bluuebunny/crossref_metadata_2025 huggingface dataset:
Accounting for delay of energy transfer between coupled rooms in statistical-acoustics models of reverberant-energy decay
Authors: Summers Jason E.
Published: July 2012

A statistical-acoustics model for energy decay in systems of two or more coupled rooms is introduced, which accounts for the distribution of delay in the transfer of energy between subrooms that results from the finite speed of sound. The method extends previous models based on systems of coupled ordinary differential equations by using functional differential equations to explicitly model dependence on prior values of energy in adjacent subrooms. Predictions of the model are illustrated for a two-room coupled system and compared with the predictions of a benchmark computational geometrical-acoustics model.
Ice Volume and Sea Level During the Last Interglacial
Authors: Dutton A. , Lambeck K.
Published: July 2012

More Melting

The last interglacial period, around 125,000 years ago, was 1° to 2°C warmer than the present, and the sea level was thought to be 4 to 6 meters higher. However,
Dutton and Lambeck
(p.
216
), now suggest that sea level was possibly as much as 10 meters above current levels. Such a large excess of seawater would mean that the Greenland and Antarctic ice sheets melted much more than previously assumed, which has implications for how much sea-level rise we should expect with anthropogenic climate warming.
Extinction Debt and Windows of Conservation Opportunity in the Brazilian Amazon
Authors: Wearn Oliver R. , Reuman Daniel C. , Ewers Robert M.
Published: July 2012

Growing Extinction Debt

Predicting, and potentially preventing, extinction is a central goal of conservation biology.

Wearn
et al.

(p.
228
; see the Perspective by

Rangel

) describe a mathematical approach for predicting the time lags in extinction following habitat loss. The model was applied to the highly biodiverse Brazilian Amazon region, and used to reconstruct the spatial and temporal patterns of extinction and the accumulation of extinction debt from 1970 through to the present, and to extrapolate to 2050 under four deforestation scenarios. The Amazon basin sits at a critical point: Few species have been driven extinct to date, but an extinction debt is rapidly accumulating, which could lead to an increasing rate of extinction in the next four decades.
Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
Authors: Liu Wei , Chun Eugene , Thompson Aaron A. , Chubukov Pavel , Xu Fei , Katritch Vsevolod , Han Gye Won , Roth Christopher B. , Heitman Laura H. , IJzerman Adriaan P. , Cherezov Vadim , Stevens Raymond C.
Published: July 2012

GPCR Close-Up

Structures of G protein–coupled receptors (GPCRs) determined in the past few years, have provided insight into the function of this important family of membrane proteins.

Liu
et al.

(p.
232
) used a protein-engineering strategy to produce a stabilized version of the human A
2A
adenosine receptor (A
2A
AR). The high-resolution structure reveals the position of about 60 internal waters, which suggests an almost continuous channel in the GPCR and can explain the allosteric effects of Na
+
on ligand binding and how cholesterol may contribute to GPCR stabilization.
Response to Comment on “Plant Species Richness and Ecosystem Multifunctionality in Global Drylands”
Authors: Maestre Fernando T. , Soliveres Santiago , Gotelli Nicholas J. , Quero José L. , Berdugo Miguel
Published: July 2012

Jucker and Coomes claim that the relationship between plant species richness (biodiversity) and ecosystem multifunctionality (B-EMf) reported in our study changes along environmental gradients. We point out flaws in their analytical approach and then reanalyze our data to further demonstrate that the B-EMf relationship does not substantially change along environmental gradients.
Quantitative Modulation of Polycomb Silencing Underlies Natural Variation in Vernalization
Authors: Coustham Vincent , Li Peijin , Strange Amy , Lister Clare , Song Jie , Dean Caroline
Published: July 2012

Is Winter Past?

Some plants are adapted to wait through the winter before their genetic programs for flowering are initiated. But the duration of winter varies with location, and thus, to avoid flowering too late into the summer or exposing blossoms to frost, the adaptation needs to hold the flowers off for just the right amount of time. Working with
Arabidopsis thaliana
,

Coustham
et al.

(p.
584
, published online 12 July) identified a quantitative mechanism that “counts” off the duration of winter. FLC, a repressor of flowering, carries sequence polymorphisms that direct epigenetic events. Plants with fewer of these polymorphisms are adapted to short winters, and plants with all four polymorphisms are adapted to long winters.
Cartwheel Architecture of
Trichonympha
Basal Body
Authors: Guichard Paul , Desfosses Ambroise , Maheshwari Aditi , Hachet Virginie , Dietrich Carsten , Brune Andreas , Ishikawa Takashi , Sachse Carsten , Gönczy Pierre
Published: July 2012

Electron microscopy provides a close-up view of the ninefold-symmetric stacked rings at the base of cilia and flagella.
Molecular Architecture and Assembly Principles of
Vibrio cholerae
Biofilms
Authors: Berk Veysel , Fong Jiunn C. N. , Dempsey Graham T. , Develioglu Omer N. , Zhuang Xiaowei , Liphardt Jan , Yildiz Fitnat H. , Chu Steven
Published: July 2012

Biofilms Up Close

Many bacterial infections involve biofilm formation. Cells within a biofilm are significantly more resistant to immune clearance and antibiotics compared to unattached, planktonic cells.

Berk
et al.

