bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of the Type IX Secretion System in Capnocytophaga ochracea Gliding Motility and Biofilm Formation
Authors: Kita Daichi , Shibata Satoshi , Kikuchi Yuichiro , Kokubu Eitoyo , Nakayama Koji , Saito Atsushi , Ishihara Kazuyuki 
Published: January 2016

ABSTRACT

Capnocytophaga ochracea
is a Gram-negative, rod-shaped bacterium that demonstrates gliding motility when cultured on solid agar surfaces.
C. ochracea
possesses the ability to form biofilms; however, factors involved in biofilm formation by this bacterium are unclear. A type IX secretion system (T9SS) in
Flavobacterium johnsoniae
was shown to be involved in the transport of proteins (e.g., several adhesins) to the cell surface. Genes orthologous to those encoding T9SS proteins in
F. johnsoniae
have been identified in the genome of
C. ochracea
; therefore, the T9SS may be involved in biofilm formation by
C. ochracea
. Here we constructed three ortholog-deficient
C. ochracea
mutants lacking
sprB
(which encodes a gliding motility adhesin) or
gldK
or
sprT
(which encode T9SS proteins in
F. johnsoniae
). Gliding motility was lost in each mutant, suggesting that, in
C. ochracea
, the proteins encoded by
sprB
,
gldK
, and
sprT
are necessary for gliding motility, and SprB is transported to the cell surface by the T9SS. For the Δ
gldK
, Δ
sprT
, and Δ
sprB
strains, the amounts of crystal violet-associated biofilm, relative to wild-type values, were 49%, 34%, and 65%, respectively, at 48 h. Confocal laser scanning and scanning electron microscopy revealed that the biofilms formed by wild-type
C. ochracea
were denser and bacterial cells were closer together than in those formed by the mutant strains. Together, these results indicate that proteins exported by the T9SS are key elements of the gliding motility and biofilm formation of
C. ochracea
.
Case definitions in Swedish register data to identify systemic lupus erythematosus
Authors: Arkema Elizabeth V , Jönsen Andreas , Rönnblom Lars , Svenungsson Elisabet , Sjöwall Christopher , Simard Julia F 
Published: January 2016

ObjectiveTo develop and investigate the utility of several different case definitions for systemic lupus erythematosus (SLE) using national register data in Sweden.MethodsThe reference standard consisted of clinically confirmed SLE cases pooled from four major clinical centres in Sweden (n=929), and a sample of non-SLE comparators randomly selected from the National Population Register (n=24 267). Demographics, comorbidities, prescriptions and autoimmune disease family history were obtained from multiple registers and linked to the reference standard. We first used previously published SLE definitions to create algorithms for SLE. We also used modern data mining techniques (penalised least absolute shrinkage and selection operator logistic regression, elastic net regression and classification trees) to objectively create data-driven case definitions. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for the case definitions identified.ResultsDefining SLE by using only hospitalisation data resulted in the lowest sensitivity (0.79). When SLE codes from the outpatient register were included, sensitivity and PPV increased (PPV between 0.97 and 0.98, sensitivity between 0.97 and 0.99). Addition of medication information did not greatly improve the algorithm's performance. The application of data mining methods did not yield different case definitions.ConclusionsThe use of SLE International Classification of Diseases (ICD) codes in outpatient clinics increased the accuracy for identifying individuals with SLE using Swedish registry data. This study implies that it is possible to use ICD codes from national registers to create a cohort of individuals with SLE.
Carbohydrate intake, obesity, metabolic syndrome and cancer risk? A two-part systematic review and meta-analysis protocol to estimate attributability
Authors: Sartorius B , Sartorius K , Aldous C , Madiba T E , Stefan C , Noakes T 
Published: January 2016

