Michael , Hiott Lari M. , Humayoun Shaheen B. , Frye Jonathan G.
Published: July 2016

Here, we report a 4.98 Mbp draft genome sequence of
Salmonella enterica
subsp.
enterica
serovar Lille strain CRJJGF_000101, isolated from ground beef in 2007.
Draft Whole-Genome Sequence of the Type Strain
Bacillus horikoshii
DSM 8719
Authors: Hernández-González Ismael L. , Olmedo-Álvarez Gabriela
Published: July 2016

Members of the
Bacillus
genus have been extensively studied because of their ability to produce enzymes with high biotechnological value. Here, we report the draft of the whole-genome sequence of the type strain
Bacillus horikoshii
DSM 8719, an alkali-tolerant strain.
Whole-Genome Sequence of
Escherichia coli
Serotype O157:H7 Strain EDL932 (ATCC 43894)
Authors: Uhlich Gaylen A. , Paoli George C. , Chen Chin-Yi , Cottrell Bryan J. , Zhang Xinmin , Yan Xianghe
Published: July 2016

The genome sequence of
Escherichia coli
serotype O157:H7 EDL933, a ground beef isolate from a 1983 hemorrhagic colitis outbreak, is a standard reference for comparative genomic studies of Shiga toxin-producing
E. coli
strains. Here, we report the genome sequence of a patient stool isolate from that outbreak, strain EDL932.
Complete Genome Sequence of
Bacillus velezensis
CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea
Authors: Hwangbo Kyeong , Um Yurry , Kim Ki Yoon , Madhaiyan Munusamy , Sa Tong Min , Lee Yi
Published: July 2016

Bacillus velezensis
CBMB205 (= KACC 13105
T
= NCCB 100236
T
) was isolated from the rhizoplane of rice (
Oryza sativa
L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of
B. velezensis
CBMB205.
Complete Genome Sequence of
Sphingomonas
sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium
Authors: Zhu Xiongyu , Wang Weiwei , Xu Ping , Tang Hongzhi
Published: July 2016

Sphingomonas
sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from tobacco leaves. Here, we present the complete genome sequence of strain NIC1, which contains one circular chromosome and two circular plasmids. The genomic information will provide insights into its molecular mechanism for nicotine degradation.
Whole-Genome Sequence of
Filimonas lacunae,
a Bacterium of the Family
Chitinophagaceae
Characterized by Marked Colony Growth under a High-CO
2
Atmosphere
Authors: Shiratori-Takano Hatsumi , Takano Hideaki , Ueda Kenji
Published: July 2016

We report here the genome sequence of
Filimonas lacunae
, a bacterium of the family
Chitinophagaceae
characterized by high-CO
2
-dependent growth. The 7.81-Mb circular genome harbors many genes involved in carbohydrate degradation and related genetic regulation, suggesting the role of the bacterium as a carbohydrate degrader in diverse environments.
Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type)
Emiliania huxleyi
CCMP1516
Authors: Orata Fabini D. , Rosana Albert Remus R. , Xu Yue , Simkus Danielle N. , Bramucci Anna R. , Boucher Yan , Case Rebecca J.
Published: July 2016

Strains of
Sulfitobacter
spp.,
Erythrobacter
sp., and
Marinobacter
sp. were isolated from a polymicrobial culture of the naked (N-type) haptophyte
Emiliania huxleyi
strain CCMP1516. The genomes encode genes for the production of phytohormones, vitamins, and the consumption of their hosts' metabolic by-products, suggesting symbiotic interactions within this polymicrobial culture.
Transvenous ethanol sclerotherapy of feeding arteries for treatment of a dural arteriovenous fistula
Authors: Alexander Matthew David , Halbach Van , Nicholson Andrew , Settecase Fabio , Darflinger Robert J , Amans Matthew R
Published: July 2016

Dural arteriovenous fistulas (DAVFs) can be complex lesions that require a well trained eye for proper characterization and management decisions. With numerous possible arteries to supply and veins to drain them, DAVFs are often complex lesions. To best treat these complex lesions, the neurointerventionalist should be adept at treating them with multiple techniques. This report describes a unique case in which a DAVF was treated with arterial sclerotherapy using ethanol from a transvenous approach.
Intramesosigmoid hernia complicated by strangulated small-bowel obstruction
Authors: Kheok Si Wei , Haja Mohideen Salahudeen Mohd , Lim Jason Wei-Min , Santhosh Raj Seela Raj
Published: July 2016

An intramesosigmoid hernia is 1 of the 3 rare types of sigmoid-related hernias that could be complicated by intestinal obstruction. Our patient presented with a clinical picture of intestinal obstruction. CT scan showed features of strangulated small-bowel obstruction secondary to a sigmoid-related hernia. This was confirmed intraoperatively to be an intramesosigmoid hernia. We share the radiological findings with intraoperative surgical correlation and discuss the imaging features described in the literature.
PERS&O (PERsistent Sitagliptin treatment & Outcomes): observational retrospective study on cardiovascular risk evolution in patients with type 2 diabetes on persistent sitagliptin treatment
Authors: Buonaiuto Giulia , De Mori Valentina , Braus Alessandra , Balini Annalisa , Berzi Denise , Carpinteri Rita , Forloni Franco , Meregalli Giancarla , Ronco Gian Luca , Bossi Antonio C
Published: July 2016

Objectives

The UK Prospective Diabetes Study (UKPDS) Risk Engine (RE) provides the best risk estimates available for people with type 2 diabetes (T2D), so it was applied to patients on persistent sitagliptin treatment.