(p.
236
) applied superresolution optical methods to image living bacteria with nanometer-scale precision as they form a biofilm.
Vibrio cholerae
biofilms were observed to have three distinct levels of spatial organization: cells, clusters of cells, and collections of clusters. Each cell cluster was wrapped in a flexible, elastic envelope. Several
V. cholerae
matrix proteins played complementary architectural roles during biofilm development. RbmA provided cell-cell adhesion, Bap1 allowed the developing biofilm to adhere to surfaces, and heterogeneous mixtures of VPS, RbmC, and Bap1 formed the dynamic, flexible, and ordered envelopes that encase the cell clusters.
Spin-Polarized Light-Emitting Diode Based on an Organic Bipolar Spin Valve
Authors: Nguyen Tho D. , Ehrenfreund Eitan , Vardeny Z. Valy
Published: July 2012

Spin-Dependent Light Emission

Spintronic devices exploit electronic currents that are spin polarized, which have an excess of one spin current over the other. One way to detect this polarization would be to create a light-emitting diode that is sensitive to spin polarization. Along these lines,

Nguyen
et al.

(p.
204
) constructed a bipolar device in which an organic semiconductor was sandwiched between two ferromagnetic contacts whose relative polarization could be controlled by an applied magnetic field. Magneto-electroluminescence of the order of ∼1% was observed at a bias voltage of ∼3.5 V. The use of a deuterated organic polymer interlayer improved spin transport relative to polymers with hydrogen side groups, and a thin LiF buffer layer on the ferromagnetic cathode improved electron injection efficiency.
The Provenances of Asteroids, and Their Contributions to the Volatile Inventories of the Terrestrial Planets
Authors: Alexander C. M. O’D. , Bowden R. , Fogel M. L. , Howard K. T. , Herd C. D. K. , Nittler L. R.
Published: July 2012

Constraining the Birthplace of Asteroids

Many primitive meteorites originating from the asteroid belt once contained abundant water that is now stored as OH in hydrated minerals.

Alexander
et al.

(p.
721
, published online 12 July) estimated the hydrogen isotopic compositions in 86 samples of primitive meteorites that fell in Antarctica and compared the results to those of comets and Saturn's moon, Enceladus. Water in primitive meteorites was less deuteriumrich than that in comets and Enceladus, implying that, in contradiction to recent models of the dynamical evolution of the solar system, the parent bodies of primitive meteorites cannot have formed in the same region as comets. The results also suggest that comets were not the principal source of Earth's water.
Long-Range Incommensurate Charge Fluctuations in (Y,Nd)Ba
2
Cu
3
O
6+

x
Authors: Ghiringhelli G. , Le Tacon M. , Minola M. , Blanco-Canosa S. , Mazzoli C. , Brookes N. B. , De Luca G. M. , Frano A. , Hawthorn D. G. , He F. , Loew T. , Sala M. Moretti , Peets D. C. , Salluzzo M. , Schierle E. , Sutarto R. , Sawatzky G. A. , Weschke E. , Keimer B. , Braicovich L.
Published: July 2012

A State of High

T
c

Superconductivity

There are strong indications that high-temperature superconductivity in the cuprates is formed amid competing orders, but only two have been observed unambiguously. The so-called stripe order has been observed in a Lanthanum-based cuprate family and consists of coexisting charge-and-spin modulations and occurs at a characteristic dopant concentration in which the critical temperature

T
c

has a dip. Now,

Ghiringhelli
et al.

(p.
821
, published online 12 July; see the Perspective by

Tranquada

) have used resonant inelastic x-ray scattering to uncover a related but apparently two-dimensional charge order in the much cleaner YBCO cuprate family. The charge fluctuations were not commensurate with the lattice and did not originate in the characteristic oxygen chains of YBCO. The order appeared only in a narrow interval of dopant concentrations and competed with superconductivity, which provides a natural explanation for a plateau in

T
c

observed in the same range.
Identification of Small Molecule Activators of Cryptochrome
Authors: Hirota Tsuyoshi , Lee Jae Wook , St. John Peter C. , Sawa Mariko , Iwaisako Keiko , Noguchi Takako , Pongsawakul Pagkapol Y. , Sonntag Tim , Welsh David K. , Brenner David A. , Doyle Francis J. , Schultz Peter G. , Kay Steve A.
Published: July 2012

Modulating the Clock

Because of the close association of the circadian clock with a wide range of physiological processes, identification of clock-modulating small molecules may prove useful for the treatment of circadian-related disorders, which include circadian sleep disorders, cardiovascular disease, cancer, and metabolic disease.

Hirota
et al.

(p.
1094
, published online 12 July) screened for chemical compounds that affected the period of the circadian clock in a human osteosarcoma cell line. A carbazole derivative named KL001 appeared to act by inhibiting proteolytic degradation of the cryptochrome proteins, which in turn caused a lengthening of the circadian period. KL001 also inhibited glucagon-induced gluconeogenesis in primary cultures of mouse hepatocytes.
Driving Dislocations in Graphene
Authors: Bonilla Luis L. , Carpio Ana
Published: July 2012

Electron microscopy has revealed time-resolved glide and climb motion of dislocations in graphene and imaged their strain and rotation fields.
Amazonian Extinction Debts
Authors: Rangel Thiago F.
Published: July 2012

How many species are headed for extinction as a result of past and future deforestation in the Brazilian Amazon?
Broadly Neutralizing Antibodies Present New Prospects to Counter Highly Antigenically Diverse Viruses
Authors: Burton Dennis R. , Poignard Pascal , Stanfield Robyn L. , Wilson Ian A.
Published: July 2012

