bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical properties of soil freshly amended with Miscanthus biochar
Authors: Menon M. , Tatari A. , Smith C. C.
Published: November 2018

Biochar has been shown to have multiple, positive benefits on soil physico‐chemical and biological properties. However, mechanical behaviour of biochar‐amended soils has been given relatively less attention. Therefore, in this study, we aimed to describe these properties of soil freshly amended with Miscanthus biochar in the context of compaction mitigation through a comprehensive laboratory study. In particular, for the first time, we evaluated the short‐term loading and unloading responses of replicated biochar‐amended soils using a modified oedometer, using different rates of application of biochar (2, 6 and 10% w/w, dry weight basis), in two types of soil (humus‐free loam and field loam) prepared at two different (10 and 22% w/w) soil moisture contents. From the experiment, dry density (ρd), void ratio (e), compression index (Cc) and relaxation ratio (R) were derived and statistically analysed. The addition of biochar was shown to reduce ρd, while e increased with the amount of added biochar. The addition of biochar increased Cc and R. The effect of soil moisture content and soil types was also found to be statistically significant on the above parameters. However, field studies are needed to understand the long‐term mechanical behaviour of biochar‐amended soils and further studies are required to examine the performance of different biochar types and soil types.
Locals get travellers’ diarrhoea too: risk factors for diarrhoeal illness and pathogenic Escherichia coli infection across an urban‐rural gradient in Ecuador
Authors: Smith Shanon M. , Montero Lorena , Paez Maritza , Ortega Estefania , Hall Eric , Bohnert Kate , Sanchez Xavier , Puebla Edison , Endara Pablo , Cevallos William , Trueba Gabriel , Levy Karen
Published: November 2018

Objectives

Diarrhoea is a common and well‐studied cause of illness afflicting international travellers. However, traveller's diarrhoea can also result from travel between high and low disease transmission regions within a country, which is the focus of this study.

Methods

We recruited participants for a case‐control study of diarrhoea at four sites along an urban‐rural gradient in Northern Ecuador: Quito, Esmeraldas, Borbón and rural communities outside of Borbón. At each of these sites, approximately 100 subjects with diarrhoea (cases) were recruited from Ministry of Health clinics and were age‐matched with subjects visiting the same clinics for other complaints (controls).

Results

Travellers to urban destinations had higher risk of diarrhoea and diarrhoeagenic Escherichia coli (DEC) infections. Travel to Quito was associated with diarrhoea (aOR = 2.01, 95% CI = 1.10–3.68) and travel to Guayaquil (another urban centre in Ecuador) was associated with Diffuse Adherent E. coli infection (OR = 2.09, 95% CI = 1.01–4.33). Compared to those not travelling, urban origins were also associated with greater risk of diarrhoea in Esmeraldas (aOR = 2.28, 95% CI = 1.20–4.41), and with higher risk of diarrhoeagenic E. coli infections in Quito (aOR = 2.61, 95% CI = 1.16–5.86), with >50% of travel from Quito and Esmeraldas specified to another urban destination.

Conclusions

This study suggests that individuals travelling from lower‐transmission regions (rural areas) to higher transmission regions (urban centres) within a single country are at a greater risk of acquiring a diarrhoea‐related illness. Investments to improve water, sanitation and hygiene conditions in urban areas could have impacts on outlying rural areas within a given country.
Evolutionary and ecological functional genomics, from lab to the wild
Authors: Zaidem Maricris L. , Groen Simon C. , Purugganan Michael D.
Published: November 2018

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
Chinese trade price and Yuan's valuation
Authors: Gao Yichen , Gan Li , Li Qi
Published: November 2018

This paper studies how the major economic events would have affected Chinese yuan's nominal exchange rate against US dollar from 1989 to 2013. The traditional average treatment effect estimation methods cannot be used to consistently estimate yuan's pegged exchange rate. We develop a new estimation strategy by combining a novel panel data method (proposed by Hisao, Ching and Wan) and the purchasing power parity theory. Based on this new estimation strategy, we find that during the period of pegging to US dollar, Chinese yuan were undervalued. Before the 1997 Asian Financial Crisis, the pegged exchange rate regime starting from January 1994 made the yuan undervalued by 2.62%. China's accession to WTO caused yuan undervalued by 36.60%. After the reform of Chinese exchange rate policy in July 2005, the undervaluation of the yuan was reduced to only 0.76%. Yuan was undervalued again by 20.43% because of 2008 China's economy stimulus package. The policy reform in June 2010 made yuan overvalued by 14.40%. We conclude that Chinese fixed exchange rate policy indeed undervalued the yuan, especially after its accession to WTO. The recent reforms of Chinese exchange rate policy made progresses in re‐evaluating the yuan.
Low damage patterning of In0.53Ga0.47As film for its integration as n-channel in a fin metal oxide semiconductor field effect transistor architecture
Authors: Bizouerne Maxime , Pargon Erwine , Petit-Etienne Camille , Labau Sébastien , David Sylvain , Martin Mickael , Burtin Pauline
Published: November 2018