Design

A ‘real-world’ retrospective, observational, single-center study.

Setting

The study was performed in a general hospital in Northern Italy in order: (1) to validate UKPDS RE in a cohort of Italian participants with T2D without prespecified diabetes duration, with/without cardiovascular (CV) disease, treated with sitagliptin; (2) to confirm CV risk gender difference; (3) to evaluate the effect on metabolic control and on CV risk evolution obtained by ‘add-on’ persistent sitagliptin treatment.

Participants

Sitagliptin 100 mg once a day was taken by 462 participants with T2D: 170 of them (males: 106; age: 63.6±8.8; T2D duration: 11.58±7.33; females: 64; age: 65.6±7.95; T2D duration 13.5±7.9) were treated for 48 months with the same dosage.

Interventions

An analysis of normality was performed both for continuous, and for groups variables on UKPDS RE percentage values, defining the requirement of a base log10transformation to normalize risk factor values for analysis validation.

Results

The evaluation of CV risk evolution by gender (t-test) confirmed the expected statistical difference (p<0.0001). Sitagliptin obtained significant results after 12 months, and at the end of the observation, both on metabolic control (expressed by glycated hemoglobin) and on UKPDS RE. Analysis of variance test revealed a significant effect on CV risk after 12 months (p=0.003), and after 48 months (p=0.04). A bivariate correlation analysis revealed a correlation index (r)=0.2 between the two variables (p<0.05).

Conclusions

These ‘real-world’ data obtained applying UKPDS RE may reflect patients’ and clinicians’ interest in realizing individual CV risk, and its evolution. Sitagliptin-persistent treatment for a medium–long period obtained an improvement on metabolic control, as well as a reduction on CV risk.
Physicians' assessments of work capacity in patients with severe subjective health complaints: a cross-sectional study on differences between five European countries
Authors: Werner Erik L , Merkus Suzanne L , Mæland Silje , Jourdain Maud , Schaafsma Frederieke , Canevet Jean Paul , Weerdesteijn Kristel H N , Rat Cédric , Anema Johannes R
Published: July 2016

Objectives

A comparison of appraisals made by general practitioners (GPs) in France and occupational physicians (OPs) and insurance physicians (IPs) in the Netherlands with those made by Scandinavian GPs on work capacity in patients with severe subjective health complaints (SHCs).

Setting

GPs in France and OPs/IPs in the Netherlands gathered to watch nine authentic video recordings from a Norwegian general practice.

Participants

46 GPs in France and 93 OPs/IPs in the Netherlands were invited to a 1-day course on SHC.

Outcomes

Recommendation of sick leave (full or partial) or no sick leave for each of the patients.

Results

Compared with Norwegian GPs, sick leave was less likely to be granted by Swedish GPs (OR 0.51, 95% CI 0.30 to 0.86) and by Dutch OPs/IPs (OR 0.53, 95% CI 0.37 to 0.78). The differences between Swedish and Norwegian GPs were maintained in the adjusted analyses (OR 0.43, 95% CI 0.23 to 0.79). This was also true for the differences between Dutch and Norwegian physicians (OR 0.55, 95% CI 0.36 to 0.86). Overall, compared with the GPs, the Dutch OPs/IPs were less likely to grant sick leave (OR 0.60, 95% CI 0.45 to 0.87).

Conclusions

Swedish GPs and Dutch OPs/IPs were less likely to grant sick leave to patients with severe SHC compared with GPs from Norway, while GPs from Denmark and France were just as likely to grant sick leave as the Norwegian GPs. We suggest that these findings may be due to the guidelines on sick-listing and on patients with severe SHC which exist in Sweden and the Netherlands, respectively. Differences in the working conditions, relationships with patients and training of specialists in occupational medicine may also have affected the results. However, a pattern was observed in which of the patients the physicians in all countries thought should be sick-listed, suggesting that the physicians share tacit knowledge regarding sick leave decision-making in patients with severe SHC.
Complex social intervention for multidisciplinary teams to improve patient referrals in obstetrical care: protocol for a stepped wedge study design
Authors: Romijn Anita , de Bruijne Martine C , Teunissen Pim W , de Groot Christianne J M , Wagner Cordula
Published: July 2016

Introduction

In obstetrics, patients often experience referral situations between different care professionals. In these multidisciplinary teams, a focus on communication and interprofessional collaboration is needed to ensure care of high quality. Crew resource management team training is increasingly being applied in healthcare settings to improve team performance and coordination. Efforts to improve communication also include tools for standardisation such as SBAR (situation, background, assessment, recommendation). Despite the growing adoption of these interventions, evidence on their effectiveness is limited, especially on patient outcomes. This article describes a study protocol to examine the effectiveness of a crew resource management team training intervention aimed at implementing the SBAR tool for structured communication during patient referrals in obstetrical care.

