bluuebunny/crossref_metadata_2025 huggingface dataset:
Ontological Insecurity, Racial Tension, and Confidence in the Police in the Shadow of Urban Unrest
Authors: Wozniak Kevin H.
Published: August 2016

According to the theory of “ontological insecurity,” people who worry that society is in a state of decline or upheaval will also support punitive social control of deviants. I test the relationship between several measures of people's anxiety about the state of society, their perception of racial tension, and their confidence in the police (as enforcers of social control) during the period of social unrest following the death of Michael Brown in Ferguson, Missouri. I use ordinary least squares regression to analyze data from a nationally representative public opinion poll gathered for the Pew Research Center for the People and the Press during August, 2014. I find that pessimism about the state of the economy, pessimism about race relations, and the experience of personal hardship are related to decreased confidence in the police, while pessimism about the state of morals in society is related to increased confidence. I conclude that public confidence in the police is intertwined with public confidence in the stability of the country, more generally. This study supports a “neo‐Durkheimian” model of policing. The opposite findings of economic versus moral insecurity also call for refinement of the ontological insecurity theory.
Affective ties and social information processing
Authors: Lemerise Elizabeth A. , Thorn Amanda , Maulden Costello Jennifer
Published: August 2016

We examined whether second‐ and fifth‐graders could display differentiated social information processing (SIP) about known peers varying in affective ties. Children's response evaluation and decision (RED) and goal importance ratings were obtained for nine ambiguous provocations involving their best friends, neutral peers, and enemies (three stories for each relationship). For each story, RED was assessed for hostile, competent and passive responses to provocation, and the importance of four social goals was rated. Both second‐ and fifth‐graders displayed RED that depended on both the type of relationship they had with the provocateur and on the type of response (hostile, competent or passive). Children's social goals were affected by their relationship with the provocateur. Younger children's failure to display sensitivity to situational cues in previous studies is likely due to the cognitive demands of reasoning about hypothetical characters rather than an insensitivity to situational cues, per se.
Apple (Malus domestica) MdERF2 negatively affects ethylene biosynthesis during fruit ripening by suppressing MdACS1 transcription
Authors: Li Tong , Jiang Zhongyu , Zhang Lichao , Tan Dongmei , Wei Yun , Yuan Hui , Li Tianlai , Wang Aide
Published: August 2016

Ripening in climacteric fruit requires the gaseous phytohormone ethylene. Although ethylene signaling has been well studied, knowledge of the transcriptional regulation of ethylene biosynthesis is still limited. Here we show that an apple (Malus domestica) ethylene response factor, MdERF2, negatively affects ethylene biosynthesis and fruit ripening by suppressing the transcription of MdACS1, a gene that is critical for biosynthesis of ripening‐related ethylene. Expression of MdERF2 was suppressed by ethylene during ripening of apple fruit, and we observed that MdERF2 bound to the promoter of MdACS1 and directly suppressed its transcription. Moreover, MdERF2 suppressed the activity of the promoter of MdERF3, a transcription factor that we found to bind to the MdACS1 promoter, thereby increasing MdACS1 transcription. We determined that the MdERF2 and MdERF3 proteins directly interact, and this interaction suppresses the binding of MdERF3 to the MdACS1 promoter. Moreover, apple fruit with transiently downregulated MdERF2 expression showed higher ethylene production and faster ripening. Our results indicate that MdERF2 negatively affects ethylene biosynthesis and fruit ripening in apple by suppressing the transcription of MdACS1 via multiple mechanisms, thereby acting as an antagonist of positive ripening regulators. Our findings offer a deep understanding of the transcriptional regulation of ethylene biosynthesis during climacteric fruit ripening.
Cochlear hearing loss and the detection of sinusoidal versus random amplitude modulation
Authors: Grose John H. , Porter Heather L. , Buss Emily , Hall Joseph W.
Published: August 2016

This study assessed the effect of cochlear hearing loss on detection of random and sinusoidal amplitude modulation. Listeners with hearing loss and normal-hearing listeners (eight per group) generated temporal modulation transfer functions (TMTFs) for envelope fluctuations carried by a 2000-Hz pure tone. TMTFs for the two groups were similar at low modulation rates but diverged at higher rates presumably because of differences in frequency selectivity. For both groups, detection of random modulation was poorer than for sinusoidal modulation at lower rates but the reverse occurred at higher rates. No evidence was found that cochlear hearing loss, per se, affects modulation detection.
Relative velocity measurement from the spectral phase of a match-filtered linear frequency modulated pulse
Authors: Pinson Samuel , Holland Charles W.
Published: August 2016

Linear frequency modulated signals are commonly used to perform underwater acoustic measurements since they can achieve high signal-to-noise ratios with relatively low source levels. However, such signals present a drawback if the source or receiver or target is moving. The Doppler effect affects signal amplitude, delay, and resolution. To perform a correct match filtering that includes the Doppler shift requires prior knowledge of the relative velocity. In this paper, the relative velocity is extracted directly from the Doppler cross-power spectrum. More precisely, the quadratic coefficient of the Doppler cross-power-spectrum phase is proportional to the relative velocity. The proposed method achieves velocity estimates that compare favorably with Global Positioning System ground truth and the ambiguity method.
Peripheral motor neuropathy is associated with defective kinase regulation of the KCC3 cotransporter
Authors: Kahle Kristopher T. , Flores Bianca , Bharucha-Goebel Diana , Zhang Jinwei , Donkervoort Sandra , Hegde Madhuri , Begum Gulnaz , Duran Daniel , Liang Bo , Sun Dandan , Bönnemann Carsten G. , Delpire Eric
Published: August 2016

