bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Silico Proteome-Wide Amino aCid and Elemental Composition (PACE) Analysis of Expression Proteomics Data Provides A Fingerprint of Dominant Metabolic Processes
Authors: Good David M. , Mamdoh Anwer , Budamgunta Harshavardhan , Zubarev Roman A. 
Published: August 2013

Abstract
Proteome-wide Amino aCid and Elemental composition (PACE) analysis is a novel and informative way of interrogating the proteome. The PACE approach consists of in silico decomposition of proteins detected and quantified in a proteomics experiment into 20 amino acids and five elements (C, H, N, O and S), with protein abundances converted to relative abundances of amino acids and elements. The method is robust and very sensitive; it provides statistically reliable differentiation between very similar proteomes. In addition, PACE provides novel insights into proteome-wide metabolic processes, occurring, e.g., during cell starvation. For instance, both Escherichia coli and Synechocystis down-regulate sulfur-rich proteins upon sulfur deprivation, but E. coli preferentially down-regulates cysteine-rich proteins while Synechocystis mainly down-regulates methionine-rich proteins. Due to its relative simplicity, flexibility, generality and wide applicability, PACE analysis has the potential of becoming a standard analytical tool in proteomics.
Temperature and Microstructures Dependent Thermal Shock Resistance Models for Ultra-High-Temperature Ceramics Considering Effect of Residual Stress
Authors: Wang R. Z. , Ai S. G. , W. G. Li  , Zheng J. , Zhang C. Z. 
Published: August 2013

ABSTRACTBased on the researches on the temperature and microstructures dependent fracture strength and temperature dependent thermal shock resistance, the new thermal shock resistance models for ultra-high-temperature ceramics were proposed. The effect of density on the fracture strength of material was investigated. A damage term was introduced to reveal the effects of uncertain factors on fracture strength. The roles of residual stress and microstructure sizes at different initial thermal shock temperatures in the thermal shock resistance were studied using the models. The study showed that the models can reveal the relationships among the residual stress, microstructure sizes and the temperature dependent thermal shock resistance well. The better thermal shock resistance is found for ultra-high-temperature ceramics having small SiC grains and relatively large micro-cracks around SiC grains. Large enhancement in thermal shock resistance can be achieved through our studies.
SPEED GOVERNORS: ROAD SAFETY AND INFRASTRUCTURAL OVERLOAD IN POST-COLONIAL KENYA, c. 1963–2013
Authors: Lamont Mark 
Published: August 2013

ABSTRACTIn this article, I focus on the place of road safety in Kenyan legislative history since independence in 1963 as a way of illustrating the analytic value of speed for the anthropology of the state. Road safety, a highly visible public concern in Kenya since the 1960s, offers us a way to rethink the temporal dangers and uncertainties of automotive travel under global capitalism, but also to go further in seeking out historical continuities in Kenya's post-colonial aspirations for safer and more efficient roads. This focus on road safety takes us from Africanization, in the 1960s and 1970s, to the regulatory reforms of the 1990s and 2000s in the guise of neo-liberalism. From the vociferous complaints and debates of Kenyan politicians about imported Peugeots being dangerous to drive on Kenya's rough and sparsely tarmacked roads in 1964, to the much publicized traffic crackdown of 2003, the so-called ‘Michuki Rules’, road safety is a field of study ideally suited to the analysis of infrastructural power and its transformations and continuities over a four-decade period. What is of analytic interest here is the new value of speed in an East African region that has aggressively embraced automobility as a vehicle for enhancing state sovereignty in a globalized economy.
Land restitution, traditional leadership and belonging: defining Barokologadi identity
Authors: Turner Robin L. 
Published: August 2013

ABSTRACTHow do government policies and practices affect struggles over collective identity and struggles over land? Examining the interconnections among collective identity struggles, land struggles and state policies and practices in post-apartheid South Africa, this paper argues that the government's contradictory policies and ambivalent practices have aggravated collective struggles over the boundaries of belonging. Specifically, the differing definitions of community set forth in traditional leadership, land tenure and land restitution policies exacerbate existing divisions among ‘communities’ concurrently subject to these policies and create practical policy dilemmas for decision-makers. This paper illustrates the interplay between public policies and collective identity struggles through close examination of struggles among the Barokologadi ba ga Maotwe, a so-called traditional community. The Barokologadi case underscores the necessity of attending to these interactions.
A Working Democracy: Jane Addams on the Meaning of Work
Authors: Winkelman Joel 
Published: August 2013

