bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Studies Neglect Apparently Gram-Negative Populations in the Human Gut Microbiota
Authors: Hugon Perrine , Lagier Jean-Christophe , Robert Catherine , Lepolard Catherine , Papazian Laurent , Musso Didier , Vialettes Bernard , Raoult Didier
Published: July 2013

Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the
Bacteroidetes
and
Firmicutes
phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10
10
prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive prokaryote ratio (ρ = 0.3282,
P
= 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the
Bacteroidetes
/
Firmicutes
ratio (ρ = 0.6057,
P
= 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies.
Cardiac Device-Related Endocarditis Caused by Paenibacillus glucanolyticus
Authors: Ferrand Janina , Hadou Tahar , Selton-Suty Christine , Goehringer François , Sadoul Nicolas , Alauzet Corentine , Lozniewski Alain
Published: July 2013

We report the first case of
Paenibacillus glucanolyticus
infection in a 65-year-old patient with type 2 diabetes who developed a cardiac device-related endocarditis. The identification of the isolate was performed using phenotypic methods, including mass spectrometry-based methods, and 16S rRNA gene sequencing.
Absence of Frequent Herpesvirus Transmission in a Nonhuman Primate Predator-Prey System in the Wild
Authors: Murthy Sripriya , Couacy-Hymann Emmanuel , Metzger Sonja , Nowak Kathrin , De Nys Helene , Boesch Christophe , Wittig Roman , Jarvis Michael A. , Leendertz Fabian H. , Ehlers Bernhard
Published: July 2013

Emergence of viruses into the human population by transmission from nonhuman primates (NHPs) represents a serious potential threat to human health that is primarily associated with the increased bushmeat trade. Transmission of RNA viruses across primate species appears to be relatively frequent. In contrast, DNA viruses appear to be largely host specific, suggesting low transmission potential. Herein, we use a primate predator-prey system to study the risk of herpesvirus transmission between different primate species in the wild. The system was comprised of western chimpanzees (
Pan troglodytes verus
) and their primary (western red colobus,
Piliocolobus badius badius
) and secondary (black-and-white colobus,
Colobus polykomos
) prey monkey species. NHP species were frequently observed to be coinfected with multiple beta- and gammaherpesviruses (including new cytomegalo- and rhadinoviruses). However, despite frequent exposure of chimpanzees to blood, organs, and bones of their herpesvirus-infected monkey prey, there was no evidence for cross-species herpesvirus transmission. These findings suggest that interspecies transmission of NHP beta- and gammaherpesviruses is, at most, a rare event in the wild.
Vaccinia Virus A19 Protein Participates in the Transformation of Spherical Immature Particles to Barrel-Shaped Infectious Virions
Authors: Satheshkumar P. S. , Weisberg Andrea S. , Moss Bernard
Published: July 2013

The A19L open reading frame of vaccinia virus encodes a 9-kDa protein that is conserved in all sequenced chordopoxviruses, yet until now it has not been specifically characterized in any species. We appended an epitope tag after the start codon of the A19L open reading frame without compromising infectivity. The protein was synthesized after viral DNA replication and was phosphorylated independently of the vaccinia virus F10 kinase. The A19 protein was present in purified virions and was largely resistant to nonionic detergent extraction, suggesting a location within the core. A conditional lethal mutant virus was constructed by placing the A19 open reading frame under the control of the
Escherichia coli lac
repressor system. A19 synthesis and infectious virus formation were dependent on inducer. In the absence of inducer, virion morphogenesis was interrupted, and spherical dense particles that had greatly reduced amounts of the D13 scaffold accumulated in place of barrel-shaped mature virions. The infectivity of purified A19-deficient particles was more than 2 log units less than that of A19-containing virions. Nevertheless, the A19-deficient particles contained DNA, and except for the absence of A19 and decreased core protein processing, they appeared to have a similar protein composition as A19-containing virions. Thus, the A19 protein participates in the maturation of immature vaccinia virus virions to infectious particles.
Herpesvirus 6 Glycoproteins B (gB), gH, gL, and gQ Are Necessary and Sufficient for Cell-to-Cell Fusion
Authors: Tanaka Yuki , Suenaga Tadahiro , Matsumoto Misako , Seya Tsukasa , Arase Hisashi
Published: July 2013

The human herpesvirus 6 (HHV-6) envelope glycoprotein gH/gL/gQ1/gQ2 complex associates with host cell CD46 as its cellular receptor. Although gB has been suggested to be involved in HHV-6 infection, its function in membrane fusion has remained unclear. Here, we have developed an HHV-6A (strain GS)and HHV-6B (strain Z29) virus-free cell-to-cell fusion assay and demonstrate that gB and the gH/gL/gQ1/gQ2 complex are the minimum components required for membrane fusion by HHV-6.
ORIGIN OF GRANITIC ROCKS OF THE NORTHWEST ADIRONDACKS
Authors: BUDDINGTON A. F.
Published: July 2013