Evaluation of a patient with peripheral motor weakness reveals a key role for phosphorylation-dependent regulation of the transporter KCC3 in the peripheral nervous system.
Paper of note in
Science Translational Medicine
Authors: Ferrarelli Leslie K.
Published: August 2016

This week’s article describes how exposure to near-infrared laser light might be therapeutic for patients with thrombocytopenia.
Astrocytes donate mitochondria
Authors: VanHook Annalisa M.
Published: August 2016

Astrocytes release mitochondria that help neurons survive stroke.
HIV-1 Coinfection Does Not Reduce Exposure to Rifampin, Isoniazid, and Pyrazinamide in South African Tuberculosis Outpatients
Authors: Rockwood Neesha , Meintjes Graeme , Chirehwa Maxwell , Wiesner Lubbe , McIlleron Helen , Wilkinson Robert J. , Denti Paolo
Published: August 2016

There are contrasting data in the literature about antituberculosis plasma drug concentrations in HIV-1-coinfected patients. We report the pharmacokinetics of rifampin, isoniazid, and pyrazinamide in a cohort of patients being treated for active tuberculosis, the majority of whom were coinfected with HIV-1 and had commenced antiretroviral therapy within 2 months of starting antituberculosis treatment. We also examined the association between antituberculosis drug concentrations and reported drug side effects at the 2-month clinical review. One hundred patients with pulmonary tuberculosis (65% coinfected with HIV-1) were intensively sampled to determine rifampin, isoniazid, and pyrazinamide plasma concentrations after 7 to 8 weeks of a daily quadruple-therapy regimen dosed according to World Health Organization (WHO) weight bands. Pharmacokinetic parameters were determined for each patient by using nonlinear mixed-effects models. HIV-1-coinfected patients had lower clearance rates for rifampin (21% decrease) and isoniazid (23% decrease) than HIV-1-uninfected patients, with resulting higher areas under the concentration-time curve from 0 to 24 h (AUC0–24) and maximum concentrations of drug in serum (Cmax). Antiretroviral therapy (ART) that included double-standard-dose lopinavir/ritonavir further lowered rifampin clearance, by 46%, and increased the AUC0–24. The current uniform dosing (per kilogram of body weight) across WHO weight bands was associated with a trend of decreased pharmacokinetic exposures for the lowest weight band. Use of fat-free mass as opposed to total body weight for allometric scaling of clearance significantly improved the model. Ambulant HIV-1-coinfected patients, the majority of whom were coprescribed ART, did not have reduced antituberculosis drug concentrations compared to HIV-1-uninfected patients.
Peak Plasma Concentration of Azithromycin and Treatment Responses in Mycobacterium avium Complex Lung Disease
Authors: Jeong Byeong-Ho , Jeon Kyeongman , Park Hye Yun , Moon Seong Mi , Kim Su-Young , Lee Soo-Youn , Shin Sung Jae , Daley Charles L. , Koh Won-Jung
Published: August 2016

Macrolides, such as azithromycin (AZM) and clarithromycin, are the cornerstones of treatment for
Mycobacterium avium
complex lung disease (MAC-LD). Current guidelines recommend daily therapy with AZM for cavitary MAC-LD and intermittent therapy for noncavitary MAC-LD, but the effectiveness of these regimens has not been thoroughly investigated. This study evaluated associations between microbiological response and estimated peak plasma concentrations (
C
max
) of AZM. The AZM
C
max
was measured in patients receiving daily therapy (250 mg of AZM daily,
n
= 77) or intermittent therapy (500 mg of AZM three times weekly,
n
= 89) for MAC-LD and daily therapy for
Mycobacterium abscessus
complex LD (MABC-LD) (250 mg of AZM daily,
n
= 55). The AZM
C
max
was lower with the daily regimen for MAC-LD (median, 0.24 μg/ml) than with the intermittent regimen for MAC-LD (median, 0.65 μg/ml;
P
< 0.001) or daily therapy for MABC-LD (median, 0.53 μg/ml;
P
< 0.001). After adjusting for confounding factors, AZM
C
max
was independently associated with favorable microbiological responses in MAC-LD patients receiving a daily regimen (adjusted odds ratio [aOR], 1.58; 95% confidence interval [CI], 1.01 to 2.48;
P
= 0.044) but not an intermittent regimen (aOR, 0.85; 95% CI, 0.58 to 1.23,
P
= 0.379). With the daily AZM-based multidrug regimen for MAC-LD, a low AZM
C
max
was common, whereas a higher AZM
C
max
was associated with favorable microbiologic responses. The results also suggested that the addition of rifampin may lower AZM
C
max
. When a daily AZM-based multidrug regimen is used for treating severe MAC-LD, such as cavitary disease, the currently recommended AZM dose might be suboptimal. (This study has been registered at ClinicalTrials.gov under identifier NCT00970801.)
Novel Structure of Enterococcus faecium-Originated
ermB
-Positive Tn
1546
-Like Element in Staphylococcus aureus
Authors: Wan Tsai-Wen , Hung Wei-Chun , Tsai Jui-Chang , Lin Yu-Tzu , Lee Hao , Hsueh Po-Ren , Lee Tai-Fen , Teng Lee-Jene
Published: August 2016