Methods and analysis

The intervention is rolled out sequentially in five hospitals and surrounding primary care midwifery practices in the Netherlands, using a stepped wedge design. The intervention involves three phases over a period of 24 months: (1) preparation, (2) training and (3) follow-up with repeated measurements. The primary outcomes are perinatal and maternal outcomes calculated using the Adverse Outcome Index. The secondary outcomes are the reaction of participating professionals to the training programme, attitudes towards safety and teamwork (Safety Attitudes Questionnaire), cohesion (Interprofessional Collaboration Measurement Scale), use of the tool for structured communication (self-reported questionnaire) and patient experiences. These secondary outcomes from professional and patient level allow triangulation and an increased understanding of the effect of the intervention on patient outcomes.

Ethics and dissemination

The study was approved by the Medical Ethical Committee of the VU University Medical Centre in the Netherlands and the protocol is in accordance with Dutch privacy regulations. Study findings will be presented in publications in peer-reviewed journals and presentations at scientific conferences.

Trial registration number

NTR4256; Pre-results.
Second‐year student diary
Authors: Perrett Rosie
Published: July 2016

Directly after her exams finished, Rosie Perrett started EMS. She wrote her diary one month in, with her exam results due within days. She reveals how she was feeling as results day approached.
Flow behavior downstream of two side-by-side circular cylinders in shallow water
Authors: Akar Mustafa Atakan , Oguz Burcu , Akilli Huseyin , Sahin Besir
Published: July 2016

Investigations of bistable flow structure past a pair of cylinders positioned side-by-side in shallow water is conducted experimentally applying dye observation and the particle image velocimetry (PIV) method. For the gap ratio of G/D = 1.25, the jet-like flow between cylinders deflects asymmetrical flow structures forming a large-scale wake as well as a small-scale wake downstream of cylinders. The small vortices around the right cylinder get closer to each other forming a larger vortex in the large-scale wake region, which leads the jet-like flow to changeover side to side. The small frequency (f = 0.352 Hz) associated with frequency of vortex shedding of cylinder with wider wake and the higher frequency (f = 0.793 Hz) which depicts the smaller wakes frequency.
Synergistic effect in B and N co-doped Ib-type diamond single crystal: A density function theory calculation
Authors: Zongbao Li , Yong Li , Ying Wang , xia Wang
Published: July 2016

Using the first principles density functional theory, diamond crystal doping with B or N atoms, and B/N with different ratios were investigated, based on previous experimental structure results. The formation energies were calculated while the most stable doped structures were obtained for the lowest energy. For comparison, the electronic structures and the micro-mechanism of the doping crystals were discussed. The electronic results show that the doping of N atom is prior to B while the symmetry B–N–B stable structure appears with the N:B = 1:2 doping ratio. And also, the absorption spectrum gives the same results with the experiment for the distinct redshift.
Emergence of Narrowband High Frequency Oscillations from Asynchronous, Uncoupled Neural Firing
Authors: Gliske Stephen V. , Stacey William C. , Lim Eugene , Holman Katherine A. , Fink Christian G.
Published: July 2016

Previous experimental studies have demonstrated the emergence of narrowband local field potential oscillations during epileptic seizures in which the underlying neural activity appears to be completely asynchronous. We derive a mathematical model explaining how this counterintuitive phenomenon may occur, showing that a population of independent, completely asynchronous neurons may produce narrowband oscillations if each neuron fires quasi-periodically, without requiring any intrinsic oscillatory cells or feedback inhibition. This quasi-periodicity can occur through cells with similar frequency–current ([Formula: see text]–[Formula: see text]) curves receiving a similar, high amount of uncorrelated synaptic noise. Thus, this source of oscillatory behavior is distinct from the usual cases (pacemaker cells entraining a network, or oscillations being an inherent property of the network structure), as it requires no oscillatory drive nor any specific network or cellular properties other than cells that repetitively fire with continual stimulus. We also deduce bounds on the degree of variability in neural spike-timing which will permit the emergence of such oscillations, both for action potential- and postsynaptic potential-dominated LFPs. These results suggest that even an uncoupled network may generate collective rhythms, implying that the breakdown of inhibition and high synaptic input often observed during epileptic seizures may generate narrowband oscillations. We propose that this mechanism may explain why so many disparate epileptic and normal brain mechanisms can produce similar high frequency oscillations.
Vanishing theorems of generalized Witten genus for generalized complete intersections in flag manifolds
Authors: Zhuang Xiaobo
Published: July 2016

We propose a potential function [Formula: see text] for the cohomology ring of partial flag manifolds. We prove a formula expressing integrals over partial flag manifolds by residues, which generalizes [E. Witten, The Verlinde algebra and the cohomology of the Grassmannian, in Geometry, Topology, Physics (International Press, 1995), pp. 357–422]. Using this formula, we prove a Landweber–Stong type vanishing theorem for generalized [Formula: see text] complete intersections in flag manifolds, which serves as evidence for the [Formula: see text] version of Stolz conjecture [Q. Chen, F. Han and W. Zhang, Generalized Witten genus and vanishing theorems, J. Differential Geom. 88(1) (2011) 1–39].
Measure expansive symplectic diffeomorphisms and Hamiltonian systems
Authors: Lee Manseob , Park Junmi
Published: July 2016