AbstractBy exploring Addams's lifelong fascination with work, this essay analyzes the ways in which her understanding of work fundamentally shaped her wider political vision. For Addams, work was the foundation of not only a personal sense of identity, but also a collective democratic character. The workplace had the potential to be the model of a cooperative community, providing a venue for social solidarity and civic reciprocity. By working together, Americans would develop a more cosmopolitan and inclusive politics. In short, the essay argues that Addams's political thought was an attempt to revitalize democracy by giving meaning to work. It concludes by suggesting that her arguments can be applied to many contemporary political problems, and that today's democratic theory and practice would be enlivened by a renewed attention to work.
Utility of Intraindividual Reaction Time Variability to Predict White Matter Hyperintensities: A Potential Assessment Tool for Clinical Contexts?
Authors: Bunce David , Bielak Allison A. M. , Cherbuin Nicolas , Batterham Philip J. , Wen Wei , Sachdev Perminder , Anstey Kaarin J. 
Published: August 2013

AbstractIntraindividual variability (IIV) refers to reaction time (RT) variation across the trials of a given cognitive task. Little research has contrasted different measures of IIV or assessed how many RT trials are required to provide a robust measure of the construct. We, therefore, investigated three measures of IIV (raw SD, coefficient of variation, and intraindividual SD statistically removing time-on-task effects) in relation to frontal white matter hyperintensities (obtained through structural MRI) in 415 cognitively normal community-dwelling adults aged 44 to 48 years. Results indicated the three IIV measures did not differ greatly in predictions of white matter hyperintensities, although it is possible that time-on-task effects were influential. As few as 20 trials taking approximately 52 s to administer provided a reliable prediction of frontal white matter hyperintensities. We conclude that future work should evaluate the comparative utility of different IIV measures in relation to persons exhibiting clear neuropathology. (JINS, 2013, 19, 1–6)
Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters
Authors: Unrein Fernando , Gasol Josep M , Not Fabrice , Forn Irene , Massana Ramon 
Published: August 2013

Abstract
Grazing rate estimates indicate that approximately half of the bacterivory in oligotrophic oceans is due to mixotrophic flagellates (MFs). However, most estimations have considered algae as a single group. Here we aimed at opening the black-box of the phytoflagellates (PFs) &lt;20 μm. Haptophytes, chlorophytes, cryptophytes and pigmented dinoflagellates were identified using fluorescent in situ hybridization or by standard 4′,6-diamidino-2-phenylindole staining. Their fluctuations in abundance, cell size, biomass and bacterivory rates were measured through an annual cycle in an oligotrophic coastal system. On average, we were able to assign to these groups: 37% of the total pico-PFs and 65% of the nano-PFs composition. Chlorophytes were mostly picoplanktonic and they never ingested fluorescently labeled bacteria. About 50% of the PF &lt;20 μm biomass was represented by mixotrophic algae. Pigmented dinoflagellates were the least abundant group with little impact on bacterioplankton. Cryptophytes were quantitatively important during the coldest periods and explained about 4% of total bacterivory. Haptophytes were the most important mixotrophic group: (i) they were mostly represented by cells 3–5 μm in size present year-round; (ii) cell-specific grazing rates were comparable to those of other bacterivorous non-photosynthetic organisms, regardless of the in situ nutrient availability conditions; (iii) these organisms could acquire a significant portion of their carbon by ingesting bacteria; and (iv) haptophytes explained on average 40% of the bacterivory exerted by MFs and were responsible for 9–27% of total bacterivory at this site. Our results, when considered alongside the widespread distribution of haptophytes in the ocean, indicate that they have a key role as bacterivores in marine ecosystems.
Aetiologies of Central Nervous System infections in adults in Kathmandu, Nepal: A prospective hospital-based study
Authors: Giri Abhishek , Arjyal Amit , Koirala Samir , Karkey Abhilasha , Dongol Sabina , Thapa Sudeep Dhoj , Shilpakar Olita , Shrestha Rishav , van Tan Le , Thi Thuy Chinh Bkrong Nguyen , Krishna K. C. Radheshyam , Pathak Kamal Raj , Shakya Mila , Farrar Jeremy , Van Doorn H. Rogier , Basnyat Buddha 
Published: August 2013

AbstractWe conducted a prospective hospital based study from February 2009-April 2011 to identify the possible pathogens of central nervous system (CNS) infections in adults admitted to a tertiary referral hospital (Patan Hospital) in Kathmandu, Nepal. The pathogens of CNS infections were confirmed in cerebrospinal fluid (CSF) using molecular diagnostics, culture (bacteria) and serology. 87 patients were recruited for the study and the etiological diagnosis was established in 38% (n = 33). The bacterial pathogens identified were Neisseria meningitidis (n = 6); Streptococcus pneumoniae (n = 5) and Staphylococcus aureus (n = 2) in 13/87(14%). Enteroviruses were found in 12/87 (13%); Herpes Simplex virus (HSV) in 2/87(2%). IgM against Japanese encephalitis virus (JEV) was detected in the CSF of 11/73 (15%) tested samples. This is the first prospective molecular and serology based CSF analysis in adults with CNS infections in Kathmandu, Nepal. JEV and enteroviruses were the most commonly detected pathogens in this setting.
The Relationship Between Parent Report of Adaptive Behavior and Direct Assessment of Reading Ability in Children With Autism Spectrum Disorder
Authors: Arciuli Joanne , Stevens Kirsten , Trembath David , Simpson Ian Craig 
Published: August 2013