We determined the resistance determinants in 274 erythromycin-resistant methicillin-susceptible
Staphylococcus aureus
(MSSA) isolates during a 13-year period, 2000 to 2012. The resistance phenotypes, inducible macrolide-lincosamide-streptogramin (iMLS), constitutive MLS (cMLS), and macrolide-streptogramin (MS) resistance phenotypes, were examined by a double-disk diffusion D test. The
ermB
gene was more frequent (35%; 97/274) than
ermC
(27%; 75/274) or
ermA
(21%; 58/274). All 97
ermB
-positive isolates harbored Tn
551
and IS
1216V
. The majority (89/97) of
ermB
-positive isolates displayed the cMLS phenotype and carried mobile element structure (MES)-like structures, which has been previously reported in sequence type 59 (ST59) methicillin-resistant
S. aureus
(MRSA). The remaining 8
ermB
-carrying isolates, belonging to ST7 (
n
= 4), ST5 (
n
= 3), and ST59 (
n
= 1), were
sasK
intact and did not carry MES-like structures. Unlike a MES-like structure that was located on the chromosome, the
ermB
elements on
sasK
-intact isolates were located on plasmids by S1 nuclease pulsed-field gel electrophoresis (PFGE) analysis and conjugation tests. Sequence data for the
ermB
-containing region (14,566 bp) from ST59 NTUH_3874 revealed that the best match was a Tn
1546
-like element in plasmid pMCCL2 DNA (GenBank accession number
AP009486
) of
Macrococcus caseolyticus
. Tn
1546
is recognized as an enterococcal transposon and was known from the vancomycin resistance gene cluster in vancomycin-resistant
Enterococcus
(VRE). So far, acquisitions of Tn
1546
in
S. aureus
have occurred in clonal complex 5 (CC5) MRSA, but not in MSSA. This is the first report that MSSA harbors an
Enterococcus faecium
-originated
ermB
-positive Tn
1546
-like element located on a plasmid.
In Vitro
and
In Vivo
Drug Interaction Study of Two Lead Combinations, Oxantel Pamoate plus Albendazole and Albendazole plus Mebendazole, for the Treatment of Soil-Transmitted Helminthiasis
Authors: Cowan Noemi , Vargas Mireille , Keiser Jennifer
Published: August 2016

The current treatments against
Trichuris trichiura
, albendazole and mebendazole, are only poorly efficacious. Therefore, combination chemotherapy was recommended for treating soil-transmitted helminthiasis. Albendazole-mebendazole and albendazole-oxantel pamoate have shown promising results in clinical trials. However,
in vitro
and
in vivo
drug interaction studies should be performed before their simultaneous treatment can be recommended. Inhibition of human recombinant cytochromes P450 (CYPs) CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 was tested by exposure to albendazole, albendazole sulfoxide, mebendazole, and oxantel pamoate, as well as albendazole-mebendazole, albendazole sulfoxide-mebendazole, albendazole-oxantel pamoate, and albendazole sulfoxide-oxantel pamoate. A high-pressure liquid chromatography (HPLC)-UV/visible spectroscopy method was developed and validated for simultaneous quantification of albendazole sulfoxide, albendazole sulfone, mebendazole, and oxantel pamoate in plasma. Albendazole, mebendazole, oxantel pamoate, albendazole-mebendazole, and albendazole-oxantel pamoate were orally applied to rats (100 mg/kg) and pharmacokinetic parameters calculated. CYP1A2 showed a 2.6-fold increased inhibition by albendazole-oxantel pamoate (50% inhibitory concentration [IC
50
] = 3.1 μM) and a 3.9-fold increased inhibition by albendazole sulfoxide-mebendazole (IC
50
= 3.8 μM) compared to the single drugs. In rats, mebendazole's area under the concentration-time curve (AUC) and maximal plasma concentration (
C
max
) were augmented 3.5- and 2.8-fold, respectively (
P
= 0.02 for both) when coadministered with albendazole compared to mebendazole alone. Albendazole sulfone was slightly affected by albendazole-mebendazole, displaying a 1.3-fold-elevated AUC compared to albendazole alone. Oxantel pamoate could not be quantified, translating to a bioavailability below 0.025% in rats. Elevated plasma levels of albendazole sulfoxide, albendazole sulfone, and mebendazole in coadministrations are probably not mediated by CYP-based drug-drug interaction. Even though this study indicates that it is safe to coadminister albendazole-oxantel pamoate and albendazole-mebendazole, human pharmacokinetic studies are recommended.
Tyrphostin AG1478 Inhibits Encephalomyocarditis Virus and Hepatitis C Virus by Targeting Phosphatidylinositol 4-Kinase IIIα
Authors: Dorobantu Cristina M. , Harak Christian , Klein Rahel , van der Linden Lonneke , Strating Jeroen R. P. M. , van der Schaar Hilde M. , Lohmann Volker , van Kuppeveld Frank J. M.
Published: August 2016