IntroductionLinkages between carbohydrates, obesity and cancer continue to demonstrate conflicting results. Evidence suggests inconclusive direct linkages between carbohydrates and specific cancers. Conversely, obesity has been strongly linked to a wide range of cancers. The purpose of the study is to explore linkages between carbohydrate intake and cancer types using a two-step approach. First the study will evaluate the linkages between carbohydrate intake and obesity, potentially stratified by metabolic syndrome status. Second, the estimated attributable fraction of obesity ascribed to carbohydrate intake will be multiplied against obesity attributable fractions for cancer types to give estimated overall attributable fraction for carbohydrate versus cancer type.Methods and analysisWe will perform a comprehensive search to identify all possible published and unpublished studies that have assessed risk factors for obesity including dietary carbohydrate intake. Scientific databases, namely PubMed MEDLINE, EMBASE, EBSCOhost and ISI Web of Science will be searched. Following study selection, paper/data acquisition, and data extraction and synthesis, we will appraise the quality of studies and risk of bias, as well as assess heterogeneity. Meta-weighted attributable fractions of obesity due to carbohydrate intake will be estimated after adjusting for other potential confounding factors (eg, physical inactivity, other dietary intake). Furthermore, previously published systematic reviews assessing the cancer-specific risk associated with obesity will also be drawn. These estimates will be linked with the attributability of carbohydrate intake in part 1 to estimate the cancer-specific burden that can be attributed to dietary carbohydrates. This systematic review protocol has been developed according to the ‘Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P) 2015’.Ethics and disseminationThe current study will be based on published literature and data, and, as such, ethics approval is not required. The final results of this two part systematic review (plus multiplicative calculations) will be published in a relevant international peer-reviewed journal.Trial registration numberPROSPERO CRD42015023257.
Factors associated with presenting late or with advanced HIV disease in the Netherlands, 1996–2014: results from a national observational cohort
Authors: Op de Coul Eline L M , van Sighem Ard , Brinkman Kees , Benthem Birgit H van , Ende Marchina E van der , Geerlings Suzanne , Reiss Peter 
Published: January 2016

ObjectivesEarly testing for HIV and entry into care are crucial to optimise treatment outcomes of HIV-infected patients and to prevent spread of HIV. We examined risk factors for presentation with late or advanced disease in HIV-infected patients in the Netherlands.MethodsHIV-infected patients registered in care between January 1996 and June 2014 were selected from the ATHENA national observational HIV cohort. Risk factors for late presentation and advanced disease were analysed by multivariable logistic regression. Furthermore, geographical differences and time trends were examined.ResultsOf 20 965 patients, 53% presented with late-stage HIV infection, and 35% had advanced disease. Late presentation decreased from 62% (1996) to 42% (2013), while advanced disease decreased from 46% to 26%. Late presentation only declined significantly among men having sex with men (MSM; p <0.001), but not among heterosexual males (p=0.08) and females (p=0.73). Factors associated with late presentation were: heterosexual male (adjusted OR (aOR), 1.59; 95% CI 1.44 to 1.75 vs MSM), injecting drug use (2.00; CI 1.69 to 2.38), age ≥50 years (1.46; CI 1.33 to 1.60 vs 30–49 years), region of origin (South-East Asia 2.14; 1.80 to 2.54, sub-Saharan Africa 2.11; 1.88 to 2.36, Surinam 1.59; 1.37 to 1.84, Caribbean 1.31; 1.13 to 1.53, Latin America 1.23; 1.04 to 1.46 vs the Netherlands), and location of HIV diagnosis (hospital 3.27; 2.94 to 3.63, general practitioner 1.66; 1.50 to 1.83, antenatal screening 1.76; 1.38 to 2.34 vs sexually transmitted infection clinic). No association was found for socioeconomic status or level of urbanisation. Compared with Amsterdam, 2 regions had higher adjusted odds and 2 regions had lower odds of late presentation. Results were highly similar for advanced disease.ConclusionsAlthough the overall rate of late presentation is declining in the Netherlands, targeted programmes to reduce late HIV diagnoses remain needed for all risk groups, but should be prioritised for heterosexual males, migrant populations, people aged ≥50 years and certain regions in the Netherlands.
Comparison of self-reported and biomedical data on hypertension and diabetes: findings from the China Health and Retirement Longitudinal Study (CHARLS)
Authors: Ning Meng , Zhang Qiang , Yang Min 
Published: January 2016