The hypotheses of the formation of granite by consolidation of magma derived from depth and of granite formed by granitization in association with magma intrusion are accepted as valid concepts. The results of a study of over 2000 square miles of the northwest Adirondack Highlands pre-Cambrian igneous complex are presented, and the two concepts are found far more appropriate to explain the source of the introduced material of the widespread granite masses occurring there than recourse to the hypothesis of “emanations” (hydrothermal solutions, gases, or migrating atoms and ions) from depth. It is concluded that over 85 per cent of the northwest Adirondack granitic rocks are the product of consolidation and differentiation of magma intruded as sheets or phacoliths and that less than 15 per cent is the product of migmatization and granitization of metasediments and amphibolite.
New onset refractory status epilepticus (NORSE) as the heralding manifestation of herpes simplex encephalitis
Authors: Verma Rajesh , Raut Tushar Premraj , Giri Prithvi , Praharaj Heramba Narayan
Published: July 2013

New onset refractory status epilepticus (NORSE) is a relatively novel concept used to describe a cohort of previously healthy young adults mostly women presenting with denovo refractory status epilepticus which has a miserable impact on the outcome. Various infectious and non-infectious causes have been considered to be responsible for this dreaded syndrome; however, many a times the exact cause is not identified. As therapy with antiepileptic and anaesthetic drugs is not so successful, identifying and treating the exact cause could improve the outcome. Here the authors describe a woman who presented with NORSE. Investigations confirmed the diagnosis of herpes simplex encephalitis (HSE) and she responded drastically to acyclovir along with complete control of seizures. In this case, NORSE was the presenting feature of HSE and the refractoriness of her seizures was terminated only after treating the exact cause, that is, encephalitis.
Management of large segmental tibial defects using locking IM nail and absorbable mesh
Authors: Whately Chris , Abdallah Mohamed Attia , Alwatari Yahya Ahmed
Published: July 2013

Tibia accounts for the majority of open fractures with long segmental defects. The management of such defects imposes several challenges due to their associations with extensive soft tissue damage and high infection risk. In this report, we describe a new technique for the reconstruction of tibia in a young patient with 10 cm defect. The patient had a history of Gustilo Anderson type IIIB open fracture following a motorcycle accident. He was initially managed with multiple debridements and application of an external fixator. The defect was treated with the insertion of an antibiotic-coated intramedullary nail along with posterolateral bone grafting using an absorbable mesh. Six months postoperative, radiological assessment showed excellent callus formation diffusely around the intramedullary nail along with optimal alignment. The preliminary follow-up data are quite encouraging and the technique described in our case can be considered as a reasonable option in managing long segmental bone defects.
Capillary haemangioma in a 13-year-old boy
Authors: Haddad Charles , Haddad-Lacle Judella , Webb Fern
Published: July 2013

This case presents a 13-year-old boy who developed an unusual skin lesion on his chest that occurred after 2–3 weeks following a traumatic injury. The lesion was raised and bled easily. It was surgically removed via shave excision and treated with electrocautery. The patient healed with no recurrence and minimal scarring. Pathology determined the skin lesion to be a capillary haemangioma.
Asthma and atopic dermatitis are associated with increased risk of clinicalPlasmodium falciparummalaria
Authors: Herrant Magali , Loucoubar Cheikh , Bassène Hubert , Gonçalves Bronner , Boufkhed Sabah , Diene Sarr Fatoumata , Fontanet Arnaud , Tall Adama , Baril Laurence , Mercereau-Puijalon Odile , Mécheri Salaheddine , Sakuntabhai Anavaj , Paul Richard
Published: July 2013

Objectives

To assess the impact of atopy and allergy on the risk of clinical malaria.

Design

A clinical and immunological allergy cross-sectional survey in a birth cohort of 175 children from 1 month to 14 years of age followed for up to 15 years in a longitudinal open cohort study of malaria in Senegal. Malaria incidence data were available for 143 of these children (aged 4 months to 14 years of age) for up to 15 years. Mixed-model regression analysis was used to determine the impact of allergy status on malaria incidence, adjusting for age, gender, sickle-cell trait and force of infection.

Main outcome measures

Asthma, allergic rhinoconjunctivitis and atopic dermatitis status, the number of clinicalPlasmodium falciparummalaria episodes since birth and associated parasite density.

Results

12% of the children were classified as asthmatic and 10% as having atopic dermatitis. These groups had respectively a twofold (OR 2.12 95%; CI 1.46 to 3.08; p=8×10−5) and threefold (OR 3.15; 1.56 to 6.33; p=1.3×10−3) increase in the risk of clinicalP falciparummalaria once older than the age of peak incidence of clinical malaria (3–4 years of age). They also presented with higherP falciparumparasite densities (asthma: mean 105.3 parasites/μL±SE 41.0 vs 51.3±9.7; p=6.2×10−3. Atopic dermatitis: 135.4±70.7 vs 52.3±11.0; p=0.014). There was no effect of allergy on the number of non-malaria clinical presentations. Individuals with allergic rhinoconjunctivitis did not have an increased risk of clinical malaria nor any difference in parasite densities.