Encephalomyocarditis virus (EMCV), like hepatitis C virus (HCV), requires phosphatidylinositol 4-kinase IIIα (PI4KA) for genome replication. Here, we demonstrate that tyrphostin AG1478, a known epidermal growth factor receptor (EGFR) inhibitor, also inhibits PI4KA activity, both
in vitro
and in cells. AG1478 impaired replication of EMCV and HCV but not that of an EMCV mutant previously shown to escape PI4KA inhibition. This work uncovers novel cellular and antiviral properties of AG1478, a compound previously regarded only as a cancer chemotherapy agent.
Secretion Chaperones PrsA2 and HtrA Are Required for Listeria monocytogenes Replication following Intracellular Induction of Virulence Factor Secretion
Authors: Ahmed Jana K. , Freitag Nancy E.
Published: August 2016

The Gram-positive bacterium
Listeria monocytogenes
transitions from an environmental organism to an intracellular pathogen following its ingestion by susceptible mammalian hosts. Bacterial replication within the cytosol of infected cells requires activation of the central virulence regulator PrfA followed by a PrfA-dependent induction of secreted virulence factors. The PrfA-induced secreted chaperone PrsA2 and the chaperone/protease HtrA contribute to the folding and stability of select proteins translocated across the bacterial membrane.
L. monocytogenes
strains that lack both
prsA2
and
htrA
exhibit near-normal patterns of growth in broth culture but are severely attenuated
in vivo
. We hypothesized that, in the absence of PrsA2 and HtrA, the increase in PrfA-dependent protein secretion that occurs following bacterial entry into the cytosol results in misfolded proteins accumulating at the bacterial membrane with a subsequent reduction in intracellular bacterial viability. Consistent with this hypothesis, the introduction of a constitutively activated allele of
prfA
(
prfA*
) into Δ
prsA2
Δ
htrA
strains was found to essentially inhibit bacterial growth at 37°C in broth culture. Δ
prsA2
Δ
htrA
strains were additionally found to be defective for cell invasion and vacuole escape in selected cell types, steps that precede full PrfA activation. These data establish the essential requirement for PrsA2 and HtrA in maintaining bacterial growth under conditions of PrfA activation. In addition, chaperone function is required for efficient bacterial invasion and rapid vacuole lysis within select host cell types, indicating roles for PrsA2/HtrA prior to cytosolic PrfA activation and the subsequent induction of virulence factor secretion.
A Zebrafish Model of Cryptococcal Infection Reveals Roles for Macrophages, Endothelial Cells, and Neutrophils in the Establishment and Control of Sustained Fungemia
Authors: Davis J. Muse , Huang Mingwei , Botts Michael R. , Hull Christina M. , Huttenlocher Anna
Published: August 2016

Cryptococcal meningoencephalitis is a fungal infection that predominantly affects immunocompromised patients and is uniformly fatal if left untreated. Timely diagnosis is difficult, and screening or prophylactic measures have generally not been successful. Thus, we need a better understanding of early, asymptomatic pathogenesis. Inhaled cryptococci must survive the host immune response, escape the lung, and persist within the bloodstream in order to reach and invade the brain. Here we took advantage of the zebrafish larval infection model to assess the process of cryptococcal infection and disease development sequentially in a single host. Using yeast or spores as infecting particles, we discovered that both cell types survived and replicated intracellularly and that both ultimately established a sustained, low-level fungemia. We propose that the establishment and maintenance of this sustained fungemia is an important stage of disease progression that has been difficult to study in other model systems. Our data suggest that sustained fungemia resulted from a pattern of repeated escape from, and reuptake by, macrophages, but endothelial cells were also seen to play a role as a niche for cryptococcal survival. Circulating yeast collected preferentially in the brain vasculature and eventually invaded the central nervous system (CNS). As suggested previously in a mouse model, we show here that neutrophils can play a valuable role in limiting the sustained fungemia, which can lead to meningoencephalitis. This early stage of pathogenesis—a balanced interaction between cryptococcal cells, macrophages, endothelial cells, and neutrophils—could represent a window for timely detection and intervention strategies for cryptococcal meningoencephalitis.
Patient and carer experience of hospital-based rehabilitation from intensive care to hospital discharge: mixed methods process evaluation of the RECOVER randomised clinical trial
Authors: Ramsay Pam , Huby Guro , Merriweather Judith , Salisbury Lisa , Rattray Janice , Griffith David , Walsh Timothy
Published: August 2016

Objectives

To explore and compare patient/carer experiences of rehabilitation in the intervention and usual care arms of the RECOVER trial (ISRCTN09412438); a randomised controlled trial of a complex intervention of post-intensive care unit (ICU) acute hospital-based rehabilitation following critical illness.

Design

Mixed methods process evaluation including comparison of patients' and carers' experience of usual care versus the complex intervention. We integrated and compared quantitative data from a patient experience questionnaire (PEQ) with qualitative data from focus groups with patients and carers.

Setting

Two university-affiliated hospitals in Scotland.