Certain human pathogens avoid elimination by our immune system by rapidly mutating the surface protein sites targeted by antibody responses, and consequently they tend to be problematic for vaccine development. The behavior described is prominent for a subset of viruses—the highly antigenically diverse viruses—which include HIV, influenza, and hepatitis C viruses. However, these viruses do harbor highly conserved exposed sites, usually associated with function, which can be targeted by broadly neutralizing antibodies. Until recently, not many such antibodies were known, but advances in the field have enabled increasing numbers to be identified. Molecular characterizations of the antibodies and, most importantly, of the sites of vulnerability that they recognize give hope for the discovery of new vaccines and drugs.
Rising Acidity Brings an Ocean of Trouble
Authors: Service Robert F.
Published: July 2012

Carbon dioxide emissions have changed the chemistry of the world's oceans in ways that are already harming shell-building organisms and could lead to broad impacts on marine ecosystems.
The View From the Top of the HIV/AIDS World
Authors: Cohen Jon
Published: July 2012

Science
spends a day with immunologist and clinician Anthony Fauci, head of the single largest funder of HIV/AIDS research.
Life in the Fast Lane: HIV and Meth
Authors: Cohen Jon
Published: July 2012

Methamphetamine use on the West Coast has become intimately linked to HIV in men who have sex with men (MSM). HIV prevalence in MSM has climbed in lockstep with the intensity of meth use.
My Virus Is Your Virus
Authors: Cohen Jon
Published: July 2012

An 8-year-old U.S.-government-funded HIV/AIDS research study has shown how readily the virus makes a mockery of the U.S.-Mexico border and creates one regional epidemic.
Acyclovir-induced acute renal failure and the importance of an expanding waist line: Table 1
Authors: Seedat Ahmed , Winnett Georgia
Published: July 2012

A 23-year-old gentleman with no significant medical history other than obesity was admitted with a history of balance problems, double vision and strange behaviour following a fall from bed. Systems examination was unremarkable. The patient was given intravenous acyclovir and intravenous ceftriaxone given the suspicion of encephalitis/meningitis. Investigations including routine bloods, CT/MRI Head and lumbar puncture were unremarkable. Within 48 h of commencing intravenous acyclovir, there was a marked deterioration in renal function. On stopping acyclovir therapy, renal function improved back to baseline. No other cause for deterioration in renal function was identified. The most likely cause for acute renal failure was secondary to acyclovir therapy. This has been well documented and is due to intratubular crystal precipitation. Moreover, in this case nephrotoxicity is likely secondary to the large boluses of intravenous acyclovir that had been given as prescribed according to the total body weight.
The role of haemoglobin mass on VO2max following normobaric ‘live high–train low’ in endurance-trained athletes
Authors: Robach Paul , Siebenmann Christoph , Jacobs Robert A , Rasmussen Peter , Nordsborg Nikolai , Pesta Dominik , Gnaiger Erich , Díaz Víctor , Christ Andreas , Fiedler Julia , Crivelli Nadine , Secher Niels H , Pichon Aurélien , Maggiorini Marco , Lundby Carsten
Published: July 2012

It remains unclear by which mechanism ‘live high–train low’ (LHTL) altitude training increases exercise performance. Haematological and skeletal muscle adaptations have both been proposed. To test the hypotheses that (i) LHTL improves maximal oxygen uptake (VO2max) and (ii) this improvement is related to hypoxia-induced increases in total haemoglobin mass (Hbmass) and not to improved maximal oxidative capacity of skeletal muscle, we determined VO2max before LHTL and after LHTL, before and after the altitude-induced increases in Hbmass(measured by carbon-monoxide rebreathing) had been abolished by isovolumic haemodilution. We obtained skeletal muscle biopsies to quantify mitochondrial oxidative capacity and efficiency. Sixteen endurance-trained athletes were assigned (double-blinded, placebo controlled) to ≥16 h/day over 4 weeks to normoxia (placebo, n=6) or normobaric hypoxia equivalent to 3000 m altitude (LHTL, n=10). Four-week LHTL did not increase VO2max, irrespective of treatment (LHTL: 1.5%; placebo: 2.0%). Hbmasswas slightly increased (4.6%) in 5 (of 10) LHTL subjects but this was not accompanied by a concurrent increase in VO2max. In the subjects demonstrating an increase in Hbmass, isovolumic haemodilution elicited a 5.8% decrease in VO2max. Cycling efficiency was altered neither with time nor by LHTL. Neither maximal capacity of oxidative phosphorylation nor mitochondrial efficiency was modified by time or LHTL. The present results suggest that LHTL has no positive effect on VO2max in endurance-trained athletes because (i) muscle maximal oxidative capacity is not improved following LHTL and (ii) erythrocyte volume expansion after LHTL, if any, is too small to alter O2transport.
Going glass to digital: virtual microscopy as a simulation-based revolution in pathology and laboratory science
Authors: Nelson Danielle , Ziv Amitai , Bandali Karim S
Published: July 2012

The recent technological advance of digital high resolution imaging has allowed the field of pathology and medical laboratory science to undergo a dramatic transformation with the incorporation of virtual microscopy as a simulation-based educational and diagnostic tool. This transformation has correlated with an overall increase in the use of simulation in medicine in an effort to address dwindling clinical resource availability and patient safety issues currently facing the modern healthcare system. Virtual microscopy represents one such simulation-based technology that has the potential to enhance student learning and readiness to practice while revolutionising the ability to clinically diagnose pathology collaboratively across the world. While understanding that a substantial amount of literature already exists on virtual microscopy, much more research is still required to elucidate the full capabilities of this technology. This review explores the use of virtual microscopy in medical education and disease diagnosis with a unique focus on key requirements needed to take this technology to the next level in its use in medical education and clinical practice.
Expression of cyclin-dependent kinase 2-associated protein 1 confers an independent prognosticator in nasopharyngeal carcinoma: a cohort study
Authors: Wu Li-Ching , Chen Yi-Ling , Wu Wen-Ren , Li Chien-Feng , Huang Hsuan-Ying , Lee Sung-Wei , Chang Shih-Lun , Lin Ching-Yih , Chen Yi-Hsien , Hsu Han-Ping , Lu Pei-Jung , Shiue Yow-Ling
Published: July 2012

Background and aim

Low expression of cyclin-dependent kinase 2-associated protein (CDK2AP1) is associated with tumour progression in oral and oesophageal carcinomas, but is not well studied in patients with head and neck cancer and nasopharyngeal carcinoma (NPC).