Let [Formula: see text] be a [Formula: see text]-dimensional ([Formula: see text]), compact smooth Riemannian manifold endowed with a symplectic form [Formula: see text]. In this paper, we show that, if a symplectic diffeomorphism [Formula: see text] is [Formula: see text]-robustly measure expansive, then it is Anosov and a [Formula: see text] generic measure expansive symplectic diffeomorphism [Formula: see text] is mixing Anosov. Moreover, for a Hamiltonian systems, if a Hamiltonian system [Formula: see text] is robustly measure expansive, then [Formula: see text] is Anosov.
Extracting Information in Agricultural Data Using Fuzzy-Rough Sets Hybridization and Clonal Selection Theory Inspired Algorithms
Authors: Lasisi Ayodele , Ghazali Rozaida , Deris Mustafa Mat , Herawan Tutut , Lasisi Fola
Published: July 2016

Mining agricultural data with artificial immune system (AIS) algorithms, particularly the clonal selection algorithm (CLONALG) and artificial immune recognition system (AIRS), form the bedrock of this paper. The fuzzy-rough feature selection (FRFS) and vaguely quantified rough set (VQRS) feature selection are coupled with CLONALG and AIRS for improved detection and computational efficiencies. Comparative simulations with sequential minimal optimization and multi-layer perceptron reveal that the CLONALG and AIRS produced significant results. Their respective FRFS and VQRS upgrades namely, FRFS-CLONALG, FRFS-AIRS, VQRS-CLONALG, and VQRS-AIRS, are able to generate the highest detection rates and lowest false alarm rates. Thus, gathering useful information with the AIS models can help to enhance productivity related to agriculture.
Performance Enhancement of a Multichannel Uncoordinated Code Hopping DSSS Signaling Scheme Using Multipath Fading Compensator
Authors: Kalita S. , Kaushik R. , Jajoo M. , Sahu P. P.
Published: July 2016

In this paper, a multipath fading compensator(MFC) has been introduced and demonstrated to reduce the signal distortion which arose due to Doppler effect, multipath propagation and self-interference for a multichannel uncoordinated code hopping direct sequence spread spectrum (UCH-DSSS) signaling in underwater communication. The bit error rate (BER) performance analysis of the proposed system obtained both analytically and using P-Spice circuit simulation model with and without jamming signal is presented. It is observed that the BER is independent of the frequencies (used in focused acoustic field (FAF) experiments FAF-06 and FAF-05) and is also less than those of the previous works. Oscilloscope traces indicate that the experimental waveform of the proposed four-channel UCH-DSSS transceiver is almost close to those obtained using P-Spice circuit simulation. The experimental values of BER measured by BER meter also matched well with the BER obtained theoretically. Noise margin and distortion performance also are analyzed from the eye pattern which shows that noise margin and distortion also are independent of frequencies (used in both FAF-06 and FAF-05) and the bandwidth of operation of FAF-06 is [Formula: see text]5.5 times more than that of FAF-05.
Electronic Circuit Experiments and SPICE Simulation of Double Covering Bifurcation of 2-Torus Quasi-Periodic Flow in Phase-Locked Loop Circuit
Authors: Kamiyama Kyohei , Endo Tetsuro , Imai Isao , Komuro Motomasa
Published: July 2016

Double covering (DC) bifurcation of a 2-torus quasi-periodic flow in a phase-locked loop circuit was experimentally investigated using an electronic circuit and via SPICE simulation; in the circuit, the input radio-frequency signal was frequency modulated by the sum of two asynchronous sinusoidal baseband signals. We observed both DC and period-doubling bifurcations of a discrete map on two Poincaré sections, which were realized by changing the sample timing from one baseband sinusoidal signal to the other. The results confirm the DC bifurcation of the original flow.
Local Entropy, Metric Entropy and Topological Entropy for Countable Discrete Amenable Group Actions
Authors: Ren Xiankun , Sun Wenxiang
Published: July 2016

Let [Formula: see text] be a compact metric space and [Formula: see text] a countable infinite discrete amenable group acting on [Formula: see text]. Like in the [Formula: see text]-action cases we define the notion of local entropy and by it we bound the difference between metric entropy and that of a partition, and bound the difference between topological entropy and that of a separated set, which generalize Theorems 1(1) and 1(2) in [Newhouse, 1989] from [Formula: see text]-actions to amenable group actions. We further prove that the entropy function [Formula: see text] is upper semi-continuous on [Formula: see text] for an asymptotic entropy expansive amenable group action.
Stability and Bifurcation Analysis in a Diffusive Brusselator-Type System
Authors: Liao Maoxin , Wang Qi-Ru
Published: July 2016