Participants

240 patients discharged from ICU who required ≥48 hours of mechanical ventilation were randomised into the trial (120 per trial arm). Exclusion criteria comprised: primary neurologic diagnosis, palliative care, current/planned home ventilation and age <18 years. 182 patients completed the PEQ at 3 months postrandomisation. 22 participants (14 patients and 8 carers) took part in focus groups (2 per trial group) at >3 months postrandomisation.

Interventions

A complex intervention of post-ICU acute hospital rehabilitation, comprising enhanced physiotherapy, nutritional care and information provision, case-managed by dedicated rehabilitation assistants (RAs) working within existing ward-based clinical teams, delivered between ICU discharge and hospital discharge. Comparator was usual care.

Outcome measures

A novel PEQ capturing patient-reported aspects of quality care.

Results

The PEQ revealed statistically significant between-group differences across 4 key intervention components: physiotherapy (p=0.039), nutritional care (p=0.038), case management (p=0.045) and information provision (p<0.001), suggesting greater patient satisfaction in the intervention group. Focus group data strongly supported and helped explain these findings. Specifically, case management by dedicated RAs facilitated greater access to physiotherapy, nutritional care and information that cut across disciplinary boundaries and staffing constraints. Patients highly valued its individualisation according to their needs, abilities and preferences.

Conclusions

Case management by dedicated RAs improves patients' experiences of post-ICU hospital-based rehabilitation and increases perceived quality of care.

Trial registration number

ISRCTN09412438.
Rewinding Frankenstein and the body-machine: organ transplantation in the dystopian young adult fiction seriesUnwind
Authors: Wohlmann Anita , Steinberg Ruth
Published: August 2016

While the separation of body and mind (and the entailing metaphor of the body as a machine) has been a cornerstone of Western medicine for a long time, reactions to organ transplantation among others challenge this clear-cut dichotomy. The limits of the machine-body have been negotiated in science fiction, most canonically in Mary Shelley's Frankenstein (1818). Since then, Frankenstein's monster itself has become a motif that permeates both medical and fictional discourses. Neal Shusterman's contemporary dystology for young adults,Unwind, draws on traditional concepts of the machine-body and the Frankenstein myth. This article follows one of the young protagonists in the series, who is entirely constructed from donated tissue, and analyses how Shusterman explores the complicated relationship between body and mind and between self and other as the teenager matures into an adult. It will be shown that, by framing the story of a transplanted individual along the lines of a coming-of-age narrative, Shusterman inter-relates the acceptance of a donor organ with the transitional space of adolescence and positions the quest for embodied selfhood at the centre of both developments. By highlighting the interconnections between medical discourse and a literary tradition, the potential contribution of the series to the treatment and understanding of post-transplant patients will be addressed.
Risk stratification for major adverse cardiac events and ventricular tachyarrhythmias by cardiac MRI in patients with cardiac sarcoidosis
Authors: Yasuda Masakazu , Iwanaga Yoshitaka , Kato Takao , Izumi Toshiaki , Inuzuka Yasutaka , Nakamura Takashi , Miyaji Yuki , Kawamura Takayuki , Ikeguchi Shigeru , Inoko Moriaki , Kurita Takashi , Miyazaki Shunichi
Published: August 2016

Background

The presence of myocardial fibrosis by cardiac MRI has prognostic value in cardiac sarcoidosis, and localisation may be equally relevant to clinical outcomes.

Objective

We aimed to analyse cardiac damage and function in detail and explore the relationship with clinical outcomes in patients with cardiac sarcoidosis using cardiac MRI.

Methods

We included 81 consecutive patients with cardiac sarcoidosis undergoing cardiac MR. Left ventricular mass and fibrosis mass were calculated, and localisation was analysed using a 17-segment model. Participants underwent follow-up through 2015, and the development of major adverse cardiac events including ventricular tachyarrhythmias was recorded.

Results

Increased left ventricular fibrosis mass was associated with increased prevalence of ventricular tachyarrhythmias (p<0.001). When localisation was defined as the sum of late gadolinium enhancement in the left ventricular basal anterior and basal anteroseptal areas, or the right ventricular area, it was associated with ventricular tachyarrhythmias (p<0.001). Kaplan-Meier analysis during a median follow-up of 22.1 months showed that both the mass and localisation groupings for fibrosis were significantly associated with major adverse cardiac events or ventricular tachyarrhythmias and that when combined, the risk stratification was better than for each variable alone (p<0.001, respectively). By Cox-proportional hazard risk analysis, the localisation grouping was an independent predictor for the both.