One of the challenges of InGaAs integration as a channel in a fin field effect transistor architecture is the patterning of the III–V fin with nanometer scale definition, vertical sidewalls, and undamaged surfaces. In this work, the authors propose a two-step process to etch anisotropically and with minimal damage thin layers of InGaAs material. The first step of the process aims to modify the InGaAs surface on a well-defined thickness with limited sputtering by implanting light ions generated by a low pressure He/O2 plasma. The depth of the material modification is well controlled by the ion energy and saturates with process time, giving to this step a self-limited behavior. The second step uses aqueous HF solution to remove the modified oxidized InGaAs layer with infinite selectivity over the nonmodified InGaAs layer. The repetition of cycles of the two-step process was applied to etch the thin film of InGaAs as well as pattern using a SiN hard mask. Blanket experiments show that each cycle of the two-step process allows to remove a fixed and reproducible InGaAs thickness of 5.7 nm, while blanket SiN films are not consumed. After the process, the InGaAs surface roughness is kept intact, but the surface stoichiometry is slightly degraded with Arsenic enrichment because of the wet chemical reactions between the III-As semiconductors and the acids. The results on the pattern show that it is possible to transfer the SiN hard mask into the InGaAs layer using cycles of the two-step process with a reproducible consumed InGaAs thickness at each cycle and low sidewalls surface damage. However, the process leads to tapered InGaAs profile because of the lateral consumption of the SiN hard mask due to preferential sputtering at grazing incidence angle.
Role of reactive gas on the structure and properties of titanium nitride films grown by plasma enhanced atomic layer deposition
Authors: Krylov Igor , Xu Xianbin , Zoubenko Ekaterina , Weinfeld Kamira , Boyeras Santiago , Palumbo Felix , Eizenberg Moshe , Ritter Dan
Published: November 2018

The authors report on the role of various reactive gases on the structure and properties of TiN thin films prepared by plasma enhanced atomic layer deposition (PEALD) from tetrakis(dimethylamido)titanium. The reactive gas plays an important role determining the film structure and properties. Nitrogen-based plasma (N­2 and NH3) resulted in low oxygen (∼3%) and carbon (∼2%) contamination and well-defined columnar grain structure. A nitrogen excess (∼4%) was found in the films deposited using N2 plasma. The stoichiometric films and lowest resistivity (∼80 μΩ cm) were achieved using NH3 plasma. Deposition using H2 plasma resulted in higher carbon and oxygen contamination (∼6% for each element). The reactive gas also plays an important role in determining the grain size and preferential orientation. By varying the plasma chemistry, either (111) or (100) oriented films can be obtained. A mechanism determining the PEALD TiN preferential orientation is proposed. Finally, plasma induced degradation of the underlying dielectric layer is evaluated.
ACOUSTICAL STANDARDS NEWS
Authors: Struck Christopher J.
Published: November 2018

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, S3/SC 1, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, animal bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes a catalog of Acoustical American National Standards. To receive a copy of the latest Standards catalog, please contact asastds@acousticalsociety.org.

Comments are welcomed on all material in Acoustical Standards News.

This Acoustical Standards News section in JASA and other information on the Standards Program of the Acoustical Society of America are available via the ASA home page: http://acousticalsociety.org.
Multicenter Clinical Evaluation of the Automated Aries Group A Strep PCR Assay from Throat Swabs
Authors: Kanwar N. , Crawford J. , Ulen C. , Uphoff T. S. , Dien Bard J. , Dunn R. , Drain A. , Selvarangan R.
Published: November 2018

Group A
Streptococcus
(GAS) is one of the leading causes of bacterial pharyngitis. Early GAS diagnosis is critical for appropriate antibiotic administration that reduces the risk of GAS sequelae and limits spread of the infection.
Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing
Authors: Monk Jonathan M.
Published: November 2018

Thanks to the genomics revolution, thousands of strain-specific whole-genome sequences are now accessible for a wide range of pathogenic bacteria. This availability enables big data informatics approaches to be used to study the spread and acquisition of antimicrobial resistance (AMR).
The Ectodomain of the Vaccinia Virus Glycoprotein A34 Is Required for Cell Binding by Extracellular Virions and Contains a Large Region Capable of Interaction with Glycoprotein B5
Authors: Monticelli Stephanie R. , Earley Amalia K. , Tate Jessica , Ward Brian M.
Published: November 2018

Previous studies have shown that the vaccinia virus glycoproteins A34 and B5 interact, and in the absence of A34, B5 is mislocalized and not incorporated into extracellular virions. Here, using a transient-transfection assay, residues 80 to 130 of the ectodomain of A34 were determined to be sufficient for interaction with B5. Recombinant viruses expressing A34 with a full, partial, or no B5 interaction site were constructed and characterized. All of the A34 truncations interacted with B5 as predicted by the transient-transfection studies but had a small-plaque phenotype. Further analysis revealed that all of the recombinants incorporated detectable levels of B5 into released virions but were defective in cell binding and extracellular virion (EV) dissolution. This study is the first to directly demonstrate that A34 is involved in cell binding and implicate the ectodomain in this role.
Defective Viral Genomes Alter How Sendai Virus Interacts with Cellular Trafficking Machinery, Leading to Heterogeneity in the Production of Viral Particles among Infected Cells
Authors: Genoyer Emmanuelle , López Carolina B.
Published: November 2018