Methods

A rabbit anti-human CDK2AP1 polyclonal antibody was prepared. Immunoblotting of CDK2AP1 was examined in three cell lines and immunoexpression was retrospectively assessed in biopsies of 124 consecutive NPC patients without initial distant metastasis and treated with consistent guidelines.

Results

Higher CDK2AP1 expression level was identified in dysplastic oral keratinocytes, compared with two NPC-derived HONE-1 and TW01 cell lines. Low expression of CDK2AP1 (50.8%) was correlated with advanced nodal status (p=0.002) and American Joint Committee on Cancer (AJCC) stage (p=0.004). In multivariate analyses, low CDK2AP1 expression emerged as an independent prognosticator for worse disease-specific survival (DSS; p=0.037) and local recurrence-free survival (LRFS; p=0.042), along with AJCC stage III–IV (p=0.034, DSS; p=0.029, LRFS).

Conclusions

Low CDK2AP1 expression is common and associated with adverse prognosticators, conferring tumour aggressiveness through cycle cycle, cell growth or apoptosis cellular processes.
Longitudinal patterns in physical activity and sedentary behaviour from mid-life to early old age: a substudy of the Whitehall II cohort
Authors: Hamer Mark , Kivimaki Mika , Steptoe Andrew
Published: July 2012

Background

There are few longitudinal data on physical activity patterns from mid-life into older age. The authors examined associations of self-reported physical activity, adiposity and socio-demographic factors in mid-life with objectively assessed measures of activity in older age.

Methods

Participants were 394 healthy men and women drawn from the Whitehall II population-based cohort study. At the baseline assessment in 1997 (mean age 54 years), physical activity was assessed through self-report and quantified as metabolic equivalent of task hours/week. At the follow-up in 2010 (mean age 66 years), physical activity was objectively measured using accelerometers worn during waking hours for seven consecutive days (average daily wear time 891±68 min/day).

Results

Self-reported physical activity at baseline was associated with objectively assessed activity at follow-up in various activity categories, including light-, moderate- and vigorous-intensity activity (all ps<0.04). Participants in the highest compared with lowest quartile of self-reported activity level at baseline recorded on average 64.1 (95% CI 26.2 to 102.1) counts per minute more accelerometer-assessed activity at follow-up and 9.0 (2.0–16.0) min/day more moderate-to-vigorous daily activity, after adjusting for baseline covariates. Lower education, obesity and self-perceived health status were also related to physical activity at follow-up. Only age and education were associated with objectively measured sedentary time at follow-up.

Conclusion

Physical activity behaviour in middle age was associated with objectively measured physical activity in later life after 13 years of follow-up, suggesting that the habits in adulthood are partly tracked into older age.
Mechanical endovascular treatment of acute stroke due to cardiac myxoma
Authors: Garcia-Ptacek Sara , Matias-Guiu Jordi A , Valencia-Sánchez Cristina , Gil Alberto , Bernal-Becerra Israel , De las Heras-Revilla Virginia , Serna-Candel Carmen
Published: July 2012

Background

Myxomas are rare cardiac tumors which often present with stroke caused by tumorous or thrombotic emboli. Treatment with intravenous recombinant tissue plasminogen activator (rtPA) and intra-arterial thrombolysis has been described previously but mechanical thrombectomy has not yet been reported, and treatment of myxoma-related ischemic stroke remains a clinical and technical challenge.

Methods

Two patients with ischemic stroke due to cardiac myxoma in which mechanical thrombectomy was performed are presented.

Results

Endovascular thrombectomy after intravenous rtPA (bridging therapy) was safely achieved in both cases, although with different clinical outcomes and degrees of recanalization.

Conclusions

In stroke secondary to cardiac myxoma, mechanical thrombectomy might represent a safe and effective treatment option. The authors suggest the use of histological examination of the clot for diagnosis as its composition may explain the differences in treatment outcome.
Ab initio calculation of the low-lying electronic states of the ZrN molecule
Authors: Farhat A. , Korek M. , Marques M.A.L. , Abdul-Al S.N.
Published: July 2012

An ab initio calculation of the low-lying electronic states of zirconium nitride (ZrN) were performed by using a complete active space self-consistent field with multireference single and double excitation configuration interaction (MRSDCI). The potential energy curves of 21 low-lying electronic states of the ZrN molecule with different spin and spatial symmetries, in the representation 2s+1Λ(+/−) and below 30 000 cm–1, were identified. The harmonic frequency (ωe), the equilibrium internuclear distance (Re), the rotational constants (Be), the electronic energy with respect to the ground state (Te), and the permanent dipole moment (µ) were calculated for the considered electronic states. The comparison of these values with those available in the literature shows a very good agreement with either theoretical or experimental data. Fifteen new electronic states were studied here for the first time.
Preparation of (Z)-1,2-dichloroalkenes from terminal alkynes
Authors: Zhou Ningzhang , Wang Qiang , Lough Alan J. , Yan Hongbin
Published: July 2012