Conclusions

These results demonstrate that asthma and atopic dermatitis delay the development of clinical immunity toP falciparum. Despite the encouraging decrease in malaria incidence rates in Africa, a significant concern is the extent to which the increase in allergy will exacerbate the burden of malaria. Given the demonstrated antiparasitic effect of antihistamines, administration to atopic children will likely reduce the burden of clinical malaria in these children, increase the efficacy of first-line treatment antimalarials and alleviate the non-infectious consequences of atopy.
Virtual colleagues, virtually colleagues—physicians’ use of Twitter: a population-based observational study
Authors: Brynolf Anne , Johansson Stefan , Appelgren Ester , Lynoe Niels , Edstedt Bonamy Anna-Karin
Published: July 2013

Objective

To investigate potential violations of patient confidentiality or other breaches of medical ethics committed by physicians and medical students active on the social networking site Twitter.

Design

Population-based cross-sectional observational study.

Setting

The social networking site Twitter (Swedish-speaking users, n=298819).

Population

Physicians and medical students (Swedish-speaking users, n=237) active on the social networking site Twitter between July 2007 and March 2012.

Main outcome measure

Postings that reflect unprofessional behaviour and ethical breaches among physicians and medical students.

Results

In all, 237 Twitter accounts were established as held by physicians and medical students and a total of 13 780 tweets were analysed by content. In all, 276 (1.9%) tweets were labelled as ‘unprofessional’. Among these, 26 (0.2%) tweets written by 15 (6.3%) physicians and medical students included information that could violate patient privacy. No information on the personal ID number or names was disclosed, but parts of the patient documentation or otherwise specific indicatory information on patients were found. Unprofessional tweets were more common among users writing under a pseudonym and among medical students.

Conclusions

In this study of physicians and medical students on Twitter, we observed potential violations of patient privacy and other breaches of medical ethics. Our findings underline that every physician and medical student has to consider his or her presence on social networking sites. It remains to be investigated if the introduction of social networking site guidelines for medical professionals will improve awareness.
‘Have you seen what is on Facebook?’ The use of social networking software by healthcare professions students
Authors: White Jonathan , Kirwan Paul , Lai Krista , Walton Jennifer , Ross Shelley
Published: July 2013

Objective

The use of social networking software has become ubiquitous in our society. The aim of this study was to explore the attitudes and experiences of healthcare professional students using Facebook at our school, to determine if there is a need for development of policy to assist students in this area.

Design

A mixed-methods approach was employed, using semistructured interviews to identify themes which were explored using an online survey. A combination of descriptive statistics and thematic analysis was used for analysis.

Setting

Healthcare professions education programmes at a large Canadian university.

Participants

Students of medicine, nursing, pharmacy, speech and language pathology, occupational therapy, physical therapy, dentistry, dental hygiene and medical laboratory Science were invited to participate. 14 participants were interviewed, and 682 participants responded to an online survey; the female:male balance was 3 : 1.

Results

14 interviews were analysed in-depth, and 682 students responded to the survey (17% response rate). 93% reported current Facebook use. Themes identified included patterns of use and attitudes to friendship, attitudes to online privacy, breaches of professional behaviour on Facebook and attitudes to guidelines relating to Facebook use. A majority considered posting of the following material unprofessional: use of alcohol/drugs, crime, obscenity/nudity/sexual content, patient/client information, criticism of others. 44% reported seeing such material posted by a colleague, and 27% reported posting such material themselves. A majority of participants agreed that guidelines for Facebook use would be beneficial.

Conclusions

Social networking software use, specifically Facebook use, was widespread among healthcare students at our school who responded to our survey. Our results highlight some of the challenges which can accompany the use of this new technology and offer potential insights to help understand the pedagogy and practices of Facebook use in this population, and to help students navigate the dilemmas associated with becoming 21st century healthcare professionals.
ELECTRONIC AND OPTICAL PROPERTIES OFC–N-CODOPEDTiO2: A FIRST-PRINCIPLES GGA+U INVESTIGATION
Authors: GUO MEILI , DU JIULIN
Published: July 2013

Electronic structures and optical properties of C – N -codoped anatase TiO2were calculated by using GGA+U method based on the density functional theory. The calculated results showed that the N -doped, C -doped and C – N -codoped TiO2produced 2p states in band gap, and the band gaps of the three doped systems decreased compared with the pure TiO2. According to the optical results, the band edges of the three doped systems shifted to the long wavelength region, and the visible optical absorption from 450 nm to 800 nm was observed. Moreover, the visible light response of C – N -codoped TiO2was better than the C or N single doped TiO2, indicating that there was a synergistic effect for the C – N -codoped TiO2, which offseted the deficiencies of C - or N -doped TiO2.
THE PREPARATION OF ULTRAFINE TUNGSTEN CARBIDE NANOPARTICLES BY DC ARC DISCHARGE PLASMA PROCESS
Authors: ZHAO S. Q. , JIN S. W. , WANG Y. X.
Published: July 2013