Defective viral genomes (DVGs) generated during Sendai virus infections accumulate in the cytoplasm of some infected cells and stimulate antiviral immunity and cell survival. DVGs are packaged and released as defective particles and have a significant impact on infection outcome. We show that the subpopulation of DVG-high cells poorly engages the virus packaging and budding machinery and do not effectively produce viral particles. In contrast, cells enriched in full-length genomes are the primary producers of both standard and defective viral particles during infection. This study demonstrates heterogeneity in the molecular interactions occurring within infected cells and highlights distinct functional roles for cells as either initiators of immunity or producers and perpetuators of viral particles depending on their content of viral genomes and their intracellular localization.
Epidemiology of injuries, treatment (costs) and outcome in burn patients admitted to a hospital with or without dedicated burn centre (Burn-Pro): protocol for a multicentre prospective observational study
Authors: Van Lieshout Esther MM , Van Yperen Daan T , Van Baar Margriet E , Polinder Suzanne , Boersma Doeke , Cardon Anne YMVP , De Rijcke Piet AR , Guijt Marc , Klem Taco MAL , Lansink Koen WW , Ringburg Akkie N , Staarink Maarten , Van de Schoot Leon , Van der Veen Alexander H , Van Eijck Floortje C , Van Eerten Percy V , Vegt Paul A , Vos Dagmar I , Waleboer Marco , Verhofstad Michael HJ , Van der Vlies Cornelis H
Published: November 2018

Introduction

The Emergency Management of Severe Burns (EMSB) referral criteria have been implemented for optimal triaging of burn patients. Admission to a burn centre is indicated for patients with severe burns or with specific characteristics like older age or comorbidities. Patients not meeting these criteria can also be treated in a hospital without burn centre. Limited information is available about the organisation of care and referral of these patients. The aims of this study are to determine the burn injury characteristics, treatment (costs), quality of life and scar quality of burn patients admitted to a hospital without dedicated burn centre. These data will subsequently be compared with data from patients with<10% total bodysurface area (TBSA) burned who are admitted (or secondarily referred) to a burn centre. If admissions were in agreement with the EMSB, referral criteria will also be determined.

Methods and analysis

In this multicentre, prospective, observational study (cohort study), the following two groups of patients will be followed: 1) all patients (no age limit) admitted with burn-related injuries to a hospital without a dedicated burn centre in the Southwest Netherlands or Brabant Trauma Region and 2) all patients (no age limit) with<10% TBSA burned who are primarily admitted (or secondarily referred) to the burn centre of Maasstad Hospital. Data on the burn injury characteristics (primary outcome), EMSB compliance, treatment, treatment costs and outcome will be collected from the patients’ medical files. At 3 weeks and at 3, 6 and 12 months after trauma, patients will be asked to complete the quality of life questionnaire (EuroQoL-5D), and the patient-reported part of the Patient and Observer Scar Assessment Scale (POSAS). At those time visits, the coordinating investigator or research assistant will complete the observer-reported part of the POSAS.

Ethics and dissemination

This study has been exempted by the medical research ethics committee Erasmus MC (Rotterdam, The Netherlands). Each participant will provide written consent to participate and remain encoded during the study. The results of the study are planned to be published in an international, peer-reviewed journal.

Trial registration number

NTR6565.
Near-infrared spectroscopy monitoring during out-of-hospital cardiac arrest: can the initial cerebral tissue oxygenation index predict ROSC?
Authors: Tsukuda Jumpei , Fujitani Shigeki , Morisawa Kenichiro , Shimozawa Nobuhiko , Lohman Brandon D , Okamoto Kentaro , Kawaguchi Takeshi , Takamatsu Yuka , Fujii Shuichi , Ozaki Masayuki , Rahman Mahbubur , Taira Yasuhiko
Published: November 2018

Study objectives

Near-infrared spectroscopy is a modality that can monitor tissue oxygenation index (TOI) and has potential to evaluate return of spontaneous circulation (ROSC) during cardiopulmonary resuscitation (CPR). This study’s objectives were to evaluate whether TOI could be associated with ROSC and used to help guide the decision to either terminate CPR or proceed to extracorporeal CPR (ECPR).

Methods

In this observational study, we assessed the patients with out-of-hospital cardiac arrest with non-traumatic cause receiving CPR on arrival at our ED between 2013 and 2016. TOI monitoring was discontinued either on CPR termination after ROSC was reached or on patient death. Patients were classified into two groups: ROSC and non-ROSC group.

Results

Out of 141 patients, 24 were excluded and the remaining 117 were classified as follows: ROSC group (n=44) and non-ROSC group (n=73). ROSC group was significantly younger and more likely to have their event witnessed and bystander CPR. ROSC group showed a higher initial TOI than non-ROSC group (60.5%±17.0% vs 37.9%±13.7%: p<0.01). Area under the curve analysis was more accurate with the initial TOI than without it for predicting ROSC (0.88, 95% CI 0.82 to 0.95 vs 0.79, 95% CI 0.70 to 0.87: p<0.01). TOI cut-off value ≥59% appeared to favour survival to hospital discharge whereas TOI ≤24% was associated with non-ROSC.