(Z)-1,2-Dihaloalkenes are thermodynamically disfavoured of the two stereoisomers. This paper reports the synthesis of some (Z)-1,2-dichloroalkene analogues from mucochloric acid. A more versatile approach involved the chloroboration of terminal alkynes to yield corresponding (Z)-chloroboronic acid as a first step. Treatment of the organoboronic acid with potassium hydrogen difluoride followed by tetrabutylammonium trichloride gave (Z)-1,2-dichloroalkenes in moderate to good yields in a stereospecific manner.
Analysis Technique for Wavelength Dispersion of Refractive Indices by Renormalized Transmission Spectroscopic Ellipsometry
Authors: Goda Kazuya , Kimura Munehiro , Akahane Tadashi
Published: July 2012

An improved analysis technique to determine the wavelength dispersion of refractive indices based on renormalized transmission spectroscopic ellipsometry was demonstrated. Twelve device parameters, including cell gap, twist angle, and rotation angle, nine Cauchy coefficients for birefringence, and refractive indices for ordinary and extraordinary rays are determined in a three-step manner. The refractive index for an ordinary ray at the wavelength λ=589.0 nm, which is measured by using an Abbe refractometer, is substituted as an original refractive index to guarantee the accuracy of the analysis for the absolute value of refractive indices. Compared with our previous technique, this analysis procedure is more simplified; as a result, the reproducibility and applicability were remarkably enhanced.
Catalytic Decomposition of PH3 on Heated Tungsten Wire Surfaces
Authors: Umemoto Hironobu , Nishihara Yushin , Ishikawa Takuma , Yamamoto Shingo
Published: July 2012

The catalytic decomposition processes of PH3 on heated tungsten surfaces were studied to clarify the mechanisms governing phosphorus doping into silicon substrates. Mass spectrometric measurements show that PH3 can be decomposed by more than 50% over 2000 K. H, P, PH, and PH2 radicals were identified by laser spectroscopic techniques. Absolute density measurements of these radical species, as well as their PH3 flow rate dependence, show that the major products on the catalyst surfaces are P and H atoms, while PH and PH2 are produced in secondary processes in the gas phase. In other words, catalytic decomposition, unlike plasma decomposition processes, can be a clean source of P atoms, which can be the only major dopant precursors. In the presence of an excess amount of H2, the apparent decomposition efficiency is small. This can be explained by rapid cyclic reactions including decomposition, deposition, and etching to reproduce PH3.
A dynamic reputation system with built-in attack resilience to safeguard buyers in e-market
Authors: Sharma Neeraj Kumar , Gaur Vibha , Muttoo S. K.
Published: July 2012

Reputation systems aim to reduce the risk of loss due to untrustworthy participants by providing a mechanism for establishing trustworthiness between mutually unknown online entities in an information asymmetric e-market. These systems encourage honest behavior and discourage malicious behavior of buyer and seller agents by laying a foundation for security and stability in the e-market. However, the success of a reputation system depends on its built-in resilience capabilities to foil various attacks. This paper focuses on how to safeguard buyers from dishonest sellers and advisors by incorporating an attack resilient reputation computation methodology. The objectives of the proposed dynamic reputation system in the distributed environment are to reduce the incentive for behaving dishonestly, and to minimize harm in case of attacks by dishonest participants with the inherent purpose of improving the quality of services in the e-market.
Strongly consistent transformation of partial scenarios
Authors: Bowles Juliana , Meedeniya Dulani
Published: July 2012

We present a formal approach for partial transformation of scenario-based specifications. Scenarios are captured as sequence diagrams (SDs) and (partially) transformed into coloured Petri nets (CPNs). Partial transformation is of interest for local analysis, or within an incremental development approach where interaction specifications are built incrementally and combined with previous iteration models. In previous work we defined a strongly consistent trans- formation from SDs to CPNs. In this paper, we extend the approach for partial transformation whilst preserving the strongly consistent nature of the transformation.
Formalizing and verifying compatibility and consistency of SysML blocks
Authors: Carrillo Oscar , Chouali Samir , Mountassir Hassan
Published: July 2012

The objective of this paper is to define an approach to formalize and verify the SysML blocks in a refinement process. We propose to specify system architecture with SysML Block Definition Diagram, this diagram is then analyzed and decomposed into several sub-blocks in order to verify their compatibility. The structural architecture of an abstract block is given by the Internal Block Diagram (IBD) which defines the communication links between sub-blocks. The compatibility verification between sub-blocks is only made on linked sub-blocks. The behaviour of each sub-block is described by an interface automaton which species the invocations exchanged with its environment. The verification between blocks is translated into consistency verification between the blocks and compatibility verification between their interface automata. Incompatibilities can be inconsistent at architecture level and at communication level if there are deadlocks during the interaction between sub-blocks. Once the verification is established between the sub-blocks, the abstract block can be then substituted by the sub-blocks which compose it.
Formalizing non-concurrent UML state machines using colored petri nets
Authors: André Étienne , Choppy Christine , Klai Kais
Published: July 2012