In this paper, the dynamic properties for a Brusselator-type system with diffusion are investigated. By employing the theory of Hopf bifurcation for ordinary and partial differential equations, we mainly obtain some conditions of the stability and Hopf bifurcation for the ODE system, diffusion-driven instability of the equilibrium solution, and the direction of the Hopf bifurcation and the stability of the bifurcating periodic solutions for the PDE system. Finally, some numerical simulations are presented to verify our results.
Dynamics of the Zeraoulia–Sprott Map Revisited
Authors: Chen Guanrong , Kudryashova Elena V. , Kuznetsov Nikolay V. , Leonov Gennady A.
Published: July 2016

In the paper “Some Open Problems in Chaos Theory and Dynamics” by Zeraoulia and Sprott, the two-dimensional map [Formula: see text] was considered and the problem on the analytical study of the boundedness of its attractors was formulated. In the present paper, the boundedness of its attractors is studied, the corresponding analytical estimation of absorbing set is obtained, and thus an answer to the problem is given.
IMPURITY INDUCED WRINKLING PATTERNS IN METAL FILMS DEPOSITED ON SOFT ELASTIC SUBSTRATES
Authors: ZHANG YONG-JU , YU SEN-JIANG , CHEN MIAO-GEN , CAI PING-GEN , ZHOU HONG
Published: July 2016

Metal (iron and nickel) films have been deposited on soft elastic polydimethylsiloxane (PDMS) substrates by direct current sputtering technique and the impurity induced wrinkling patterns are investigated by using optical microscopy and atomic force microscopy. It is found that the metal films can spontaneously form disordered wrinkles due to the isotropic compressive stress. In the vicinity of film impurities such as extraneous particles, linear defects, cracks and thickness-gradient film edges, the stress field becomes anisotropic owing to symmetry breaking and thus complex wrinkling patterns including straight stripes, herringbones, crossings, labyrinths and their transitions can be observed. The morphological evolutions, structural characteristics and physical mechanisms of the impurity induced wrinkles have been discussed and analyzed based on the continuum elastic theory.
A theoretical study on the antioxidant properties of methoxy-substituted chalcone derivatives: A case study of kanakugiol and pedicellin through their Fe (II and III) coordination ability
Authors: Serobatse Kemoabetswe R. N. , Kabanda Mwadham M.
Published: July 2016

A theoretical study on the antioxidant properties of two chalcone derivatives, kanakugiol and pedicellin, is performed by considering their Fe[Formula: see text] and Fe[Formula: see text] coordination ability. The objective of the study is to elucidate the factors influencing the stability of the isolated conformers, the nature of the complexes, metal[Formula: see text]ligand stability, metal ion affinities (MIA) and electronic properties of the cations before and after coordination to the ligand. The study is performed using the B3LYP/6–311[Formula: see text]G(2d,p)//B3LYP/6–31[Formula: see text]G(d,p) method. The LANL2DZ pseudopotential is selected to describe the Fe[Formula: see text] ions. Time-dependent density functional theory (TDDFT) method is used to assess the electronic UV–Vis spectra of the isolated chalcones and their complexes with Fe[Formula: see text] ions. The results suggest that the preferred complexes are those in which the Fe ion is coordinated at the hydroxyl-methoxy and hydroxyl-keto sites for kanakugiol and methoxy-keto site for pedicellin. Both kanakugiol and pedicellin have potential to chelate iron ions as demonstrated by their high MIA values in vacuo and in water solution. However, the ability of pedicellin to chelate iron is slightly lower than that of kanakugiol, indicating that the presence of the hydroxyl group has an effect of enhancing the metal binding abilities of the chalcone derivatives. In all the complexes obtained in vacuo, kanakugiol and pedicellin exhibit the ability to reduce the Fe[Formula: see text] ion. In water solution (which mimics the environment in biological systems or studies performed in vivo), Fe[Formula: see text] is reduced to Fe[Formula: see text] upon coordination to the ligand while the oxidation number of Fe[Formula: see text] upon coordination to the ligand remains virtually unchanged.
A model on the biological treatment of saline wastewater
Authors: Goyal Ashish , Sharma Pawan
Published: July 2016

Water scarcity is not a new issue, neither is water pollution. While 70% of the earth’s surface is covered with water, only 3% of it is available as fresh water. Moreover the pollution of water resources has dramatically increased the problem of water scarcity over the last century. Bioremediation presents a cheap and effective solution of this problem. In particular, halophiles have been found to be effective in hypersaline wastewater treatment. Therefore, in this paper, we propose a nonlinear mathematical model to study the removal of a pollutant using halophiles in the hypersaline environment. The analysis of the model is being carried out using stability theory of differential equations. The results indicate that halophiles not only help in removing the organic pollutant, but also help in conversion of saline water into fresh water. The numerical simulations along with sensitivity analysis are performed to support the analytical results.
SNAP
Authors: Leskovec Jure , Sosič Rok
Published: July 2016

Large networks are becoming a widely used abstraction for studying complex systems in a broad set of disciplines, ranging from social-network analysis to molecular biology and neuroscience. Despite an increasing need to analyze and manipulate large networks, only a limited number of tools are available for this task.