Conclusions

This study demonstrated an association between higher initial TOI and ROSC. Initial TOI could increase the accuracy of ROSC prognosis and may be a clinical factor in the decision to terminate CPR and select patients who are to proceed to ECPR.
Why caesarean is more unequally concentrated among better-off people in Tehran? A concentration index decomposition approach
Authors: Omani-Samani Reza , Almasi-Hashiani Amir , Safiri Saeid , Rezaeinejad Mahroo , Shokri Fatemeh , Khedmati Morasae Esmaeil , Maroufizadeh Saman , Sepidarkish Mahdi
Published: November 2018

Background

Iran, as one of the low-income and middle-income countries, has experienced a remarkable increase in the caesarean section (CS) rate during the past three decades. Although several studies have been conducted on the prevalence and risk factors affecting CS, but few studies were done regarding socioeconomic factors influencing the CS rate. The aim of this study was to identify socioeconomic inequalities and its determinants in CS in Tehran, capital of Iran.

Methods

A population-based cross-sectional study was conducted on 5170 pregnancies in Tehran, since 2015. Principal component analysis was applied to measure the asset-based economic status. Concentration index was used to measure socioeconomic inequality in CS and then decomposed in to its determinants.

Results

The concentration index and its 95% CI for CS history was 0.102 (0.091 to 0.112). Decomposition of the concentration index showed that economic status had the largest contribution (49.2%) to socioeconomic inequality in CS. Mother’s education (14.9%), father’s occupation (13.3%) and father’s nationality (9.7%) had the next high positive contribution to measured inequality in CS, respectively.

Conclusions

CS is mostly concentrated among women with high economic status. The identified contributing factors should be addressed to decrease the socioeconomic inequalities as possible.
Government social assistance programmes are failing to protect the health of low-income populations: evidence from the USA and Canada (2003–2014)
Authors: Vahid Shahidi Faraz , Sod-Erdene Odmaa , Ramraj Chantel , Hildebrand Vincent , Siddiqi Arjumand
Published: November 2018

Background

Social policies that improve the availability and distribution of key socioeconomic resources such as income, wealth and employment are believed to present the most promising avenue for reducing health inequalities. The present study aims to estimate the effect of social assistance recipiency on the health of low-income earners in the USA and Canada.

Methods

Drawing on nationally representative survey data (National Health Interview Survey and the Canadian Community Health Survey), we employed propensity score matching to match recipients of social assistance to comparable sets of non-recipient ‘controls’. Using a variety of matching algorithms, we estimated the treatment effect of social assistance recipiency on self-rated health, chronic conditions, hypertension, obesity, smoking, binge drinking and physical inactivity.

Results

After accounting for underlying differences in the demographic and socioeconomic characteristics of recipients and non-recipients, we found that social assistance recipiency was associated with worse health status or, at best, the absence of a clear health advantage. This finding was consistent across several different matching strategies and a diverse range of health outcomes.

Conclusions

From a public health perspective, our findings suggest that interventions are warranted to improve the scope and generosity of existing social assistance programmes. This may include reversing welfare reforms implemented over the past several decades, increasing benefit levels and untethering benefit recipiency from stringent work conditionalities.
A new control method of rotor re-suspension after short failure of active magnetic bearing system
Authors: Zhu Yi-Li , Zhang Yan-Hong , Liu Yi-Lin
Published: November 2018

As it is difficult for traditional control method to realize rotor resuspension after short failure of Active Magnetic Bearing (AMB) system, a new control method containing rotor collision force evaluation algorithm module, rotor position control algorithm module and rotor vibration speed control algorithm module was proposed. Through the evaluation of rotor collision force, the controller automatically selects rotor positon control mode or rotor speed control mode. Based on rigid rotor theory, rotor dynamic model was established to analyze the dynamic responses after short failure of AMB system utilizing different control method. The results proved that the proposed control method can successfully realize rotor re-suspension.
Research on fault diagnosis of diesel engine based on PCA-RBF neural network
Authors: Zhang Meifeng , Li Yongxin , Cai Jianwen , Chen Fuhao , Miao Xin
Published: November 2018

In order to improve the fault diagnosis rate and efficiency of diesel engine, the PCA-RBF neural network as a new algorithm was constructed by combing the character extraction ability of PCA with the nonlinear approximation ability of RBF neural network. Firstly, eight factors which affected the fault types of diesel engine were analyzed and three principal components were extracted by PCA. Secondly, the data obtained from the three principal components were taken as the input of RBF neural network which was trained and tested. Finally, the PCA-RBF neural network was verified through simulation. The simulation results show that the network has fewer training steps, less training and higher training accuracy.
Stochastic operational matrix of Chebyshev wavelets for solving multi-dimensional stochastic Itô–Volterra integral equations
Authors: Singh S. , Saha Ray S.
Published: November 2018

In this paper, the numerical solutions of multi-dimensional stochastic Itô–Volterra integral equations have been obtained by second kind Chebyshev wavelets. The second kind Chebyshev wavelets are orthonormal and have compact support on [Formula: see text]. The block pulse functions and their relations to second kind Chebyshev wavelets are employed to derive a general procedure for forming stochastic operational matrix of second kind Chebyshev wavelets. The system of integral equations has been reduced to a system of nonlinear algebraic equations and solved for obtaining the numerical solutions. Convergence and error analysis of the proposed method are also discussed. Furthermore, some examples have been discussed to establish the accuracy and efficiency of the proposed scheme.
Adaptive Static Analysis via Learning with Bayesian Optimization
Authors: Heo Kihong , Oh Hakjoo , Yang Hongseok , Yi Kwangkeun
Published: November 2018

Building a cost-effective static analyzer for real-world programs is still regarded an art. One key contributor to this grim reputation is the difficulty in balancing the cost and the precision of an analyzer. An ideal analyzer should be adaptive to a given analysis task and avoid using techniques that unnecessarily improve precision and increase analysis cost. However, achieving this ideal is highly nontrivial, and it requires a large amount of engineering efforts.