Tungsten carbide nanoparticles were synthesized successfully by DC arc discharge plasma process with 23 A discharge current at atmospheric pressure, in which tungsten positive electrode reacted with carbon black produced from the benzene cracking. The XRD results indicate that the samples consist of carbon black, WC and W 2 C . The TEM micrographs show that the tungsten carbide particles range from 3 to 7 nm in size, and are composed of WC and W 2 C .
SURFACE MODIFICATION OF NITINOL BY CHEMICAL AND ELECTROCHEMICAL ETCHING
Authors: YANG ZHENDI , WEI XIAOJIN , CAO PENG , GAO WEI
Published: July 2013

In this paper, Nitinol, an equiatomic binary alloy of nickel and titanium, was surface modified for its potential biomedical applications by chemical and electrochemical etching. The main objective of the surface modification is to reduce the nickel content on the surface of Nitinol and simultaneously to a rough surface microstructure. As a result, better biocompatibility and better cell attachment would be achieved. The effect of the etching parameters was investigated, using scanning electron microscopy (SEM) equipped with energy dispersive X-ray spectrometry (EDX) and X-ray photoelectron spectrometry (XPS). The corrosion property of modified Nitinol surfaces was investigated by electrochemical work station. After etching, the Ni content in the surface layer has been reduced and the oxidation of Ti has been enhanced.
ENERGY CONVERSION FOR THE TRANSITION FROM Al TO γ-Al2O3 NANOPARTICLES
Authors: WANG SHULIN , LI SHENGJUAN , XU BO , JIAN DUNLIANG , ZHU YUFANG
Published: July 2013

We have successfully converted large volume Al particles into γ- Al 2 O 3 nanostructures by vibration milling at room temperature and successive treatment. We show that there exist special relationships among stacking fault energy (SFE), strain energy (SRE), and surface energy (SE) of the materials, including interdependence, intercompetition, and interconversion during the phase transition. SFE and SRE perform the same changing tendency, while SE just does the opposite. However, it is not the particle size but the energy state that determines the reactivity of the materials. And it is the SE that can directly determine the physical chemical reaction and the conversion into the end product rather than SFE and SRE. When SE goes up, the material reactivity and the product yield will be enhanced; and when SE goes down, the reaction and the product yield will decay. However, the state of SE depends closely on the change tendency of the SFE and SRE. That is, when SFE and SRE goes up, SE will goes down; if SFE and SRE goes down, SE will goes up. It seems that energy conservation law may be followed in a sense in the particle system if the external input keeps constant. The work may be significant for energy conversion in nano-scale and mechanosynthesis of oxide nanoparticles.
LOW POWER AND HIGH PERFORMANCE SINGLE-ENDED SENSE AMPLIFIER
Authors: SINGH AJAY KUMAR , SEONG MAH MENG , PRABHU C. M. R.
Published: July 2013

This paper presents a new power efficient single ended sense amplifier (SA). The proposed circuit is based on the direct current voltage conversion technique. It has been simulated using Microwind3 and DSCH3 tools (advanced BSIM 4 level) for 90 nm CMOS technology in terms of power consumption, sense time and results were compared to other circuits. The proposed SA circuit consumes more than 50% less power and gives 90% faster sensing speed compared to other circuits. The lower power consumption is due to lower leakage current, lower voltage drop on bit-line and faster speed is due to positive feedback of the circuit. The proposed circuit is more robust against any process and temperature variation.
EFFECT OF MICRO-ARC OXIDATION COATINGS ON CORROSION RESISTANCE AND MECHANICAL PROPERTIES OF CLOSED-CELL ALUMINUM FOAMS
Authors: ZHU XIANYONG , LIU JIAAN
Published: July 2013

Micro-arc oxidation (MAO) coatings were prepared on closed-cell aluminum foams. The microstructure, elemental distribution and phase composition of the MAO coatings were analyzed by scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS) and X-ray diffraction (XRD), respectively. The corrosion resistances and compressive properties of the uncoated and coated aluminum foams were studied by electrochemical polarization test and mechanical test, respectively. The results show that the MAO coatings cover the surfaces of closed-cell aluminum foams. The average thickness of the MAO coatings is 7 μm. The MAO coatings are mainly composed of γ- Al 2 O 3 phase. The corrosion resistances of the closed-cell aluminum foams are improved by MAO treatment. The as-received foams show a low corrosion potential (-1.36 V), on contrary, the MAO coated foams get an increase corrosion potential (-0.78 V). But the MAO coated foams show the marginal variation in compressive strengths when the thickness of the coatings could be negligible compared with the total thickness of the foams.
Long-period orbital climate forcing in the early Palaeozoic?
Authors: Cherns L. , Wheeley J. R. , Popov L. E. , Ghobadi Pour M. , Owens R. M. , Hemsley A. R.
Published: July 2013