Conclusions

In patients with cardiac sarcoidosis, both fibrosis mass and its localisation to the basal anterior/anteroseptal left ventricle, or right ventricle was associated with the development of major adverse cardiac events or ventricular tachyarrhythmias. Cardiac MR with late gadolinium enhancement may be useful for improving risk stratification in patients with cardiac sarcoidosis.
Moving media: Second harmonic generation investigation
Authors: Ghalandari Mahboubeh
Published: August 2016

Because of the importance of second harmonic generation (SHG) in some nonlinear media, in this paper, we investigated induced SHG in diamond where there is no intrinsic second-order susceptibility, [Formula: see text]. The electric field is proposed to introduce moving susceptibility of the second-order and induce second harmonic generation. Then, spatiotemporal quasi-phase matching (QPM) is applied to optimize the induced SHG. Numerical results reveal that in this way, the induced second harmonic is found at the frequency of [Formula: see text] rather than [Formula: see text].
An improved global dynamic routing strategy for scale-free network with tunable clustering
Authors: Sun Lina , Huang Ning , Zhang Yue , Bai Yannan
Published: August 2016

An efficient routing strategy can deliver packets quickly to improve the network capacity. Node congestion and transmission path length are inevitable real-time factors for a good routing strategy. Existing dynamic global routing strategies only consider the congestion of neighbor nodes and the shortest path, which ignores other key nodes’ congestion on the path. With the development of detection methods and techniques, global traffic information is readily available and important for the routing choice. Reasonable use of this information can effectively improve the network routing. So, an improved global dynamic routing strategy is proposed, which considers the congestion of all nodes on the shortest path and incorporates the waiting time of the most congested node into the path. We investigate the effectiveness of the proposed routing for scale-free network with different clustering coefficients. The shortest path routing strategy and the traffic awareness routing strategy only considering the waiting time of neighbor node are analyzed comparatively. Simulation results show that network capacity is greatly enhanced compared with the shortest path; congestion state increase is relatively slow compared with the traffic awareness routing strategy. Clustering coefficient increase will not only reduce the network throughput, but also result in transmission average path length increase for scale-free network with tunable clustering. The proposed routing is favorable to ease network congestion and network routing strategy design.
Visualization of Clusters in an Educational Data Set Based on Convex-Hull Shape Preservation Algorithm
Authors: Albertini Marcelo Keese , Backes André Ricardo
Published: August 2016

We study the problem of visualization of clusters in an educational data set based on convex-hull shape preservation algorithm. This problem considers multidimensional data with pre-established classes with the requirement of elements of different classes must be presented at distinctive regions. Such problem is commonly found on economic and social data, where visualization is important to understand a phenomenon before further analysis. In this paper, we propose an algorithm that uses a nonlinear transformation to preserve some data distance properties and display in a convenient format to interpretation. The proposed visualization algorithm is a partition-conforming projection, as defined by Kleinberg [An impossibility theorem for clustering, Adv. Neural Inform. Processing Syst. 15: Proc. 2002 Conf., 2003, The MIT Press, p. 463.], and completely separates the convex hull of data classes by applying locally linear operations. We applied this algorithm to visualize data from an important exam applied for over four million students of the Brazilian educational system Exame Nacional do Ensino Médio (ENEM). Results show that the proposed algorithm successfully separates unintelligible data and presents it more accessible to further visual analysis.
A note about the uniform distribution on the intersection of a simplex and a sphere
Authors: Chatterjee Sourav
Published: August 2016

Uniform probability distributions on [Formula: see text] balls and spheres have been studied extensively and are known to behave like product measures in high dimensions. In this note we consider the uniform distribution on the intersection of a simplex and a sphere. Certain new and interesting features, such as phase transitions and localization phenomena emerge.
Enterprise Architecture Benefit Realization
Authors: Niemi Eetu I. , Pekkola Samuli
Published: August 2016

In recent years, Enterprise Architecture (EA) has been of interest to both researchers and practitioners. However, EA benefit realization has not been focused on much. Even though a few studies have addressed the subject, the results are somewhat fragmented and are subjected to limited empirical validation, particularly from the viewpoint of different theoretical constructs and their interrelations in the benefit realization process. To understand how the EA benefits accumulate and how related constructs influence each other, we propose a model and criteria for analyzing the explanatory power of the existing EA benefit realization models. Our model emerged from the data of a qualitative case study with 14 semi-structured EA stakeholder interviews. The results support earlier findings, thereby contributing to the enhancement of the relevance and generalizability of the constructs present in previous studies. However, the results also indicate that no existing EA benefit realization model fully captures the complex process of EA benefit realization. Our findings highlight the following: the importance of EA process quality; EA service quality and supportive social environment; constructs that have received less attention in previous studies.
Compensate or ignore? meeting control robustness requirements through adaptive soft-error handling
Authors: Chen Kuan-Hsun , Bönninghoff Björn , Chen Jian-Jia , Marwedel Peter
Published: August 2016

To avoid catastrophic events like unrecoverable system failures on mobile and embedded systems caused by soft-errors, software-based error detection and compensation techniques have been proposed. Methods like error-correction codes or redundant execution can offer high flexibility and allow for application-specific fault-tolerance selection without the needs of special hardware supports. However, such software-based approaches may lead to system overload due to the execution time overhead. An adaptive deployment of such techniques to meet both application requirements and system constraints is desired. From our case study, we observe that a control task can tolerate limited errors with acceptable performance loss. Such tolerance can be modeled as a (m,k) constraint which requires at least m correct runs out of any k consecutive runs to be correct. In this paper, we discuss how a given (m,k) constraint can be satisfied by adopting patterns of task instances with individual error detection and compensation capabilities. We introduce static strategies and provide a formal feasibility analysis for validation. Furthermore, we develop an adaptive scheme that extends our initial approach with online awareness that increases efficiency while preserving analysis results. The effectiveness of our method is shown in a real-world case study as well as for synthesized task sets.
Opportunity for compute partitioning in pursuit of energy-efficient systems
Authors: Chakraborty Prasenjit , Doshi Gautam , Shekhar Shashank , Kumar Vikrant
Published: August 2016