Here, we describe the Stanford Network Analysis Platform (SNAP), a general-purpose, high-performance system that provides easy-to-use, high-level operations for analysis and manipulation of large networks. We present SNAP functionality, describe its implementational details, and give performance benchmarks. SNAP has been developed for single big-memory machines, and it balances the trade-off between maximum performance, compact in-memory graph representation, and the ability to handle dynamic graphs in which nodes and edges are being added or removed over time. SNAP can process massive networks with hundreds of millions of nodes and billions of edges. SNAP offers over 140 different graph algorithms that can efficiently manipulate large graphs, calculate structural properties, generate regular and random graphs, and handle attributes and metadata on nodes and edges. Besides being able to handle large graphs, an additional strength of SNAP is that networks and their attributes are fully dynamic; they can be modified during the computation at low cost. SNAP is provided as an open-source library in C++ as well as a module in Python.

We also describe the Stanford Large Network Dataset, a set of social and information real-world networks and datasets, which we make publicly available. The collection is a complementary resource to our SNAP software and is widely used for development and benchmarking of graph analytics algorithms.
Probabilistic Directed Writebacks for Exclusive Caches
Authors: Olson Lena E. , Hill Mark D.
Published: July 2016

Energy is an increasingly important consideration in memory system design. Caches improve energy efficiency by decreasing execution time and reducing the number of main memory accesses, but they suffer from known inefficiencies: the last-level cache (LLC) tends to have a high miss ratio while simultaneously storing many blocks that are never referenced. Because these blocks are not referenced before eviction, we can write them directly to memory rather than to the LLC. To do so, we must predict which blocks will not be referenced. Previous approaches rely on additional state at the LLC and/or extra communication.

We show that by predicting working set size per program counter (PC), we can decide which blocks have low probability of being referenced. Our approach relies on the insight that it is possible to makes this prediction based solely on the address stream as seen by the level-one data cache (L1D), eliminating the need to store or communicate PC values between levels of the cache hierarchy. We require no modifications to the LLC.

Our approach uses Flajolet andMartin's probabilistic counting to keep the state small: two additional bits per L1D block, with an additional 6KB prediction table. This approach yields a large reduction in number of LLC writebacks: 25% fewer for SPEC on average, 80% fewer for graph500, and 67% fewer for an in-memory hash table.
Reduction of Parallel Computation in the Parallel Model for Ada
Authors: Taft Tucker , Moore Brad , Pinho Luis Miguel , Michell Stephen
Published: July 2016

One of the most common program constructs to be parallelized (and where most of the times gains are obtained) is parallel loops. This paper discusses different approaches to support loop parallelization in the fine-grained parallelism model for Ada currently being proposed, focusing in particular in the issues related to reducing operations.
Implementing Safety-Critical Java Missions in Ada
Authors: Wellings A. J. , Cholpanov V. , Burns A.
Published: July 2016

Critical systems written in Ada are still reluctant to use dynamic memory allocation. The Ravenscar profile, for example, prohibits the dynamic creation of tasks. This is in spite of the availability of storage pools and the strong compile-time checking of access types. The Java community has, by necessity, taken a slightly less conservative approach. Safety-Critical Java (SCJ) supports a constrained use of dynamic memory allocation. This paper takes the SCJ approach and tries to implement it using Ada's storage pools. We show that the approach is not directly transferable to Ada due to the difference in the way that SCJ and Ada handle region-based memory management. However, an equivalent approach can be developed.
Session Summary
Authors: Vardanega Tullio , Rogers Pat
Published: July 2016

This session of the 18th International Real Time Ada Workshop discussed the use of profiles in Ada, and the possibility and desirability of adding additional language profiles to Ada besides the Ravenscar Tasking Profile.
Optical-Based Analysis of Soft Tissue Structures
Authors: Goth Will , Lesicko John , Sacks Michael S. , Tunnell James W.
Published: July 2016

Fibrous structures are an integral and dynamic feature of soft biological tissues that are directly related to the tissues’ condition and function. A greater understanding of mechanical tissue behavior can be gained through quantitative analyses of structure alone, as well as its integration into computational models of soft tissue function. Histology and other nonoptical techniques have traditionally dominated the field of tissue imaging, but they are limited by their invasiveness, inability to provide resolution on the micrometer scale, and dynamic information. Recent advances in optical modalities can provide higher resolution, less invasive imaging capabilities, and more quantitative measurements. Here we describe contemporary optical imaging techniques with respect to their suitability in the imaging of tissue structure, with a focus on characterization and implementation into subsequent modeling efforts. We outline the applications and limitations of each modality and discuss the overall shortcomings and future directions for optical imaging of soft tissue structure.
Electrical Chips for Biological Point-of-Care Detection
Authors: Reddy Bobby , Salm Eric , Bashir Rashid
Published: July 2016