Purpose
This study was designed to shed light on the profile of reading ability in children with autism spectrum disorder (ASD). A key aim was to examine the relationship between parent report of adaptive behavior and direct assessment of reading ability in these children.

Method
The authors investigated children's reading ability using the Wide Range Achievement Test—Fourth Edition (Wilkinson & Robertson, 2006) and the Neale Analysis of Reading Ability—Third Edition (Neale, 2007). Parent report data was collected using the Vineland Adaptive Behavior Scales—Second Edition (Sparrow, Cicchetti, & Balla, 2005). Participants were 21 children with ASD (6–11 years) and their primary caregivers.

Results
Direct assessment of children's reading ability showed that some children with ASD have difficulty learning to read and exhibit particular weaknesses in comprehension. The results revealed positive relationships between Vineland Adaptive Behavior Scales scores in the Adaptive Communication domain and direct assessment of children's reading ability across 3 measures of reading (word-level accuracy, passage-level accuracy, and passage-level comprehension).

Conclusions
Although literacy levels vary among children with ASD, some clearly struggle with reading. There is a significant relationship between parent self-report of adaptive behavior and direct assessment of children's reading ability.
Early Predictors of Language and Social Communication Impairments at Ages 9–11 Years: A Follow-Up Study of Early-Referred Children
Authors: Chiat Shula , Roy Penny 
Published: August 2013

Purpose
In this study, the authors aimed to evaluate hypotheses that early sociocognition will predict later social communication and early phonology will predict later morphosyntax in clinically referred preschoolers.

Method
Participants were 108 children ages 9–11 years who had been referred to clinical services with concerns about language at age 2½–3½ years. Predictors at Time 1 (T1) were measures of sociocognition, word/nonword repetition, and receptive language. Outcome measures at Time 3 (T3) included a social communication questionnaire completed by parents and tests of nonword repetition, morphosyntax, and receptive language.

Results
Group- and case-level analyses revealed early sociocognition to be the strongest predictor of social communication problems, which by T3 affected almost one third of the sample. At the group level, early phonology, which was a significant problem for the majority of children at T1, was a weak predictor of morphosyntax at T3. However, at the case level the majority of children with poor morphosyntax and nonword repetition at outcome had had very low repetition scores at T1.

Conclusions
In early language referrals, it is important to identify and address sociocognitive problems, a considerable risk for later social communication and autism spectrum disorders. The majority of early-referred children had phonological problems, often severe, but these require further investigation to determine their longer term significance for language.
Metalinguistic awareness in children with differing language learning experience
Authors: Tellier Angela , Roehr-Brackin Karen 
Published: August 2013

Theoretical research concerned with the notion of second language (L2) learning difficulty has resulted in specific criteria that can be used to predict the learning difficulty of different languages in terms of both explicit and implicit knowledge. The characteristics of the constructed language Esperanto suggest that this language has lower explicit and implicit learning difficulty than other languages. It may therefore be a suitable ‘starter language’ for child L2 learning in the classroom. Specifically, we propose that Esperanto may facilitate the development of metalinguistic awareness and, as a consequence, boost children’s budding capacity for explicit learning. This would be particularly advantageous in the minimal-input setting of the average foreign language classroom. We present findings from an empirical study which compared 11 to 12-year-old English-speaking children who had learned Esperanto and a European L2 (N = 35) with children who had learned various combinations of European and non-European L2s (N = 168) in terms of their performance on a measure of metalinguistic awareness. No significant differences in overall level of metalinguistic awareness were identified, but the Esperanto group significantly outperformed the comparison group on one of the eleven metalinguistic tasks included in the measure. Moreover, the Esperanto group displayed a more homogeneous performance than the other groups of children. This suggests that learning Esperanto may have a lasting levelling effect, reducing differences between children with varying metalinguistic abilities.
A Standardized Technique to Back-Calculate Length at Age from Unsectioned Walleye Spines
Authors: Meerbeek Jonathan R. , Hawkins Kimberly A. 
Published: August 2013