In this article, we present a new learning-based approach for adaptive static analysis. In our approach, the analysis includes a sophisticated parameterized strategy that decides, for each part of a given program, whether to apply a precision-improving technique to that part or not. We present a method for learning a good parameter for such a strategy from an existing codebase via Bayesian optimization. The learnt strategy is then used for new, unseen programs. Using our approach, we developed partially flow- and context-sensitive variants of a realistic C static analyzer. The experimental results demonstrate that using Bayesian optimization is crucial for learning from an existing codebase. Also, they show that among all program queries that require flow- or context-sensitivity, our partially flow- and context-sensitive analysis answers 75% of them, while increasing the analysis cost only by 3.3× of the baseline flow- and context-insensitive analysis, rather than 40× or more of the fully sensitive version.
Static Prediction of Silent Stores
Authors: Pereira Fernando Magno Quintão , Leobas Guilherme Vieira , Gamatié Abdoulaye
Published: November 2018

A store operation is called “silent” if it writes in memory a value that is already there. The ability to detect silent stores is important, because they might indicate performance bugs, might enable code optimizations, and might reveal opportunities of automatic parallelization, for instance. Silent stores are traditionally detected via profiling tools. In this article, we depart from this methodology and instead explore the following question: is it possible to predict silentness by analyzing the syntax of programs? The process of building an answer to this question is interesting in itself, given the stochastic nature of silent stores, which depend on data and coding style. To build such an answer, we have developed a methodology to classify store operations in terms of syntactic features of programs. Based on such features, we develop different kinds of predictors, some of which go much beyond what any trivial approach could achieve. To illustrate how static prediction can be employed in practice, we use it to optimize programs running on nonvolatile memory systems.
RAGuard
Authors: Zhang Jun , Hou Rui , Song Wei , Mckee Sally A. , Jia Zhen , Zheng Chen , Chen Mingyu , Zhang Lixin , Meng Dan
Published: November 2018

Control-flow integrity (CFI) is a general method for preventing code-reuse attacks, which utilize benign code sequences to achieve arbitrary code execution. CFI ensures that the execution of a program follows the edges of its predefined static Control-Flow Graph: any deviation that constitutes a CFI violation terminates the application. Despite decades of research effort, there are still several implementation challenges in efficiently protecting the control flow of function returns (Return-Oriented Programming attacks). The set of valid return addresses of frequently called functions can be large and thus an attacker could bend the backward-edge CFI by modifying an indirect branch target to another within the valid return set. This article proposes RAGuard, an efficient and user-transparent hardware-based approach to prevent Return-Oreiented Programming attacks. RAGuard binds a message authentication code (MAC) to each return address to protect its integrity. To guarantee the security of the MAC and reduce runtime overhead: RAGuard (1) computes the MAC by encrypting the signature of a return address with AES-128, (2) develops a key management module based on a Physical Unclonable Function (PUF) and a True Random Number Generator (TRNG), and (3) uses a dedicated register to reduce MACs’ load and store operations of leaf functions. We have evaluated our mechanism based on the open-source LEON3 processor and the results show that RAGuard incurs acceptable performance overhead and occupies reasonable area.
GenMatcher
Authors: Wang Ping , McHale Luke , Gratz Paul V. , Sprintson Alex
Published: November 2018

Packet classification methods rely upon packet content/header matching against rules. Thus, throughput of matching operations is critical in many networking applications. Further, with the advent of Software Defined Networking (SDN), efficient implementation of software approaches to matching are critical for the overall system performance.

This article presents
1
GenMatcher, a generic, software-only, arbitrary matching framework for fast, efficient searches. The key idea of our approach is to represent arbitrary rules with efficient prefix-based tries. To support arbitrary wildcards, we rearrange bits within the rules such that wildcards accumulate to one side of the bitstring. Since many non-contiguous wildcards often remain, we use multiple prefix-based tries. The main challenge in this context is to generate efficient trie groupings and expansions to support all arbitrary rules. Finding an optimal mix of grouping and expansion is an NP-complete problem.

Our contribution includes a novel, clustering-based grouping algorithm to group rules based upon their bit-level similarities. Our algorithm generates near-optimal trie groupings with low configuration times and provides significantly higher match throughput compared to prior techniques. Experiments with synthetic traffic show that our method can achieve a 58.9X speedup compared to the baseline on a single core processor under a given memory constraint.
Extraction of Emotional Information via Visual Scanning Patterns
Authors: Wade Joshua , Nichols Heathman S. , Ichinose Megan , Bian Dayi , Bekele Esube , Snodgress Matthew , Amat Ashwaq Zaini , Granholm Eric , Park Sohee , Sarkar Nilanjan
Published: November 2018