Facies indicators and geochemical proxies of early Palaeozoic global climate cooling suggest episodes of fluctuating glacio-eustasy and severe cold or glaciation from the Mid–Late Cambrian to Silurian (
c
. 85 myr), with a mean frequency of 2.6 myr. Long-period orbital time series predicted through the Phanerozoic are used to generate sine waves to test against these data; the null hypothesis of no orbital influence is rejected with a high confidence level. Cooling episodes appear most frequent through the Late Ordovician leading up to the Hirnantian glacial maximum, but even ‘greenhouse’ intervals of the Early–Mid-Ordovician and early Silurian provide evidence for periodic cooling episodes.
Performance evaluation of sensor networks by statistical modeling and euclidean model checking
Authors: Kwon Youngmin , Agha Gul
Published: July 2013

Modeling and evaluating the performance of large-scale wireless sensor networks (WSNs) is a challenging problem. The traditional method for representing the global state of a system as a cross product of the states of individual nodes in the system results in a state space whose size is exponential in the number of nodes. We propose an alternative way of representing the global state of a system: namely, as a probability mass function (pmf) which represents the fraction of nodes in different states. A pmf corresponds to a point in a Euclidean space of possible pmf values, and the evolution of the state of a system is represented by trajectories in this Euclidean space. We propose a novel performance evaluation method that examines all pmf trajectories in a dense Euclidean space by exploring only finite relevant portions of the space. We call our method
Euclidean model checking
. Euclidean model checking is useful both in the design phase—where it can help determine system parameters based on a specification—and in the evaluation phase—where it can help verify performance properties of a system. We illustrate the utility of Euclidean model checking by using it to design a time difference of arrival (TDoA) distance measurement protocol and to evaluate the protocol's implementation on a 90-node WSN. To facilitate such performance evaluations, we provide a Markov model estimation method based on applying a standard statistical estimation technique to samples resulting from the execution of a system.
On the quality and value of information in sensor networks
Authors: Bisdikian Chatschik , Kaplan Lance M. , Srivastava Mani B.
Published: July 2013

The increasing use of sensor-derived information from planned, ad-hoc, and/or opportunistically deployed sensor networks provides enhanced visibility to everyday activities and processes, enabling fast-paced data-to-decision in personal, social, civilian, military, and business contexts. The value that information brings to this visibility and ensuing decisions depends on the quality characteristics of the information gathered. In this article, we highlight, refine, and extend upon our past work in the areas of quality and value of information (QoI and VoI) for sensor networks. Specifically, we present and elaborate on our two-layer QoI/VoI definition, where the former relates to context-independent aspects and the latter to context-dependent aspects of an information product. Then, we refine our taxonomy of pertinent QoI and VoI attributes anchored around a simple ontological relationship between the two. Finally, we introduce a framework for scoring and ranking information products based on their VoI attributes using the analytic hierarchy multicriteria decision process, illustrated via a simple example.
Datacenter Scale Evaluation of the Impact of Temperature on Hard Disk Drive Failures
Authors: Sankar Sriram , Shaw Mark , Vaid Kushagra , Gurumurthi Sudhanva
Published: July 2013

With the advent of cloud computing and online services, large enterprises rely heavily on their datacenters to serve end users. A large datacenter facility incurs increased maintenance costs in addition to service unavailability when there are increased failures. Among different server components, hard disk drives are known to contribute significantly to server failures; however, there is very little understanding of the major determinants of disk failures in datacenters. In this work, we focus on the interrelationship between temperature, workload, and hard disk drive failures in a large scale datacenter. We present a dense storage case study from a population housing thousands of servers and tens of thousands of disk drives, hosting a large-scale online service at Microsoft. We specifically establish correlation between temperatures and failures observed at different location granularities: (a) inside drive locations in a server chassis, (b) across server locations in a rack, and (c) across multiple racks in a datacenter. We show that temperature exhibits a stronger correlation to failures than the correlation of disk utilization with drive failures. We establish that variations in temperature are not significant in datacenters and have little impact on failures. We also explore workload impacts on temperature and disk failures and show that the impact of workload is not significant. We then experimentally evaluate knobs that control disk drive temperature, including workload and chassis design knobs. We corroborate our findings from the real data study and show that workload knobs show minimal impact on temperature. Chassis knobs like disk placement and fan speeds have a larger impact on temperature. Finally, we also show the proposed cost benefit of temperature optimizations that increase hard disk drive reliability.
How to efficiently implement dynamic circuit specialization systems
Authors: Abouelella Fatma , Davidson Tom , Meeus Wim , Bruneel Karel , Stroobandt Dirk
Published: July 2013

Dynamic circuit specialization (DCS) is a technique used to implement FPGA applications where some of the input data, called parameters, change slowly compared to other inputs. Each time the parameter values change, the FPGA is reconfigured by a configuration that is specialized for those new parameter values. This specialized configuration is much smaller and faster than a regular configuration. However, the overhead associated with the specialization process should be minimized to achieve the desired benefits of using the DCS technique. This overhead is represented by both the FPGA resources needed to specialize the FPGA at runtime and by the specialization time. The introduction of
parameterized configurations
[Bruneel and Stroobandt 2008] has improved the efficiency of DCS implementations. However, the specialization overhead still takes a considerable amount of resources and time.