ObjectivesWe examined the level of agreement between biomedical and self-reported measurements of hypertension and diabetes in a Chinese national community sample, and explored associations of the agreement and possible contextual effects among provinces and geographic regions in China.DesignSecondary analysis of a cohort sample.Setting and participantsCommunity samples were drawn from the national baseline survey of the China Health and Retirement Longitudinal Study (CHARLS, 2011–2012) through multistage probability sampling, which included households with members 45 years of age or above with a total sample size of 17 708 individuals.Outcome measuresSensitivity, specificity and κ were used as measurements of agreements or validity; variance of validity measures among provinces and communities was estimated using random-effects models.ResultsSelf-reports for hypertension and diabetes showed high specificity (96.3% and 98.3%, respectively) but low sensitivity (56.3% and 61.5%, respectively). Agreement between self-reported data and biomedical measurements was moderate for both hypertension (κ 0.57) and diabetes (κ 0.65), with respondents who were older, of higher socioeconomic status, better educated and who had hospital admissions in the past 12 months showing stronger agreements than their counterparts. Large and significant variations in the sensitivity among provinces for hypertension, and among communities for both hypertension and diabetes, could neither be attributed to the effects of respondents’ characteristics nor to the contextual effects of city–village differences.ConclusionsAs a considerable number of people in the overall sample were unaware of their conditions, self-reports will lead to an underestimation of the prevalence of hypertension and diabetes. However, in more developed communities or provinces, self-reported data can be a reliable estimate of the prevalence of the two conditions. Further investigations of contextual effects at provincial and community levels could highlight public health strategies to improve awareness of the two conditions.
Child academic achievement in association with pre-pregnancy obesity and gestational weight gain
Authors: Pugh Sarah J , Hutcheon Jennifer A , Richardson Gale A , Brooks Maria M , Himes Katherine P , Day Nancy L , Bodnar Lisa M 
Published: January 2016

BackgroundRecent data suggest that children of mothers who are obese before pregnancy, or who gain too much weight during pregnancy, may be at an increased risk of cognitive impairments.MethodsMother–infant dyads enrolled in a birth cohort study in Pittsburgh, Pennsylvania (1983–1986), were followed from early pregnancy to 14 years postpartum (n=574). Math, reading and spelling achievements were assessed at ages 6 and 10 years using the Wide Range Achievement Test-Revised, and at age 14 years using the Wechsler Individual Achievement Test Screener. Self-reported total GWG was converted to gestational age-standardised z-scores. Generalised estimating equations were used to estimate the effects of GWG and pre-pregnancy body mass index (BMI) on academic achievement at 6, 10 and 14 years, while adjusting for maternal race, child sex, parity, employment, family income, maternal intelligence, maternal depression, pre-pregnancy BMI (in GWG models only) and the home environment.ResultsThe mean (SD) BMI was 23.4 (5.7) kg/m2and the mean (SD) GWG reported at delivery was 14.4 (5.9) kg. There was a significant non-linear association between pre-pregnancy BMI and an offspring's academic achievement. At 6, 10 and 14 years, an offspring's academic scores were inversely associated with pre-pregnancy BMI beyond 22 kg/m2. High GWG (>1 SD) was associated with approximately 4-point lower reading (adjusted β (adjβ) −3.75, 95% CI −7.1 to −0.4) and spelling scores (adjβ −3.90, 95% CI −7.8 to −0.2), compared with GWG −1 to +1 SD.ConclusionsFuture studies in larger and socioeconomically diverse populations are needed to confirm maternal weight and weight gain as causal determinants of a child's academic skills, and whether this effect persists into adulthood.
The load slice core microarchitecture
Authors: Carlson Trevor E. , Heirman Wim , Allam Osman , Kaxiras Stefanos , Eeckhout Lieven 
Published: January 2016