Emotion recognition impairment is a core feature of schizophrenia (SZ), present throughout all stages of this condition, and leads to poor social outcome. However, the underlying mechanisms that give rise to such deficits have not been elucidated and hence, it has been difficult to develop precisely targeted interventions. Evidence supports the use of methods designed to modify patterns of visual attention in individuals with SZ in order to effect meaningful improvements in social cognition. To date, however, attention-shaping systems have not fully utilized available technology (e.g., eye tracking) to achieve this goal. The current work consisted of the design and feasibility testing of a novel gaze-sensitive social skills intervention system called MASI-VR. Adults from an outpatient clinic with confirmed SZ diagnosis (
n
= 10) and a comparison sample of neurotypical participants (
n
= 10) were evaluated on measures of emotion recognition and visual attention at baseline assessment, and a pilot test of the intervention system was evaluated on the SZ sample following five training sessions over three weeks. Consistent with the literature, participants in the SZ group demonstrated lower recognition of faces showing medium intensity fear, spent more time deliberating about presented emotions, and had fewer fixations in comparison to neurotypical peers. Furthermore, participants in the SZ group showed significant improvement in the recognition of fearful faces post-training. Preliminary evidence supports the feasibility of a gaze-sensitive paradigm for use in assessment and training of emotion recognition and social attention in individuals with SZ, thus warranting further evaluation of the novel intervention.
Immunotherapy for Glioblastoma: Adoptive T-cell Strategies
Authors: Choi Bryan D. , Maus Marcela V. , June Carl H. , Sampson John H.
Published: November 2018

Glioblastoma (GBM) is a devastating disease with an extremely poor prognosis. Immunotherapy via adoptive cell transfer (ACT), especially with T cells engineered to express chimeric antigen receptors (CAR), represents a particularly promising approach. Despite the recent success of CAR T cells for blood cancers, the question remains whether this powerful anticancer therapy will ultimately work for brain tumors, and whether the primary immunologic challenges in this disease, which include antigenic heterogeneity, immune suppression, and T-cell exhaustion, can be adequately addressed. Here, we contextualize these concepts by reviewing recent developments in ACT for GBM, with a special focus on pioneering clinical trials of CAR T-cell therapy.
AKT Inhibition Modulates H3K4 Demethylase Levels in PTEN-Null Prostate Cancer
Authors: Khan Mohammad Imran , Hamid Abid , Rath Suvasmita , Ateeq Bushra , Khan Qateeb , Siddiqui Imtiaz A. , Adhami Vaqar Mustafa , Choudhry Hani , Zamzami Mazin A. , Mukhtar Hasan
Published: November 2018

Hyperactivated AKT kinase due to loss of its negative regulator PTEN influences many aspects of cancer biology, including chromatin. AKT primarily regulates acetyl-CoA production and phosphorylates many histone-modulating enzymes, resulting in their activation or inhibition. Therefore, understanding the therapeutic impact of AKT inhibition on chromatin-related events is essential. Here, we report that AKT inhibition in prostate-specific PTEN knockout mice significantly induces di- and trimethylation of H3K4 with concomitant reduction in H3K9 acetylation. Mechanistically, we observed that AKT inhibition reduces expression of the H3K4 methylation-specific histone demethylases KDM5 family, especially KDM5B expression at transcriptional levels. Furthermore, we observed that AKT negatively regulates miR-137 levels, which transcriptionally represses KDM5B expression. Overexpression of miR-137 significantly reduced KDM5B and increased H3K4 methylation levels but failed to change AKT phosphorylation. Overall, we observed that AKT transcriptionally regulates KDM5B mainly via repression of miR-137. Our data identify a mechanism by which AKT kinase modulates the prostate cancer epigenome through regulating H3K4 methylation. Additional studies on AKT inhibition–mediated induction of H3K4 methylation will help in designing strategies to enhance the therapeutic efficacy of PI3K/AKT inhibitors.
Candida albicans Increases Dentine Demineralization Provoked by Streptococcus mutans Biofilm
Authors: Sampaio Aline A. , Souza Samilly E. , Ricomini-Filho Antônio P. , Del Bel Cury Altair A. , Cavalcanti Yuri W. , Cury Jaime A.
Published: November 2018

Streptococcus mutans are considered the most cariogenic bacteria, but it has been suggested that Candida albicans could increase their cariogenicity. However, the effect of this dual-species microorganisms’ combination on dentine caries has not been experimentally evaluated. Biofilms of C. albicans, S. mutans and C. albicans + S. mutans (n = 12/biofilm) were grown in ultra-filtered tryptone yeast extract broth culture medium for 96 h on root dentine slabs of known surface hardness and exposed 8 times per day for 3 min to 10% sucrose. The medium was changed 2 times per day (after the 8 cariogenic challenges and after the overnight period of famine), and aliquots were analyzed to determinate the pH (indicator of biofilm acidogenicity). After 96 h, the biofilms were collected to determine the wet weight, colony-forming units, and the amounts of extracellular polysaccharides (soluble and insoluble). Dentine demineralization was assessed by surface hardness loss (% SHL). The architecture of the biofilms was analyzed by confocal laser scanning microscopy (CLSM) and transmission electron microscopy (TEM). Data were analyzed by ANOVA followed by Tukey’s test (α = 0.05). The dual-species C. albicans + S. mutans biofilm provoked higher % SHL on dentine (p < 0.05) than the S. mutans and C. albicans biofilm. This was supported by the results of biofilm acidogenicity and the amounts of soluble (6.4 ± 2.14 vs. 4.0 ± 0.94 and 1.9 ± 0.97, respectively) and insoluble extracellular polysaccharides (24.9 ± 9.22 vs. 18.9 ± 5.92 and 0.7 ± 0.48, respectively) (p < 0.05). The C. albicans biofilm alone presented low cariogenicity. The images by CLSM and TEM, respectively, suggest that the C. albicans + S. mutans biofilm is more voluminous than the S. mutans biofilm, and S. mutans cells interact with C. albicans throughout polysaccharides from the biofilm matrix. These findings show that C. albicans enhances the cariogenic potential of the S. mutans biofilm, increasing dentine demineralization.
Mechanisms of Hydrogen Sulfide against the Progression of Severe Alzheimer’s Disease in Transgenic Mice at Different Ages
Authors: Vandini Eleonora , Ottani Alessandra , Zaffe Davide , Calevro Anita , Canalini Fabrizio , Cavallini Gian Maria , Rossi Rosario , Guarini Salvatore , Giuliani Daniela
Published: November 2018