In this article, we explore how to efficiently build DCS systems by presenting a variety of possible solutions for the specialization process and the overhead associated with each of them. We split the specialization process into two main phases: the evaluation and the configuration phase. The PowerPC embedded processor, the MicroBlaze, and a customized processor (CP) are used as alternatives in the evaluation phase. In the configuration phase, the ICAP and a custom configuration interface (SRL configuration) are used as alternatives. Each solution is used to implement a DCS system for three applications: an adaptive finite impulse response (FIR) filter, a ternary content-addressable memory (TCAM), and a regular expression matcher (RegEx). The experiments show that the use of our CP along with the SRL configuration achieves minimum overhead in terms of resources and time. Our CP is 1.8 and 3.5 times smaller than the PowerPC and the area-optimized implementation of the MicroBlaze, respectively. Moreover, the use of the CP enables a more compact representation for the parameterized configuration in comparison to both the PowerPC and the MicroBlaze processors. For instance, in the FIR, the parameterized configuration compiled for our CP is 6--7 times smaller than that for the embedded processors.
Employing circadian rhythms to enhance power and reliability
Authors: Gupta Saket , Sapatnekar Sachin S.
Published: July 2013

This article presents a novel scheme for saving architectural power by mitigating delay degradations in digital circuits due to bias temperature instability (BTI), inspired by the notion of human circadian rhythms. The method works in two alternating phases. In the first, the compute phase, the circuit is awake and active, operating briskly at a greater-than-nominal supply voltage which causes tasks to complete more quickly. In the second, the idle phase, the circuit is power-gated and put to sleep, enabling BTI recovery. Since the wakeful stage works at an elevated supply voltage, it results in greater aging than operation at the nominal supply voltage, but the sleep state involves a recovery that more than compensates for this differential. We demonstrate, both at the circuit and the architectural levels, that at about the same performance, this approach can result in appreciable BTI mitigation, thus reducing the guardbands necessary to protect against aging, which results in power savings over the conventional design.
An efficient method for analyzing on-chip thermal reliability considering process variations
Authors: Lee Yu-Min , Huang Pei-Yu
Published: July 2013

This work provides an efficient statistical electrothermal simulator for analyzing on-chip thermal reliability under process variations. Using the collocation-based statistical modeling technique, first, the statistical interpolation polynomial for on-chip temperature distribution can be obtained by performing deterministic electrothermal simulation very few times and by utilizing polynomial interpolation. After that, the proposed simulator not only provides the mean and standard deviation profiles of on-chip temperature distribution, but also innovates the concept of thermal yield profile to statistically characterize the on-chip temperature distribution more precisely, and builds an efficient technique for estimating this figure of merit. Moreover, a mixed-mesh strategy is presented to further enhance the efficiency of the developed statistical electrothermal simulator.

Experimental results demonstrate that (1) the developed statistical electrothermal simulator can obtain accurate approximations with orders of magnitude speedup over the Monte Carlo method; (2) comparing with a well-known cumulative distribution function estimation method, APEX [Li et al. 2004], the developed statistical electrothermal simulator can achieve 215× speedup with better accuracy; (3) the developed mixed-mesh strategy can achieve an order of magnitude faster over our baseline algorithm and still maintain an acceptable accuracy level.
Test compaction for small-delay defects using an effective path selection scheme
Authors: Xiang Dong , Li Jianbo , Chakrabarty Krishnendu , Lin Xijiang
Published: July 2013

Testing for small-delay defects (SDDs) requires fault-effect propagation along the longest testable paths. However, identification of the longest testable paths requires high CPU time, and the sensitization of all such paths leads to large pattern counts. Dynamic test compaction for small-delay defects is therefore necessary to reduce test-data volume. We present a new technique for identifying the longest testable paths through each gate in order to accelerate test generation for SDDs. The resulting test patterns sensitize the longest testable paths that pass through each SDD site. An efficient dynamic test compaction method based on structural analysis is presented to reduce the pattern count substantially, while ensuring that all the longest paths for each SDD are sensitized. Simulation results for a set of ISCAS 89 and IWLS 05 benchmark circuits demonstrate the effectiveness of this method.
Teaching programming the way it works outside the classroom
Authors: Guo Philip
Published: July 2013

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

http://cacm.acm.org/blogs/blog-cacm

Philip Guo offers programmers 'Opportunistic Programming' tips that typically are not shared in school.
Money models for MOOCs
Authors: Dellarocas Chrysanthos , Van Alstyne Marshall
Published: July 2013

Considering new business models for massive open online courses.
The air gap
Authors: Byres Eric
Published: July 2013

Attempting to use isolation as a security strategy for critical systems is unrealistic in an increasingly connected world.
Cherry-picking and the scientific method
Authors: Neville-Neil George V.
Published: July 2013

Software is supposed be a part of computer science, and science demands proof.
Rules for mobile performance optimization
Authors: Everts Tammy
Published: July 2013

An overview of techniques to speed page loading
Verifying cloud services
Authors: Bouchenak Sara , Chockler Gregory , Chockler Hana , Gheorghe Gabriela , Santos Nuno , Shraer Alexander
Published: July 2013