As the future of health care diagnostics moves toward more portable and personalized techniques, there is immense potential to harness the power of electrical signals for biological sensing and diagnostic applications at the point of care. Electrical biochips can be used to both manipulate and sense biological entities, as they can have several inherent advantages, including on-chip sample preparation, label-free detection, reduced cost and complexity, decreased sample volumes, increased portability, and large-scale multiplexing. The advantages of fully integrated electrical biochip platforms are particularly attractive for point-of-care systems. This review summarizes these electrical lab-on-a-chip technologies and highlights opportunities to accelerate the transition from academic publications to commercial success.
Lensless Imaging and Sensing
Authors: Ozcan Aydogan , McLeod Euan
Published: July 2016

High-resolution optical microscopy has traditionally relied on high-magnification and high–numerical aperture objective lenses. In contrast, lensless microscopy can provide high-resolution images without the use of any focusing lenses, offering the advantages of a large field of view, high resolution, cost-effectiveness, portability, and depth-resolved three-dimensional (3D) imaging. Here we review various approaches to lensless imaging, as well as its applications in biosensing, diagnostics, and cytometry. These approaches include shadow imaging, fluorescence, holography, superresolution 3D imaging, iterative phase recovery, and color imaging. These approaches share a reliance on computational techniques, which are typically necessary to reconstruct meaningful images from the raw data captured by digital image sensors. When these approaches are combined with physical innovations in sample preparation and fabrication, lensless imaging can be used to image and sense cells, viruses, nanoparticles, and biomolecules. We conclude by discussing several ways in which lensless imaging and sensing might develop in the near future.
The Virtual Physiological Human: Ten Years After
Authors: Viceconti Marco , Hunter Peter
Published: July 2016

Biomedical research and clinical practice are struggling to cope with the growing complexity that the progress of health care involves. The most challenging diseases, those with the largest socioeconomic impact (cardiovascular conditions; musculoskeletal conditions; cancer; metabolic, immunity, and neurodegenerative conditions), are all characterized by a complex genotype–phenotype interaction and by a “systemic” nature that poses a challenge to the traditional reductionist approach. In 2005 a small group of researchers discussed how the vision of computational physiology promoted by the Physiome Project could be translated into clinical practice and formally proposed the term Virtual Physiological Human. Our knowledge about these diseases is fragmentary, as it is associated with molecular and cellular processes on the one hand and with tissue and organ phenotype changes (related to clinical symptoms of disease conditions) on the other. The problem could be solved if we could capture all these fragments of knowledge into predictive models and then compose them into hypermodels that help us tame the complexity that such systemic behavior involves. In 2005 this was simply not possible—the necessary methods and technologies were not available. Now, 10 years later, it seems the right time to reflect on the original vision, the results achieved so far, and what remains to be done.
Malabsorption and intestinal adaptation after one anastomosis gastric bypass compared with Roux-en-Y gastric bypass in rats
Authors: Cavin Jean-Baptiste , Voitellier Eglantine , Cluzeaud Françoise , Kapel Nathalie , Marmuse Jean-Pierre , Chevallier Jean-Marc , Msika Simon , Bado André , Le Gall Maude
Published: July 2016

The technically easier one-anastomosis (mini) gastric bypass (MGB) is associated with similar metabolic improvements and weight loss as the Roux-en-Y gastric bypass (RYGB). However, MGB is controversial and suspected to result in greater malabsorption than RYGB. In this study, we compared macronutrient absorption and intestinal adaptation after MGB or RYGB in rats. Body weight and food intake were monitored and glucose tolerance tests were performed in rats subjected to MGB, RYGB, or sham surgery. Carbohydrate, protein, and lipid absorption was determined by fecal analyses. Intestinal remodeling was evaluated by histology and immunohistochemistry. Peptide and amino acid transporter mRNA levels were measured in the remodeled intestinal mucosa and those of anorexigenic and orexigenic peptides in the hypothalamus. The MGB and RYGB surgeries both resulted in a reduction of body weight and an improvement of glucose tolerance relative to sham rats. Hypothalamic orexigenic neuropeptide gene expression was higher in MGB rats than in RYGB or sham rats. Fecal losses of calories and proteins were greater after MGB than RYGB or sham surgery. Intestinal hyperplasia occurred after MGB and RYGB with increased jejunum diameter, higher villi, and deeper crypts than in sham rats. Peptidase and peptide or amino acid transporter genes were overexpressed in jejunal mucosa from MGB rats but not RYGB rats. In rats, MGB led to greater protein malabsorption and energy loss than RYGB. This malabsorption was not compensated by intestinal overgrowth and increased expression of peptide transporters in the jejunum.
Animal models of gastrointestinal and liver diseases. Animal models of acute and chronic pancreatitis
Authors: Zhan Xianbao , Wang Fan , Bi Yan , Ji Baoan
Published: July 2016

Animal models of pancreatitis are useful for elucidating the pathogenesis of pancreatitis and developing and testing novel interventions. In this review, we aim to summarize the most commonly used animal models, overview their pathophysiology, and discuss their strengths and limitations. We will also briefly describe common animal study procedures and refer readers to more detailed protocols in the literature. Although animal models include pigs, dogs, opossums, and other animals, we will mainly focus on rodent models because of their popularity. Autoimmune pancreatitis and genetically engineered animal models will be reviewed elsewhere.
Role of mesothelin in carbon nanotube-induced carcinogenic transformation of human bronchial epithelial cells
Authors: He Xiaoqing , Despeaux Emily , Stueckle Todd A. , Chi Alexander , Castranova Vincent , Dinu Cerasela Zoica , Wang Liying , Rojanasakul Yon
Published: July 2016