Performance of computing systems, from handhelds to supercomputers, is increasingly constrained by the energy consumed. A significant and increasing fraction of the energy is consumed in the movement of data. In a compute node, caches have been very effective in reducing data movement by exploiting the available data locality in programs. Program regions with poor data locality, then effect most of the data movement, and consequently consume an ever larger fraction of energy. In this paper we explore the energy efficiency opportunity of minimizing the data movement in precisely such program regions, by first imagining the possibility of compute near memory, and then partitioning the program’s execution between a compute core and the compute near memory (CnM). Due to the emergence of 3D stacked memory, a CnM implementation appears more realistic. Our focus is on evaluating the partitioning opportunity in applications and to do a limit study of systems enabled with CnM capabilities to understand and guide their architectural embodiment. We describe an automated method of analyzing the data access pattern of optimized workload binaries, via a binary-instrumentation tool called SnapCnM, to identify the beneficial program regions (loops) for CnM execution.We also perform a limit study to evaluate the impact of such partitioning over a range of parameters affecting CnM design choices. Our results show that compute partitioning a small (<10%) fraction of a workload can improve its energy efficiency from 3% (for compute-bound applications) to 27% (for memory-bound applications). From the study in this work we discuss the important aspects that help to shape the future CnM design space.
From Datalog to flix: a declarative language for fixed points on lattices
Authors: Madsen Magnus , Yee Ming-Ho , Lhoták Ondřej
Published: August 2016

We present Flix, a declarative programming language for specifying and solving least fixed point problems, particularly static program analyses. Flix is inspired by Datalog and extends it with lattices and monotone functions. Using Flix, implementors of static analyses can express a broader range of analyses than is currently possible in pure Datalog, while retaining its familiar rule-based syntax. We define a model-theoretic semantics of Flix as a natural extension of the Datalog semantics. This semantics captures the declarative meaning of Flix programs without imposing any specific evaluation strategy. An efficient strategy is semi-naive evaluation which we adapt for Flix. We have implemented a compiler and runtime for Flix, and used it to express several well-known static analyses, including the IFDS and IDE algorithms. The declarative nature of Flix clearly exposes the similarity between these two algorithms.
Programmatic and direct manipulation, together at last
Authors: Chugh Ravi , Hempel Brian , Spradlin Mitchell , Albers Jacob
Published: August 2016

Direct manipulation interfaces and programmatic systems have distinct and complementary strengths. The former provide intuitive, immediate visual feedback and enable rapid prototyping, whereas the latter enable complex, reusable abstractions. Unfortunately, existing systems typically force users into just one of these two interaction modes. We present a system called Sketch-n-Sketch that integrates programmatic and direct manipulation for the particular domain of Scalable Vector Graphics (SVG). In Sketch-n-Sketch, the user writes a program to generate an output SVG canvas. Then the user may directly manipulate the canvas while the system immediately infers a program update in order to match the changes to the output, a workflow we call live synchronization. To achieve this, we propose (i) a technique called trace-based program synthesis that takes program execution history into account in order to constrain the search space and (ii) heuristics for dealing with ambiguities. Based on our experience with examples spanning 2,000 lines of code and from the results of a preliminary user study, we believe that Sketch-n-Sketch provides a novel workflow that can augment traditional programming systems. Our approach may serve as the basis for live synchronization in other application domains, as well as a starting point for yet more ambitious ways of combining programmatic and direct manipulation.
Idle time garbage collection scheduling
Authors: Degenbaev Ulan , Eisinger Jochen , Ernst Manfred , McIlroy Ross , Payer Hannes
Published: August 2016

Efficient garbage collection is increasingly important in today's managed language runtime systems that demand low latency, low memory consumption, and high throughput. Garbage collection may pause the application for many milliseconds to identify live memory, free unused memory, and compact fragmented regions of memory, even when employing concurrent garbage collection. In animation-based applications that require 60 frames per second, these pause times may be observable, degrading user experience. This paper introduces idle time garbage collection scheduling to increase the responsiveness of applications by hiding expensive garbage collection operations inside of small, otherwise unused idle portions of the application's execution, resulting in smoother animations. Additionally we take advantage of idleness to reduce memory consumption while allowing higher memory use when high throughput is required. We implemented idle time garbage collection scheduling in V8, an open-source, production JavaScript virtual machine running within Chrome. We present performance results on various benchmarks running popular webpages and show that idle time garbage collection scheduling can significantly improve latency and memory consumption. Furthermore, we introduce a new metric called frame time discrepancy to quantify the quality of the user experience and precisely measure the improvements that idle time garbage collection provides for a WebGL-based game benchmark. Idle time garbage collection is shipped and enabled by default in Chrome.
Verifying bit-manipulations of floating-point
Authors: Lee Wonyeol , Sharma Rahul , Aiken Alex
Published: August 2016