Backgroud: Alzheimer disease is an age-related severe neurodegenerative pathology. The level of the third endogenous gas, hydrogen sulfide (H2S), is decreased in the brain of Alzheimer’s disease (AD) patients compared with the brain of the age-matched normal individuals; also, plasma H2S levels are negatively correlated with the severity of AD. Recently, we have demonstrated that systemic H2S injections are neuroprotective in an early phase of preclinical AD. Objectives: This study focuses on the possible neuroprotection of a chronic treatment with an H2S donor and sulfurous water (rich of H2S) in a severe transgenic 3×Tg-AD mice model. Method: 3×Tg-AD mice at 2 different ages (6 and 12 months) were daily treated intraperitoneally with an H2S donor and sulfurous water (rich of H2S) for 3 months consecutively. We investigated the cognitive ability, brain morphological alterations, amyloid/tau cascade, excitotoxic, inflammatory and apoptotic responses. Results: Three months of treatments with H2S significantly protected against impairment in learning and memory in a severe 3×Tg-AD mice model, at both ages studied, and reduced the size of Amyloid β plaques with preservation of the morphological picture. This neuroprotection appeared mainly in the cortex and hippocampus, associated with reduction in activity of c-jun N-terminal kinases, extracellular signal-regulated kinases and p38, which have an established role not only in the phosphorylation of tau protein but also in the inflammatory and excitotoxic response. Conclusion: Our findings indicate that appropriate treatments with various sources of H2S, might represent an innovative approach to counteract early and severe AD progression in humans.
New Insights into Kleefstra Syndrome: Report of Two Novel Cases with Previously Unreported Features and Literature Review
Authors: Ciaccio Claudia , Scuvera Giulietta , Tucci Arianna , Gentilin Barbara , Baccarin Marco , Marchisio Paola , Avignone Sabrina , Milani Donatella
Published: November 2018

Kleefstra syndrome (KS) is a rare genetic condition resulting from either 9q34.3 microdeletions or mutations in the EHMT1 gene located in the same genomic region. To date, approximately 100 patients have been reported, thereby allowing the core phenotype of KS to be defined as developmental delay/intellectual disability, generalized hypotonia, neuropsychiatric anomalies, and a distinctive facial appearance. Here, to further expand the knowledge on genotype and phenotype of this condition, we report 2 novel cases: one patient carrying a 46-kb 9q34.3 deletion and showing macrocephaly never described in KS, and a second patient carrying a classic 9q34.3 deletion, presenting with a previously unreported skeletal feature (postaxial polydactyly of the right foot) and an unusual brain anomaly (olfactory bulb hypoplasia) observed via magnetic resonance imaging. Further, we provide a review of the current literature regarding KS and compare these 2 patients with those previously described, thereby confirming that the genotype-phenotype correlation in KS remains difficult to determine.
Hepatitis B Virus X Protein Increases 8-Oxo-7,8-Dihydro-2ʹ-Deoxyguanosine (8-Oxodg) Level via Repressing MTH1/ MTH2 Expression in Hepatocytes
Authors: Lin Yan-Ting , Liu Wei , He Yun , Wu Yun-Li , Chen Wan-Nan , Lin Xin-Jian , Lin Xu
Published: November 2018