Driven by the motivation to expose instruction-level parallelism (ILP), microprocessor cores have evolved from simple, in-order pipelines into complex, superscalar out-of-order designs. By extracting ILP, these processors also enable parallel cache and memory operations as a useful side-effect. Today, however, the growing off-chip memory wall and complex cache hierarchies of many-core processors make cache and memory accesses ever more costly. This increases the importance of extracting memory hierarchy parallelism (MHP), while reducing the net impact of more general, yet complex and power-hungry ILP-extraction techniques. In addition, for multi-core processors operating in power- and energy-constrained environments, energy-efficiency has largely replaced single-thread performance as the primary concern.
Based on this observation, we propose a core microarchitecture that is aimed squarely at generating parallel accesses to the memory hierarchy while maximizing energy efficiency. The Load Slice Core extends the efficient in-order, stall-on-use core with a second in-order pipeline that enables memory accesses and address-generating instructions to bypass stalled instructions in the main pipeline. Backward program slices containing address-generating instructions leading up to loads and stores are extracted automatically by the hardware, using a novel iterative algorithm that requires no software support or recompilation. On average, the Load Slice Core improves performance over a baseline in-order processor by 53% with overheads of only 15% in area and 22% in power, leading to an increase in energy efficiency (MIPS/Watt) over in-order and out-of-order designs by 43% and over 4.7×, respectively. In addition, for a power- and area-constrained many-core design, the Load Slice Core outperforms both in-order and out-of-order designs, achieving a 53% and 95% higher performance, respectively, thus providing an alternative direction for future many-core processors.
CAWA
Authors: Lee Shin-Ying , Arunkumar Akhil , Wu Carole-Jean 
Published: January 2016

The ubiquity of graphics processing unit (GPU) architectures has made them efficient alternatives to chip-multiprocessors for parallel workloads. GPUs achieve superior performance by making use of massive multi-threading and fast context-switching to hide pipeline stalls and memory access latency. However, recent characterization results have shown that general purpose GPU (GPGPU) applications commonly encounter long stall latencies that cannot be easily hidden with the large number of concurrent threads/warps. This results in varying execution time disparity between different parallel warps, hurting the overall performance of GPUs -- the warp criticality problem.
To tackle the warp criticality problem, we propose a coordinated solution, criticality-aware warp acceleration (CAWA), that efficiently manages compute and memory resources to accelerate the critical warp execution. Specifically, we design (1) an instruction-based and stall-based criticality predictor to identify the critical warp in a thread-block, (2) a criticality-aware warp scheduler that preferentially allocates more time resources to the critical warp, and (3) a criticality-aware cache reuse predictor that assists critical warp acceleration by retaining latency-critical and useful cache blocks in the L1 data cache. CAWA targets to remove the significant execution time disparity in order to improve resource utilization for GPGPU workloads. Our evaluation results show that, under the proposed coordinated scheduler and cache prioritization management scheme, the performance of the GPGPU workloads can be improved by 23% while other state-of-the-art schedulers, GTO and 2-level schedulers, improve performance by 16% and -2% respectively.
Probable cause
Authors: Rahmati Amir , Hicks Matthew , Holcomb Daniel E. , Fu Kevin 
Published: January 2016

Approximate computing research seeks to trade-off the accuracy of computation for increases in performance or reductions in power consumption. The observation driving approximate computing is that many applications tolerate small amounts of error which allows for an opportunistic relaxation of guard bands (e.g., clock rate and voltage). Besides affecting performance and power, reducing guard bands exposes analog properties of traditionally digital components. For DRAM, one analog property exposed by approximation is the variability of memory cell decay times.
In this paper, we show how the differing cell decay times of approximate DRAM creates an error pattern that serves as a system identifying fingerprint. To validate this observation, we build an approximate memory platform and perform experiments that show that the fingerprint due to approximation is device dependent and resilient to changes in environment and level of approximation. To identify a DRAM chip given an approximate output, we develop a distance metric that yields a two-orders-of-magnitude difference in the distance between approximate results produced by the same DRAM chip and those produced by other DRAM chips. We use these results to create a mathematical model of approximate DRAM that we leverage to explore the end-to-end deanonymizing effects of approximate memory using a commodity system running an image manipulation program. The results from our experiment show that given less than 100 approximate outputs, the fingerprint for an approximate DRAM begins to converge to a single, machine identifying fingerprint.
Systematical follow-up in social work practices
Authors: Zimic Sheila , Dalin Rolf 
Published: January 2016