Reasoning about floating-point is difficult and becomes only more so if there is an interplay between floating-point and bit-level operations. Even though real-world floating-point libraries use implementations that have such mixed computations, no systematic technique to verify the correctness of the implementations of such computations is known. In this paper, we present the first general technique for verifying the correctness of mixed binaries, which combines abstraction, analytical optimization, and testing. The technique provides a method to compute an error bound of a given implementation with respect to its mathematical specification. We apply our technique to Intel's implementations of transcendental functions and prove formal error bounds for these widely used routines.
Configuration synthesis for programmable analog devices with Arco
Authors: Achour Sara , Sarpeshkar Rahul , Rinard Martin C.
Published: August 2016

Programmable analog devices have emerged as a powerful computing substrate for performing complex neuromorphic and cytomorphic computations. We present Arco, a new solver that, given a dynamical system specification in the form of a set of differential equations, generates physically realizable configurations for programmable analog devices that are algebraically equivalent to the specified system. On a set of benchmarks from the biological domain, Arco generates configurations with 35 to 534 connections and 28 to 326 components in 1 to 54 minutes.
Verified lifting of stencil computations
Authors: Kamil Shoaib , Cheung Alvin , Itzhaky Shachar , Solar-Lezama Armando
Published: August 2016

This paper demonstrates a novel combination of program synthesis and verification to lift stencil computations from low-level Fortran code to a high-level summary expressed using a predicate language. The technique is sound and mostly automated, and leverages counter-example guided inductive synthesis (CEGIS) to find provably correct translations. Lifting existing code to a high-performance description language has a number of benefits, including maintainability and performance portability. For example, our experiments show that the lifted summaries can enable domain specific compilers to do a better job of parallelization as compared to an off-the-shelf compiler working on the original code, and can even support fully automatic migration to hardware accelerators such as GPUs. We have implemented verified lifting in a system called STNG and have evaluated it using microbenchmarks, mini-apps, and real-world applications. We demonstrate the benefits of verified lifting by first automatically summarizing Fortran source code into a high-level predicate language, and subsequently translating the lifted summaries into Halide, with the translated code achieving median performance speedups of 4.1X and up to 24X for non-trivial stencils as compared to the original implementation.
Assessing the limits of program-specific garbage collection performance
Authors: Jacek Nicholas , Chiu Meng-Chieh , Marlin Benjamin , Moss Eliot
Published: August 2016

We consider the ultimate limits of program-specific garbage collector performance for real programs. We first characterize the GC schedule optimization problem using Markov Decision Processes (MDPs). Based on this characterization, we develop a method of determining, for a given program run and heap size, an optimal schedule of collections for a non-generational collector. We further explore the limits of performance of a generational collector, where it is not feasible to search the space of schedules to prove optimality. Still, we show significant improvements with Least Squares Policy Iteration, a reinforcement learning technique for solving MDPs. We demonstrate that there is considerable promise to reduce garbage collection costs by developing program-specific collection policies.
SDNRacer: concurrency analysis for software-defined networks
Authors: El-Hassany Ahmed , Miserez Jeremie , Bielik Pavol , Vanbever Laurent , Vechev Martin
Published: August 2016

Concurrency violations are an important source of bugs in Software-Defined Networks (SDN), often leading to policy or invariant violations. Unfortunately, concurrency violations are also notoriously difficult to avoid, detect and debug. This paper presents a novel approach and a tool, SDNRacer, for detecting concurrency violations of SDNs. Our approach is enabled by three key ingredients: (i) a precise happens- before model for SDNs that captures when events can happen concurrently; (ii) a set of sound, domain-specific filters that reduce reported violations by orders of magnitude, and; (iii) a sound and complete dynamic analyzer, based on the above, that can ensure the network is free of harmful errors such as data races and per-packet incoherence. We evaluated SDNRacer on several real-world OpenFlow controllers, running both reactive and proactive applications in large networks. We show that SDNRacer is practically effective: it quickly pinpoints harmful concurrency violations without overwhelming the user with false positives.
Cardinalities and universal quantifiers for verifying parameterized systems
Authors: Gleissenthall Klaus v. , Bjørner Nikolaj , Rybalchenko Andrey
Published: August 2016

Parallel and distributed systems rely on intricate protocols to manage shared resources and synchronize, i.e., to manage how many processes are in a particular state. Effective verification of such systems requires universally quantification to reason about parameterized state and cardinalities tracking sets of processes, messages, failures to adequately capture protocol logic. In this paper we present Tool, an automatic invariant synthesis method that integrates cardinality-based reasoning and universal quantification. The resulting increase of expressiveness allows Tool to verify, for the first time, a representative collection of intricate parameterized protocols.
Design and Anthropology
Authors: Murphy Keith M.
Published: August 2016

In this review, I examine the recent turn to design in anthropology in three different configurations: anthropology of design, anthropology for design, and design for anthropology. Although these three configurations represent different cuts in a complex set of relations between these two disciplines, I have chosen to discuss them together because they all represent—though not always obviously so—attempts to contend with the moral implications of humans intervening in the lives of other humans. One goal of this article is to specify and evaluate a long-standing but underarticulated regard for design and designed things in anthropology while also offering a framework for critically engaging anthropology's relationship with design in its multiple configurations.