UML state machines are an interesting graphical language to express dynamic systems behavior. However, using the different features available (hierarchy, internal/external transitions, entry/exit/do activities, history pseudostates, etc.) may yield quite complex behaviors that are difficult to inspect and check visually. We introduce an algorithm to automatically generate a colored Petri net model associated with a state machine description, so as to provide a formal specification. In this proposal, although we do not consider concurrent aspects (such as fork and join), we take into ac- count all the above mentioned features in a thorough and integrated way. This is illustrated on some examples.
A look to the old-world_sky
Authors: Bessani Alysson , Kapitza Rüdiger , Petcu Dana , Romano Paolo , Gogouvitis Spyridon V. , Kyriazis Dimosthenis , Cascella Roberto G.
Published: July 2012

Cloud computing is currently the most important trend in the Information and Communication Technology (ICT) industry, and it has still not fully realized its potential. Reasons for its popularity are the opportunities to rapidly allocate vast amounts of computing resources and the fact that resources are accounted per use. While cloud computing was initiated by major industry players, academia has rapidly caught up; currently we see a vast number of cloud computing-related research efforts. However, since industry pushes development and many research aspects of cloud computing demand for large compute resources and real workloads, pure academic efforts have difficulties to address the most important issues and to have a major impact. On the other hand, academia usually tends to explore disruptive ideas that would not be addressed by industry alone. This paper summarizes the approaches and methods of five EU-funded research projects that focus on cloud computing in general and address important issues such as security, dependability, and interoperability. These aspects have received limited attention by the industry so far. The key to success of these large joint efforts is the close collaboration between partners from academia and industry spread all over Europe. The specific projects are Cloud-TM, Contrail, mOASIC, TClouds and VISION Cloud. Besides presenting the individual projects and their key contributions, we provide a perspective on future ICT research in Europe.
Where does transactional memory research stand and what challenges lie ahead?
Authors: Couceiro Maria , Romano Paolo
Published: July 2012

Transactional Memory (TM) is a promising technology that aims to simplify parallel programming by providing a programmer friendly alternative to traditional lock-based concurrency. The past ten years have seen intense research work on software and hardware TM proposals, and has recently led to the first hardware TM implementation for a commodity high-performance microprocessor, and to the inclusion of TM support in the world's leading open source compiler.

EuroTM (COST Action IC1001), in collaboration with the CloudTM project1, organized the second edition of the EuroTM Workshop on Transactional Memory (WTM 2012). The objective of WTM was to discuss new developments for this era of maturing TM research.

The workshop took place on April 10, in Bern, Switzerland, in conjunction with Eurosys 2012. Below we give highlights on the topics discussed in the workshop.
HCl-induced and ATP-dependent upregulation of TRPV1 receptor expression and cytokine production by human esophageal epithelial cells
Authors: Ma Jie , Altomare Annamaria , Guarino Michele , Cicala Michele , Rieder Florian , Fiocchi Claudio , Li Dan , Cao Weibiao , Behar Jose , Biancani Piero , Harnett Karen M.
Published: July 2012

The pathogenesis of gastroesophageal reflux disease (GERD) remains elusive, but recent evidence suggests that early secretion of inflammatory cytokines and chemokines by the mucosa leads to influx of immune cells followed by tissue damage. We previously showed that exposure of esophageal mucosa to HCl causes ATP release, resulting in activation of acetyl-CoA:1- O-alkyl- sn-glycero-3-phosphocholine acetyltransferase (lyso-PAF AT), the enzyme responsible for the production of platelet-activating factor (PAF). In addition, HCl causes release of IL-8 from the esophageal mucosa. We demonstrate that esophageal epithelial cells secrete proinflammatory mediators in response to HCl and that this response is mediated by ATP. Monolayers of the human esophageal epithelial cell line HET-1A were exposed to acidified cell culture medium (pH 5) for 12 min, a total of seven times over 48 h, to simulate the recurrent acid exposure clinically occurring in GERD. HCl upregulated mRNA and protein expression for the acid-sensing transient receptor potential cation channel, subfamily vanilloid member 1 (TRPV1), lyso-PAF AT, IL-8, eotaxin-1, -2, and -3, macrophage inflammatory protein-1α, and monocyte chemoattractant protein-1. The chemokine profile secreted by HET-1A cells in response to repeated HCl exposure parallels similar findings in erosive esophagitis patients. In HET-1A cells, the TRPV1 agonist capsaicin reproduced these findings for mRNA of the inflammatory mediators lyso-PAF AT, IL-8, and eotaxin-1. These effects were blocked by the TRPV1 antagonists iodoresiniferatoxin and JNJ-17203212. These effects were imitated by direct application of ATP and blocked by the nonselective ATP antagonist suramin. We conclude that HCl/TRPV-induced ATP release upregulated secretion of various chemoattractants by esophageal epithelial cells. These chemoattractants are selective for leukocyte subsets involved in acute inflammatory responses and allergic inflammation. The data support the validity of HET-1A cells as a model of the response of the human esophageal mucosa in GERD.
Bioengineered human IAS reconstructs with functional and molecular properties similar to intact IAS
Authors: Singh Jagmohan , Rattan Satish
Published: July 2012