Carbon nanotubes (CNTs) have been likened to asbestos in terms of morphology and toxicity. CNT exposure can lead to pulmonary fibrosis and promotion of tumorigenesis. However, the mechanisms underlying CNT-induced carcinogenesis are not well defined. Mesothelin (MSLN) is overexpressed in many human tumors, including mesotheliomas and pancreatic and ovarian carcinomas. In this study, the role of MSLN in the carcinogenic transformation of human bronchial epithelial cells chronically exposed to single-walled CNT (BSW) was investigated. MSLN overexpression was found in human lung tumors, lung cancer cell lines, and BSW cells. The functional role of MSLN in the BSW cells was then investigated by using stably transfected MSLN knockdown (BSW shMSLN) cells. MSLN knockdown resulted in significantly decreased invasion, migration, colonies on soft agar, and tumor sphere formation. In vivo, BSW shMSLN cells formed smaller primary tumors and less metastases. The mechanism by which MSLN contributes to these more aggressive behaviors was investigated by using ingenuity pathway analysis, which predicted that increased MSLN could induce cyclin E expression. We found that BSW shMSLN cells had decreased cyclin E, and their proliferation rate was reverted to nearly that of untransformed cells. Cell cycle analysis showed that the BSW shMSLN cells had an increased G2 population and a decreased S phase population, which is consistent with the decreased rate of proliferation. Together, our results indicate a novel role of MSLN in the malignant transformation of bronchial epithelial cells following CNT exposure, suggesting its utility as a potential biomarker and drug target for CNT-induced malignancies.
Cooperative signaling by TGF-β1 and WNT-11 drives sm-α-actin expression in smooth muscle via Rho kinase-actin-MRTF-A signaling
Authors: Kumawat Kuldeep , Koopmans Tim , Menzen Mark H. , Prins Alita , Smit Marieke , Halayko Andrew J. , Gosens Reinoud
Published: July 2016

Airway smooth muscle (ASM) remodeling is a key feature in asthma and includes changes in smooth muscle-specific gene and protein expression. Despite this being a major contributor to asthma pathobiology, our understanding of the mechanisms governing ASM remodeling remains poor. Here, we studied the functional interaction between WNT-11 and TGF-β1 in ASM cells. We demonstrate that WNT-11 is preferentially expressed in contractile myocytes and is strongly upregulated following TGF-β1-induced myocyte maturation. Knock-down of WNT-11 attenuated TGF-β1-induced smooth muscle (sm)-α-actin expression in ASM cells. We demonstrate that TGF-β1-induced sm-α-actin expression is mediated by WNT-11 via RhoA activation and subsequent actin cytoskeletal remodeling, as pharmacological inhibition of either Rho kinase by Y27632 or actin remodeling by latrunculin A attenuated sm-α-actin induction. Moreover, we show that TGF-β1 regulates the nuclear expression of myocardin-related transcription factor-A (MRTF-A) in a Rho kinase-dependent fashion, which in turn mediates sm-α-actin expression. Finally, we demonstrate that TGF-β1-induced MRTF-A nuclear translocation is dependent on endogenous WNT-11. The present study thus demonstrates a WNT-11-dependent Rho kinase-actin-MRTF-A signaling axis that regulates the expression of sm-α-actin in ASM cells.
Physiological impact of patent foramen ovale on pulmonary gas exchange, ventilatory acclimatization, and thermoregulation
Authors: Lovering Andrew T. , Elliott Jonathan E. , Davis James T.
Published: July 2016

The foramen ovale, which is part of the normal fetal cardiopulmonary circulation, fails to close after birth in ∼35% of the population and represents a potential source of right-to-left shunt. Despite the prevalence of patent foramen ovale (PFO) in the general population, cardiopulmonary, exercise, thermoregulatory, and altitude physiologists may have underestimated the potential effect of this shunted blood flow on normal physiological processes in otherwise healthy humans. Because this shunted blood bypasses the respiratory system, it would not participate in either gas exchange or respiratory system cooling and may have impacts on other physiological processes that remain undetermined. The consequences of this shunted blood flow in PFO-positive (PFO+) subjects can potentially have a significant, and negative, impact on the alveolar-to-arterial oxygen difference (AaDO2), ventilatory acclimatization to high altitude and respiratory system cooling with PFO+ subjects having a wider AaDO2 at rest, during exercise after acclimatization, blunted ventilatory acclimatization, and a higher core body temperature (∼0.4°C) at rest and during exercise. There is also an association of PFO with high-altitude pulmonary edema and acute mountain sickness. These effects on physiological processes are likely dependent on both the presence and size of the PFO, with small PFOs not likely to have significant/measureable effects. The PFO can be an important determinant of normal physiological processes and should be considered a potential confounder to the interpretation of former and future data, particularly in small data sets where a significant number of PFO+ subjects could be present and significantly impact the measured outcomes.