Background/Aims: Chronic hepatitis B virus (HBV) infection markedly increases the risk of development of hepatocellular carcinoma (HCC). Among the seven viral proteins that HBV encodes, HBV X protein (HBx) appears to have the most oncogenic potential. The mitochondria-associated HBx can induce oxidative stress in hepatocytes, leading to the production of abundant reactive oxygen species (ROS). High levels of ROS usually induce oxidative DNA damage and 8-hydroxy-2-deoxyguanosine (8-OHdG), also known as 8-oxo-7,8-dihydro-2-deoxyguanosine (8-oxodG), which is one of the major products of DNA oxidation and an important biomarker for oxidative stress and carcinogenesis. Cells have evolved a mechanism to prevent oxidized nucleotides from their incorporation into DNA through nucleotide pool sanitization enzymes of MTH1 (NUDT1), MTH2 (NUDT15), MTH3 (NUDT18) and NUDT5. However, little is known as to whether HBx can regulate the expression of those enzymes and modulate the formation and accumulation of 8-oxodG in hepatocytes. Methods: The level of 8-oxodG was assessed by ELISA in stable HBV-producing hepatoma cell lines, an HBV infectious mouse model, HBV and HBx transgenic mice and HBV-infected patients versus their respective controls. Expression of MTH1, MTH2, MTH3 and NUDT5 was determined by a real-time quantitative PCR and western blot analysis. Transcriptional regulation of MTH1 and MTH2 expression by HBx and the effect of HBx on MTH1 and MTH2 promoter hypermethylation were examined using a luciferase reporter assay and bisulfite sequencing analysis. Results: In comparison with controls, significantly higher levels of 8-oxodG were detected in the genome and culture supernatant of stable HBV-producing HepG2.2.15 cells, in the sera and liver tissues of HBV infectious mice and HBV or HBx transgenic mice, and in the sera of HBV-infected patients. Expression of HBx in hepatocytes significantly increased 8-oxodG level and reduced the expression of MTH1 and MTH2 at both mRNA and protein levels. It was also demonstrated that HBx markedly attenuated the MTH1 or MTH2 promoter activities through hypermethylation. Furthermore, enhancement of 8-oxodG production by HBx was reversible by overexpression of MTH1 and MTH2. Conclusion: Our data show that HBx expression results in the accumulation of 8-oxodG in hepatocytes through inhibiting the expression of MTH1 and MTH2. This may implicate that HBx may act as a tumor promoter through facilitating the mutational potential of 8-oxodG thus connecting a possible link between HBV infection and liver carcinogenesis.
Cytoprotective Effects of N-Acetylcysteine on Streptozotocin- Induced Oxidative Stress and Apoptosis in RIN-5F Pancreatic β-Cells
Authors: Al-Nahdi Arwa M.T. , John Annie , Raza Haider 
Published: November 2018

Background/Aims: Numerous studies have reported overproduction of reactive oxygen species (ROS) and alterations in mitochondrial energy metabolism in the development of diabetes and its complications. The potential protective effects of N-acetylcysteine (NAC) in diabetes have been reported in many therapeutic studies. NAC has been shown to reduce oxidative stress and enhance redox potential in tissues protecting them against oxidative stress associated complications in diabetes. In the current study, we aimed to investigate the molecular mechanisms of the protective action of NAC on STZ-induced toxicity in insulin secreting Rin-5F pancreatic β-cells. Methods: Rin-5F cells were grown to 80% confluence and then treated with 10mM STZ for 24h in the presence or absence of 10mM NAC. After sub-cellular fractionation, oxidative stress, GSH-dependent metabolism and mitochondrial respiratory functions were studied using spectrophotometric, flow cytometric and Western blotting techniques. Results: Our results showed that STZ-induced oxidative stress and apoptosis caused inhibition in insulin secretion while NAC treatment restored the redox homeostasis, enhanced insulin secretion in control cells and prevented apoptosis in STZ-treated cells. Moreover, NAC attenuated the inhibition of mitochondrial functions induced by STZ through partial recovery of the mitochondrial enzymes and restoration of membrane potential. STZ-induced DNA damage and expression of apoptotic proteins were significantly inhibited in NAC-treated cells. Conclusion: Our results suggest that the cytoprotective action of NAC is mediated via suppression of oxidative stress and apoptosis and restoration of GSH homeostasis and mitochondrial bioenergetics. This study may, thus, help in better understanding the cellular defense mechanisms of pancreatic β-cells against STZ-induced cytotoxicity.
Butyrate Modulates Inflammation in Chondrocytes via GPR43 Receptor
Authors: Pirozzi Claudio  , Francisco Vera , Guida Francesca Di , Gómez Rodolfo , Lago Francisca , Pino Jesus , Meli Rosaria , Gualillo Oreste
Published: November 2018

Background/Aims: Osteoarthritis (OA) is a joint degenerative biomechanical disorder involving immunity, metabolic alterations, inflammation, and cartilage degradation, where chondrocytes play a pivotal role. OA has not effective pharmacological treatments and new therapeutic targets are needed. Adipokines contribute to the low-grade systemic inflammation in OA. Here, we explored novel molecular mechanisms of sodium butyrate (BuNa) in modulating inflammation and chemotaxis in chondrocytes, demonstrating the direct involvement of its G protein-coupled receptor (GPR)-43. Methods: ATDC5 murine chondrocytes were stimulated with interleukin (IL)-1β, in the presence or not of BuNa, for 24 h. RT-PCR and Western blot analysis was performed to evaluate the expression of inflammatory mediators and structural proteins. Results: Butyrate reduced the expression of canonic pro-inflammatory mediators (Nos2, COX-2, IL-6), pro-inflammatory adipokines (lipocalin-2 and nesfatin-1) and adhesion molecule (VCAM-1 and ICAM-1) in IL-1β-stimulated chondrocytes, inhibiting several inflammatory signalling pathways (NFκB, MAPKinase, AMPK-α, PI3K/Akt). Butyrate also reduced metalloproteinase production and limited the loss of type II collagen in IL-1β-inflamed chondrocytes. The chemoattractant effect of butyrate, after different inflammatory challenges, was revealed by increased annexin (AnxA)1 levels and chemokines expression. The chemoattractant and anti-inflammatory activities of butyrate were completely blunted by GPR43 silencing using RNA interference. Conclusion: Taken together, our data suggest the potential application of sodium butyrate as a novel candidate in a multi-target approach for the treatment of chondrocyte inflammation and cartilage degenerative process.