As cloud-based services gain popularity in both private and enterprise domains, cloud consumers are still lacking in tools to verify that these services work as expected. Such tools should consider properties such as functional correctness, service availability, reliability, performance and security guarantees. In this paper we survey existing work in these areas and identify gaps in existing cloud technology in terms of the verification tools provided to users. We also discuss challenges and new research directions that can help bridge these gaps.
Boosting energy efficiency with mirrored data block replication policy and energy scheduler
Authors: Yazd Sara Arbab , Venkatesan Subbarayan , Mittal Neeraj
Published: July 2013

Energy efficiency is one of the major challenges in big datacenters. To facilitate processing of large data sets in a distributed fashion, the MapReduce programming model is employed in these datacenters. Hadoop is an open-source implementation of MapReduce which contains a distributed file system. Hadoop Distributed File System provides a data block replication scheme to preserve reliability and data availability. The distribution of the data block replicas over the nodes is performed randomly by meeting some constraints (e.g., preventing storage of two replicas of a data block on a single node). This study makes use of flexibility in the data block placement policy to increase energy efficiency in datacenters. Furthermore, inspired by Zaharia et al.'s delay scheduling algorithm, a scheduling algorithm is introduced, which takes into account energy efficiency in addition to fairness and data locality properties. Computer simulations of the proposed method suggest its superiority over Hadoop's standard settings.
Differential gene expression by endothelial cells under positive and negative streamwise gradients of high wall shear stress
Authors: Dolan Jennifer M. , Meng Hui , Sim Fraser J. , Kolega John
Published: July 2013

Flow impingement at arterial bifurcations causes high frictional force [or wall shear stress (WSS)], and flow acceleration and deceleration in the branches create positive and negative streamwise gradients in WSS (WSSG), respectively. Intracranial aneurysms tend to form in regions with high WSS and positive WSSG. However, little is known about the responses of endothelial cells (ECs) to either positive or negative WSSG under high WSS conditions. We used cDNA microarrays to profile gene expression in cultured ECs exposed to positive or negative WSSG for 24 h in a flow chamber where WSS varied between 3.5 and 28.4 Pa. Gene ontology and biological pathway analysis indicated that positive WSSG favored proliferation, apoptosis, and extracellular matrix processing while decreasing expression of proinflammatory genes. To determine if similar responses occur in vivo, we examined EC proliferation and expression of the matrix metalloproteinase ADAMTS1 under high WSS and WSSG created at the basilar terminus of rabbits after bilateral carotid ligation. Precise hemodynamic conditions were determined by computational fluid dynamic simulations from three-dimensional angiography and mapped on immunofluorescence staining for the proliferation marker Ki-67 and ADAMTS1. Both proliferation and ADAMTS1 were significantly higher in ECs under positive WSSG than in adjacent regions of negative WSSG. Our results indicate that WSSG elicits distinct EC gene expression profiles and particular biological pathways including increased cell proliferation and matrix processing. Such EC responses may be important in understanding the mechanisms of intracranial aneurysm initiation at regions of high WSS and positive WSSG.
Protective role of small pigment epithelium-derived factor (PEDF) peptide in diabetic renal injury
Authors: Awad Alaa S. , Gao Ting , Gvritishvili Anzor , You Hanning , Liu Yanling , Cooper Timothy K. , Reeves W. Brian , Tombran-Tink Joyce
Published: July 2013

Pigment epithelium-derived factor (PEDF) is a multifunctional protein with antiangiogenic, antioxidative, and anti-inflammatory properties. PEDF is involved in the pathogenesis of diabetic retinopathy, but its direct role in the kidneys remains unclear. We hypothesize that a PEDF fragment (P78-PEDF) confers kidney protection in diabetic nephropathy (DN). The localization of the full-length PEDF protein were determined in DBA mice following multiple low doses of streptozotocin. Using immunohistochemistry, PEDF was localized in the kidney vasculature, interstitial space, glomeruli, tubules, and renal medulla. Kidney PEDF protein and mRNA expression were significantly reduced in diabetic mice. Continuous infusion of P78-PEDF for 6 wk resulted in protection from diabetic neuropathy as indicated by reduced albuminuria and blood urea nitrogen, increased nephrin expression, decreased kidney macrophage recruitment and inflammatory cytokines, and reduced histological changes compared with vehicle-treated diabetic mice. In vitro, P78-PEDF blocked the increase in podocyte permeability to albumin and disruption of the actin cytoskeleton induced by puromycin aminonucleoside treatment. These findings highlight the importance of P78-PEDF peptide as a potential therapeutic modality in early phase diabetic renal injury.
Bladder filling and voiding affect umbrella cell tight junction organization and function
Authors: Carattino Marcelo D. , Prakasam H. Sandeep , Ruiz Wily G. , Clayton Dennis R. , McGuire Meredith , Gallo Luciana I. , Apodaca Gerard
Published: July 2013