Because of its critical importance in rectoanal incontinence, we determined the feasibility to reconstruct internal anal sphincter (IAS) from human IAS smooth muscle cells (SMCs) with functional and molecular attributes similar to the intact sphincter. The reconstructs were developed using SMCs from the circular smooth muscle layer of the human IAS, grown in smooth muscle differentiation media under sterile conditions in Sylgard-coated tissue culture plates with central Sylgard posts. The basal tone in the reconstructs and its changes were recorded following 0 Ca2+, KCl, bethanechol, isoproterenol, protein kinase C (PKC) activator phorbol 12,13-dibutyrate, and Rho kinase (ROCK) and PKC inhibitors Y-27632 and Gö-6850, respectively. Western blot (WB), immunofluorescence (IF), and immunocytochemical (IC) analyses were also performed. The reconstructs developed spontaneous tone (0.68 ± 0.26 mN). Bethanechol (a muscarinic agonist) and K+depolarization produced contraction, whereas isoproterenol (β-adrenoceptor agonist) and Y-27632 produced a concentration-dependent decrease in the tone. Maximal decrease in basal tone with Y-27632 and Gö-6850 (each 10−5M) was 80.45 ± 3.29 and 17.76 ± 3.50%, respectively. WB data with the IAS constructs′ SMCs revealed higher levels of RhoA/ROCK, protein kinase C-potentiated inhibitor or inhibitory phosphoprotein for myosin phosphatase (CPI-17), phospho-CPI-17, MYPT1, and 20-kDa myosin light chain vs. rectal smooth muscle. WB, IF, and IC studies of original SMCs and redispersed from the reconstructs for the relative distribution of different signal transduction proteins confirmed the feasibility of reconstruction of IAS with functional properties similar to intact IAS and demonstrated the development of myogenic tone with critical dependence on RhoA/ROCK. We conclude that it is feasible to bioengineer IAS constructs using human IAS SMCs that behave like intact IAS.
Defective intestinal amino acid absorption in Ace2 null mice
Authors: Singer Dustin , Camargo Simone M. R. , Ramadan Tamara , Schäfer Matthias , Mariotta Luca , Herzog Brigitte , Huggel Katja , Wolfer David , Werner Sabine , Penninger Josef M. , Verrey François
Published: July 2012

Mutations in the main intestinal and kidney luminal neutral amino acid transporter B0AT1 (Slc6a19) lead to Hartnup disorder, a condition that is characterized by neutral aminoaciduria and in some cases pellagra-like symptoms. These latter symptoms caused by low-niacin are thought to result from defective intestinal absorption of its precursor l-tryptophan. Since Ace2 is necessary for intestinal B0AT1 expression, we tested the impact of intestinal B0AT1 absence in ace2 null mice. Their weight gain following weaning was decreased, and Na+-dependent uptake of B0AT1 substrates measured in everted intestinal rings was defective. Additionally, high-affinity Na+-dependent transport of l-proline, presumably via SIT1 (Slc6a20), was absent, whereas glucose uptake via SGLT1 (Slc5a1) was not affected. Measurements of small intestine luminal amino acid content following gavage showed that more l-tryptophan than other B0AT1 substrates reach the ileum in wild-type mice, which is in line with its known lower apparent affinity. In ace2 null mice, the absorption defect was confirmed by a severalfold increase of l-tryptophan and of other neutral amino acids reaching the ileum lumen. Furthermore, plasma and muscle levels of glycine and l-tryptophan were significantly decreased in ace2 null mice, with other neutral amino acids displaying a similar trend. A low-protein/low-niacin diet challenge led to differential changes in plasma amino acid levels in both wild-type and ace2 null mice, but only in ace2 null mice to a stop in weight gain. Despite the combination of low-niacin with a low-protein diet, plasma niacin concentrations remained normal in ace2 null mice and no pellagra symptoms, such as photosensitive skin rash or ataxia, were observed. In summary, mice lacking Ace2-dependent intestinal amino acid transport display no total niacin deficiency nor clear pellagra symptoms, even under a low-protein and low-niacin diet, despite gross amino acid homeostasis alterations.
Inhibition of long myosin light-chain kinase activation alleviates intestinal damage after binge ethanol exposure and burn injury
Authors: Zahs Anita , Bird Melanie D. , Ramirez Luis , Turner Jerrold R. , Choudhry Mashkoor A. , Kovacs Elizabeth J.
Published: July 2012

Laboratory evidence suggests that intestinal permeability is elevated following either binge ethanol exposure or burn injury alone, and this barrier dysfunction is further perturbed when these insults are combined. We and others have previously reported a rise in both systemic and local proinflammatory cytokine production in mice after the combined insult. Knowing that long myosin light-chain kinase (MLCK) is important for epithelial barrier maintenance and can be activated by proinflammatory cytokines, we examined whether inhibition of MLCK alleviated detrimental intestinal responses seen after ethanol exposure and burn injury. To accomplish this, mice were given vehicle or a single binge ethanol exposure followed by a sham or dorsal scald burn injury. Following injury, one group of mice received membrane permeant inhibitor of MLCK (PIK). At 6 and 24 h postinjury, bacterial translocation and intestinal levels of proinflammatory cytokines were measured, and changes in tight junction protein localization and total intestinal morphology were analyzed. Elevated morphological damage, ileal IL-1β and IL-6 levels, and bacterial translocation were seen in mice exposed to ethanol and burn injury relative to either insult alone. This increase was not seen in mice receiving PIK after injury. Ethanol-exposed and burn-injured mice had reduced zonula occludens protein-1 and occludin localization to the tight junction relative to sham-injured mice. However, the observed changes in junctional complexes were not seen in our PIK-treated mice following the combined insult. These data suggest that MLCK activity may promote morphological and inflammatory responses in the ileum following ethanol exposure and burn injury.
DHRS3, a retinal reductase, is differentially regulated by retinoic acid and lipopolysaccharide-induced inflammation in THP-1 cells and rat liver
Authors: Zolfaghari Reza , Chen Qiuyan , Ross A. Catharine
Published: July 2012