In this paper, we explore the meaning of a specific follow-up system in different social work practices. We want to gain understanding about if the system can be an empowering tool for the practitioners to learn in their professional work. We interviewed four practitioners in different teams in order to find out how they describe the follow-up system as a tool, how they describe the knowledge they produce with help of it and what this means to them.
We have found that the practitioners describe the tool as an easy way to present results which are often described as 'facts'. The teams mainly use their specific follow-ups to present their work to others and in relation to that the tool serves a purpose for the team to gain credibility and be considered as professional. Their use can be understood in light of Evidence Based Practice and performance measurement as a discourse which sets limits and have effects on professional learning.
The Microsound Synthesis Framework in the LC Computer Music Programming Language
Authors: Nishino Hiroki , Osaka Naotoshi , Nakatsu Ryohei 
Published: January 2016

Abstract
This article describes the design of a framework for sound synthesis in LC, a new computer music language we prototyped, together with concrete code examples. Unlike existing unit-generator languages, LC provides objects as well as library functions and methods that can directly represent microsounds and related manipulations that are involved in microsound synthesis. Furthermore, LC is equipped with traditional unit generators, and these two different abstractions can collaborate seamlessly. Although the framework for microsound synthesis itself is not particularly bound to the entire language design of LC, such seamless unification between the traditional concept of unit generators and LC’s microsound synthesis framework contribute to making LC’s programming model for microsound synthesis simpler and terser in comparison with existing unit-generator languages. These features of LC’s entire sound-synthesis framework can help computer musicians to creatively explore the domain of microsound synthesis and would also be beneficial for further research in computer music language as a design exemplar.
Akcentuacja zapożyczonych leksemów czasownikowych w gwarze staroobrzędowców mieszkających w regionie suwalsko-augustowskim
Authors: Paśko-Koneczniak Dorota Angelika 
Published: January 2016

<p><img src="http://ispan.waw.pl/journals/public/site/images/admin/issj004.png" alt="" /></p><p><strong>Stress patterns in loan verb lexemes in the dialect used by the Old Believers living in the Suwałki-Augustów region </strong></p><p>The aim of the article is to present the stress pattern phenomenon in loan verb lexemes which function in the Russian dialect of the Old Believers from the Suwałki-Augustów Region. In the last decades, the insular dialect, separated from the general Russian language, has been influenced by the Polish language. Such influence is visible, in particular, in the vocabulary, in the form of loan translations and idiomatic expressions. Stress patterns, along with the root vocabulary and the morphological system, still remains one of the indicators of the Russian essence of the dialect. The native vocabulary of the Old Believers’ dialect maintains Russian accentuation patterns. A similar situation is observed in the case of stress patterns in lexemes borrowed from Polish, which undergo a stress accentuation adaptation; that is, they feature a shift in the place of the stress in relation to the source language. In loan verb morphemes, one can notice the pattern of stress which is not fixed and depends upon the morphological form or, sometimes, the paroxitonic stress, which results from the influence of the Polish language.</p><p> </p><p><img src="http://ispan.waw.pl/journals/public/site/images/admin/issj003.png" alt="" /></p><p><strong>Akcentuacja zapożyczonych leksemów czasownikowych w gwarze staroobrzędowców mieszkających w regionie suwalsko-augustowskim </strong></p><p>Celem artykułu jest zaprezentowanie zjawiska akcentuacji w zapożyczonych leksemach czasownikowych, funkcjonujących w rosyjskiej gwarze staroobrzędowców z regionu suwalsko-augustowskiego. W ciągu ostatnich kilkudziesięciu lat badana gwara wyspowa, odseparowana od rosyjskiego języka ogólnego, podlega znacznemu wpływowi języka polskiego. Wpływ polszczyzny widoczny jest szczególnie w zasobie leksykalnym w postaci zapożyczeń, kalk i w idiomatyce. Akcentuacja obok rdzennego zasobu leksykalnego i systemu morfologicznego nadal pozostaje jednym z wyznaczników rosyjskości gwary. Rodzimy zasób leksykalny badanej gwary staroobrzędowców zachowuje rosyjski system akcentuacyjny. Podobnie rzecz się ma z systemem akcentuacyjnym w leksemach zapożyczonych z języka polskiego, które podlegają adaptacji akcentuacyjnej, czyli następuje w nich przesunięcie miejsca akcentu w stosunku do języka dawcy. W zapożyczonych leksemach czasownikowych mamy do czynienia ze zmiennością akcentu uzależnioną od formy morfologicznej, niekiedy również z akcentem paroksytonicznym, wynikającym z wpływu języka polskiego.</p>