Epithelial cells are continuously exposed to mechanical forces including shear stress and stretch, although the effect these forces have on tight junction (TJ) organization and function are poorly understood. Umbrella cells form the outermost layer of the stratified uroepithelium and undergo large cell shape and surface area changes during the bladder cycle. Here we investigated the effects of bladder filling and voiding on the umbrella cell TJ. We found that bladder filling promoted a significant increase in the length of the TJ ring, which was quickly reversed within 5 min of voiding. Interestingly, when isolated uroepithelial tissue was mounted in Ussing chambers and exposed to physiological stretch, we observed a 10-fold drop in both transepithelial electrical resistance (TER) and the umbrella cell junctional resistance. The effects of stretch on TER were reversible and dependent on the applied force. Furthermore, the integrity of the umbrella cell TJ was maintained in the stretched uroepithelium, as suggested by the limited permeability of biotin, fluorescein, and ruthenium red. Finally, we found that depletion of extracellular Ca2+ by EGTA completely disrupted the TER of unstretched, but not of stretched uroepithelium. Taken together, our studies indicate that the umbrella cell TJ undergoes major structural and functional reorganization during the bladder cycle. The impact of these changes on bladder function is discussed.
Exposure to diesel exhaust particulates induces cardiac dysfunction and remodeling
Authors: Bradley Jessica M. , Cryar Kipp A. , El Hajj Milad C. , El Hajj Elia C. , Gardner Jason D.
Published: July 2013

Chronic exposure to diesel exhaust particulates (DEP) increases the risk of cardiovascular disease in urban residents, predisposing them to the development of several cardiovascular stresses, including myocardial infarctions, arrhythmias, thrombosis, and heart failure. DEP contain a high level of polycyclic aromatic hydrocarbons, which activate the aryl hydrocarbon receptor (AHR). We hypothesize that exposure to DEP elicits ventricular remodeling through the activation of the AHR pathway, leading to ventricular dilation and dysfunction. Male Sprague-Dawley rats were exposed by nose-only nebulization to DEP (SRM 2975, 0.2 mg/ml) or vehicle for 20 min/day × 5 wk. DEP exposure resulted in eccentric left ventricular dilation (8% increased left ventricular internal diameter at diastole and 23% decreased left ventricular posterior wall thickness at diastole vs. vehicle), as shown by echocardiograph assessment. Histological analysis using Picrosirius red staining revealed that DEP reduced cardiac interstitial collagen (23% decrease vs. vehicle). Further assessment of cardiac function using a pressure-volume catheter indicated impaired diastolic function (85% increased end-diastolic pressure and 19% decreased Tau vs. vehicle) and contractility (57 and 48% decreased end-systolic pressure-volume relationship and maximum change in pressure over time vs. end-diastolic volume compared with vehicle, respectively) in the DEP-exposed animals. Exposure to DEP significantly increased cardiac expression of AHR (19% increase vs. vehicle). In addition, DEP significantly decreased the cardiac expression of hypoxia inducible factor-1α, the competitive pathway to the AHR, and vascular endothelial growth factor, a downstream mediator of hypoxia inducible factor-1α (26 and 47% decrease vs. vehicle, respectively). These findings indicate that exposure to DEP induced left ventricular dilation by loss of collagen through an AHR-dependent mechanism.
Role of cellular effectors in the emergence of ventilation defects during allergic bronchoconstriction
Authors: Layachi Skander , Porra Liisa , Albu Gergely , Trouillet Nathalie , Suhonen Heikki , Peták Ferenc , Sevestre Henri , Suortti Pekka , Sovijärvi Anssi , Habre Walid , Bayat Sam
Published: July 2013

It is not known whether local factors within the airway wall or parenchyma may influence the emergence and spatial distribution of ventilation defects (VDs), thereby modulating the dynamic system behavior of the lung during bronchoconstriction. We assessed the relationship between the distribution of cellular effectors and the emergence of defects in regional ventilation distribution following allergen challenge. We performed high-resolution K-edge subtraction (KES) synchrotron imaging during xenon inhalation and measured the forced oscillatory input impedance in ovalbumin (OVA)-sensitized Brown-Norway rats ( n = 12) at baseline and repeatedly following OVA challenge. Histological slices with best anatomic matching to the computed tomographic images were stained with a modified May-Grunwald Giemsa and immunohistochemical staining with monoclonal anti-rat CD68, in six rats. Slides were digitized and total cells and eosinophils were counted in the walls of bronchi and vessels randomly selected within and outside of VDs on the basis of xenon-KES images. Ventilated alveolar area decreased and ventilation heterogeneity, Newtonian resistance, tissue damping, and elastance increased following OVA challenge. Eosinophil, total cell, and CD68+ counts were significantly higher in the bronchial and vascular walls within vs. outside of the VDs. The minimal central airway diameters during OVA-induced bronchoconstriction were correlated with eosinophil ( R = −0.85; P = 0.031) and total cell densities ( R = −0.82; P = 0.046) in the airway walls within the poorly ventilated zones. Our findings suggest that allergic airway inflammation is locally heterogeneous and is topographically associated with the local emergence of VDs following allergen challenge.