Both retinoid status and inflammation have been shown to control the level of expression of retinoid homeostatic genes. In the present study, DHRS3, previously shown to possess retinal reductase activity, was identified by microarray analysis of THP-1 monocytes as a possible gene target of all- trans-retinoic acid (RA). In these cells, DHRS3 mRNA increased 30- to 40-fold after treatment with ≤20 nM RA for 24 h, while DHRS3 protein also increased. Of several synthetic retinoids tested, only Am580, a RA receptor-α-selective retinoid, increased DHRS3 mRNA expression. The full-length DHRS3 cDNA was cloned from rat liver and subjected to in vitro transcription-translation. Two major ∼30- and 35-kDa proteins were detected. In adult rat tissues, DHRS3 mRNA was most abundant in the adrenal gland, liver, and ovary. In the liver, DHRS3 is expressed in hepatocytes and possibly in all liver cells. To evaluate whether DHRS3 is regulated in the liver by RA and/or inflammatory stimuli, we treated rats for 6 h with RA or LPS or both. DHRS3 mRNA was doubled by RA but reduced by >90% after treatment with LPS in the absence and presence of RA. On the basis of our results, DHRS3 mRNA expression is regulated by RA in a tissue- or cell-type specific manner; the RA-induced increase in DHRS3 may contribute to retinoid storage; and a reduction of DHRS3 expression in the liver during inflammation may contribute to the perturbation of whole body vitamin A metabolism that has previously been shown to occur in conditions of inflammatory stress.
From Abnormal Hippocampal Synaptic Plasticity in Down Syndrome Mouse Models to Cognitive Disability in Down Syndrome
Authors: Cramer Nathan , Galdzicki Zygmunt
Published: July 2012

Down syndrome (DS) is caused by the overexpression of genes on triplicated regions of human chromosome 21 (Hsa21). While the resulting physiological and behavioral phenotypes vary in their penetrance and severity, all individuals with DS have variable but significant levels of cognitive disability. At the core of cognitive processes is the phenomenon of synaptic plasticity, a functional change in the strength at points of communication between neurons. A wide variety of evidence from studies on DS individuals and mouse models of DS indicates that synaptic plasticity is adversely affected in human trisomy 21 and mouse segmental trisomy 16, respectively, an outcome that almost certainly extensively contributes to the cognitive impairments associated with DS. In this review, we will highlight some of the neurophysiological changes that we believe reduce the ability of trisomic neurons to undergo neuroplasticity-related adaptations. We will focus primarily on hippocampal networks which appear to be particularly impacted in DS and where consequently the majority of cellular and neuronal network research has been performed using DS animal models, in particular the Ts65Dn mouse. Finally, we will postulate on how altered plasticity may contribute to the DS cognitive disability.
Amyloid‐Like Structures Formed by Azobenzene Peptides: Light‐Triggered Disassembly
Authors: Deeg Andreas A. , Schrader Tobias E. , Strzalka Halina , Pfizer Jose , Moroder Luis , Zinth Wolfgang
Published: July 2012

The light‐driven disassembly process of amyloid‐like structures formed by azobenzene model peptides is studied by time‐resolved mid‐IR spectroscopy from nanoseconds to minutes. The investigated peptide consists of two amino acid strands connected by the azobenzene switch. The peptides aggregate to amyloid‐like structures when the azobenzene chromophore is in the trans-conformation. Illumination, resulting in a trans- to cis-isomerization of the azobenzene, leads to disaggregation of the aggregated structures. After optical excitation and isomerization of the azobenzene, one finds absorption changes which recover to a large extent on the time scale of few nanoseconds. These early absorption transients are assigned to the relaxation of vibrational excess energy (heat) or to structural rearrangements of isomerized azobenzene and the aggregated surroundings. It is only on the time scale of minutes that spectral signatures appear which are characteristic for the disassembly of the aggregated structure.
Detection of Fusarium oxysporum Fungal Isolates Using ATR Spectroscopy
Authors: Salman A. , Lapidot I. , Pomerantz A. , Tsror L. , Hammody Z. , Moreh R. , Huleihel M. , Mordechai S.
Published: July 2012

Fungi are considered as serious pathogens for many plants, potentially causing severe economic damage. Early detection and identification of these pathogens is crucial for their timely control. The methods available for identification of fungi are time consuming and not always very specific. In this study, the potential of FTIR‐ATR spectroscopy was examined together with advanced mathematical principle component analysis (PCA) and statistical linear discriminant analysis (LDA) to differentiate among 10 isolates of Fusarium oxysporum. The results are encouraging and indicate that FTIR‐ATR can successfully detect different isolates of Fusarium oxysporum. Based on PCA and LDA calculations in the region 850–1775 cm−1 with 16 PC′s, the different strains from the same fungal genus could be classified with 75.3% and 69.5% success rates using the “leave one out” method and “20–80% algorithm” respectively.
Spectroscopic Studies of Methimazole Reactivity toward the Aquapentacyanoferrate (II) Ion in Aqueous Solutions
Authors: Cvijanović D. , Damjanović V. , Picek I. , Foretić B.
Published: July 2012

Methimazole (2‐mercapto‐1‐methylimidazole, MMI) and its pentacyanoferrate (II) complex have been characterized by means of UV/Vis, Raman, and NMR spectroscopy. The reaction of MMI with aquapentacyanoferrate (II), [Fe(CN)5(H2O)]3−, in buffered aqueous solutions yielded the [Fe(CN)5(MMI)]3− complex. It was found that only thione tautomer of MMI coordinates to the iron (II). The exceptionally stabile and inert complex was produced.