Abstract
The primary assumption of using back-calculated length-at-age (BCL) methods to estimate fish growth is that the body length and hard-part radius relationship is linear. Therefore, standardized techniques are required for BCL methods to be comparable over time. Recent studies have found that unsectioned dorsal spines of Sander spp. improve efficiency and provide accurate age estimates. We evaluated a simple, standardized method of using unsectioned Walleye S. vitreus (N = 162) dorsal spines to estimate age and BCL (direct-proportion and Fraser–Lee methods) by comparing these estimates with those of a sectioned spine technique. We validated the technique by comparing observed growth (measured via a mark–recapture study) with BCL growth estimated via sectioned and unsectioned techniques. The time required to process, prepare, view and perform BCL for each of the two techniques was also compared. Both reader age estimates and exact reader agreement rates were significantly better using the sectioned spine technique. Age frequencies varied significantly among readers and techniques as differences ranged up to 8 years. No difference was detected among the slopes of the back-calculation methods among techniques, but there were significant differences in the mean BCL estimates for ages &lt; 10 years old. The relationships between observed growth and growth estimated via BCL methods were significant; however, BCL methods significantly overestimated Walleye growth. Total processing time for the unsectioned technique was significantly less, but based on our poor ability to replicate ages, we do not suggest the use of our standardized unsectioned spine technique to estimate the age or BCL older Walleye. In addition, no BCL method accurately estimated annual growth regardless of technique or reader experience. We conclude that more research is necessary to validate dorsal spine-based BCL estimates on Walleye populations. Once validated, further research evaluating new or modifying our technique for unsectioned Walleye spines needs to be explored.
Received February 14, 2013; accepted June 2, 2013
Exploring the role of human miRNAs in virus–host interactions using systematic overlap analysis
Authors: Li Zhenpeng , Cui Xiuliang , Li Fei , Li Peng , Ni Ming , Wang Shengqi , Bo Xiaochen 
Published: August 2013

Abstract
Motivation: Human miRNAs have recently been found to have important roles in viral replication. Understanding the patterns and details of human miRNA interactions during virus–host interactions may help uncover novel antiviral therapies. Based on the abundance of knowledge available regarding protein–protein interactions (PPI), virus–host protein interactions, experimentally validated human miRNA-target pairs and transcriptional regulation of human miRNAs, it is possible to explore the complex regulatory network that exists between viral proteins and human miRNAs at the system level.
Results: By integrating current data regarding the virus–human interactome and human miRNA-target pairs, the overlap between targets of viral proteins and human miRNAs was identified and found to represent topologically important proteins (e.g. hubs or bottlenecks) at the global center of the human PPI network. Viral proteins and human miRNAs were also found to significantly target human PPI pairs. Furthermore, an overlap analysis of virus targets and transcription factors (TFs) of human miRNAs revealed that viral proteins preferentially target human miRNA TFs, representing a new pattern of virus–host interactions. Potential feedback loops formed by viruses, human miRNAs and miRNA TFs were also identified, and these may be exploited by viruses resulting in greater virulence and more effective replication strategies.
Contact: boxc@bmi.ac.cn or ni.ming@163.com or sqwang@bmi.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Near-infrared spectroscopy of SN 2009ip's 2012 brightening reveals a dusty pre-supernova environment
Authors: Smith Nathan , Mauerhan Jon C. , Kasliwal Mansi M. , Burgasser Adam J. 
Published: August 2013

Abstract
We present low-resolution near-infrared (IR) 0.8–2.5 μm spectra of Supernova (SN) 2009ip, taken immediately before, during and just after its rapid brightening in late September/October 2012. The first epoch shows the same general spectral characteristics as the later epochs (smooth continuum, narrow H and He i emission lines), but the IR continuum shape is substantially redder than the later epochs. The epoch 1 continuum can be approximated by reddening the peak-luminosity (epoch 3) spectrum by E(B − V) = 1.0 mag, but the blue colour seen in visual-wavelength spectra at the same time indicates that strong wavelength-dependent extinction by circumstellar dust is not the correct explanation. Instead, we favour the hypothesis that the redder colour before the brightening arises from excess emission from hot ∼2000 K circumstellar dust. The minimum radius ( ≳ 120 au) deduced from the dust temperature and observed luminosity of the transient, combined with the observed expansion speed in the precursor outbursts of SN 2009ip, is consistent with an ejection at least 1.1 yr earlier. The mass of hot dust indicated by the IR excess is ∼4 × 10−7 M⊙, although this is only a lower limit since the near-IR data do not constrain the mass of cooler dust. Thus, the observed pre-SN outbursts of this object were able to efficiently form dust into which the SN ejecta and radiation now propagate. This is consistent with the notion that the same pre-SN eruptions that generally give rise to SNe IIn also give rise to the dust needed for their commonly observed IR echoes. We also discuss some aspects of the IR line profiles, including He i λ10 830.