bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid innovation diffusion in social networks
Authors: Kreindler Gabriel E. , Young H. Peyton
Published: July 2014

Social and technological innovations often spread through social networks as people respond to what their neighbors are doing. Previous research has identified specific network structures, such as local clustering, that promote rapid diffusion. Here we derive bounds that are independent of network structure and size, such that diffusion is fast whenever the payoff gain from the innovation is sufficiently high and the agents’ responses are sufficiently noisy. We also provide a simple method for computing an upper bound on the expected time it takes for the innovation to become established in any finite network. For example, if agents choose log-linear responses to what their neighbors are doing, it takes on average less than 80 revision periods for the innovation to diffuse widely in any network, provided that the error rate is at least 5% and the payoff gain (relative to the status quo) is at least 150%. Qualitatively similar results hold for other smoothed best-response functions and populations that experience heterogeneous payoff shocks.
Synergy of aromatic residues and phosphoserines within the intrinsically disordered DNA-binding inhibitory elements of the Ets-1 transcription factor
Authors: Desjardins Geneviève , Meeker Charles A. , Bhachech Niraja , Currie Simon L. , Okon Mark , Graves Barbara J. , McIntosh Lawrence P.
Published: July 2014

Significance

Eukaryotic proteins often contain intrinsically disordered regions that lack well-defined conformations, yet still play key roles in numerous biological processes. The molecular mechanisms underlying the functions of such unstructured regions are often poorly understood. In the case of the E26 transformation-specific transcription factor, DNA binding by the ETS domain is autoinhibited through transient interactions with an adjacent disordered serine-rich region (SRR). Phosphorylation of the SRR in response to cellular signals increases these interactions and thereby reinforces autoinhibition. In this study, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine or tyrosine residues neighboring the SRR phosphoacceptor serines. This highlights a previously unrecognized role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence.
Properties of artificial networks evolved to contend with natural spectra
Authors: Morgenstern Yaniv , Rostami Mohammad , Purves Dale
Published: July 2014

Understanding why spectra that are physically the same appear different in different contexts (color contrast), whereas spectra that are physically different appear similar (color constancy) presents a major challenge in vision research. Here, we show that the responses of biologically inspired neural networks evolved on the basis of accumulated experience with spectral stimuli automatically generate contrast and constancy. The results imply that these phenomena are signatures of a strategy that biological vision uses to circumvent the inverse optics problem as it pertains to light spectra, and that double-opponent neurons in early-level vision evolve to serve this purpose. This strategy provides a way of understanding the peculiar relationship between the objective world and subjective color experience, as well as rationalizing the relevant visual circuitry without invoking feature detection or image representation.
The dynamic history of plastid genomes in the Campanulaceae
sensu lato
is unique among angiosperms
Authors: Knox Eric B.
Published: July 2014

Significance

Photosynthesis in plants occurs in the chloroplast, which is one developmental form of the eukaryotic plastid that evolved endosymbiotically from a cyanobacterium. During their algal ancestry, most plastid genes were transferred to the nucleus or otherwise lost, and genome architecture and organization stabilized prior to the origin of land plants. The plastid genome in some groups of plants subsequently became dynamic, which prompts the question: Why? This study shows that the extensive rearrangements in Campanulaceae plastid genomes include dozens of newly inserted protein-coding genes that likely originated from the nucleus. Better understanding of this unique evolutionary potential of Campanulaceae plastids to acquire new DNA may help bioengineers incorporate genes into plastids of other plants.
Pla2g16 phospholipase mediates gain-of-function activities of mutant p53
Authors: Xiong Shunbin , Tu Huolin , Kollareddy Madhusudhan , Pant Vinod , Li Qin , Zhang Yun , Jackson James G. , Suh Young-Ah , Elizondo-Fraire Ana C. , Yang Peirong , Chau Gilda , Tashakori Mehrnoosh , Wasylishen Amanda R. , Ju Zhenlin , Solomon Hilla , Rotter Varda , Liu Bin , El-Naggar Adel K. , Donehower Lawrence A. , Martinez Luis Alfonso , Lozano Guillermina
Published: July 2014

Significance

Mutations of p53 occur in approximately 50% of human cancer. p53 missense mutations exhibit gain-of-function activities. In this study, we discovered a previously unidentified mechanism of mutant p53 gain-of-function in osteosarcoma and mammary tumors. Our data indicate that mutant p53 binds to E26 transformation-specific motifs in the
Pla2g16
phospholipase promoter to induce its expression, which leads to more aggressive and metastatic phenotypes. Thus, the study implicates mutant p53 regulation of lipid metabolism in cancer cells to confer its gain-of-function. The study suggests new therapeutic options for patients with mutant p53.
Hierarchical random walks in trace fossils and the origin of optimal search behavior
Authors: Sims David W. , Reynolds Andrew M. , Humphries Nicolas E. , Southall Emily J. , Wearmouth Victoria J. , Metcalfe Brett , Twitchett Richard J.
Published: July 2014

Significance

How best to search for food in heterogeneous landscapes is a universal problem facing mobile organisms. Diverse modern animals use a random search strategy called a Lévy walk, composed of many small move steps interspersed by rare long steps, which theoretically is optimal for locating sparse resources. Here, we find the first evidence, to our knowledge, that extinct animals, in this case 50 My-old sea urchins, used a Lévy-like search strategy. Our results are important because they indicate Lévy walks likely have an ancient origin and may arise from simple behaviors observed in much older fossil trails. This foraging strategy may have adapted in response to decreased food availability after productivity collapse associated with past climate change and mass extinctions.
Accuracy of forecasts in strategic intelligence
Authors: Mandel David R. , Barnes Alan
Published: July 2014

Significance

Forecasting is a vital part of strategic intelligence, offering policy makers indications about probable future conditions and aiding sound decision making. Nevertheless, there has not been a concerted effort to study the accuracy of intelligence forecasts over a large set of assessments. This study applied quantitative measures of forecasting accuracy commonly used in other areas of expert forecasting to over 1,500 strategic intelligence forecasts spanning approximately 6 y of intelligence production by a strategic assessment unit. The findings revealed a high level of discrimination and calibration skill. We also show how calibration may be improved through postforecast transformations. The study illustrates the utility of proactively applying scoring rules to intelligence forecasts as a means of outcome-based quality control.
Transcriptomics identified a critical role for Th2 cell-intrinsic miR-155 in mediating allergy and antihelminth immunity
Authors: Okoye Isobel S. , Czieso Stephanie , Ktistaki Eleni , Roderick Kathleen , Coomes Stephanie M. , Pelly Victoria S. , Kannan Yashaswini , Perez-Lloret Jimena , Zhao Jimmy L. , Baltimore David , Langhorne Jean , Wilson Mark S.
Published: July 2014

Significance

The rising prevalence of allergic diseases throughout the world demands new approaches to treat this inflammatory disorder. CD4+Th2 cells orchestrate the allergic cascade, stimulating IgE production, activating innate cells, and stimulating local tissue. This study took a comprehensive approach to identify the unique transcriptional features of pathogenic Th2 cells with the aim of identifying novel molecular regulators. Highly purified Th1, Th2, Th9, Th17, and Treg cells isolated from mice with allergy, infection, and autoimmunity identified unique mRNA and microRNAs (miRNAs) expressed in Th2 cells. Functional and mechanistic studies using miRNA-deficient mice, luciferase assays, miRNA inhibitors, and siRNA in combination with state-of-the-art adoptive transfer systems, identified a critical role for miR-155–regulatedS1pr1in the pathogenesis of Th2-mediated allergy.
Charge transport and rectification in molecular junctions formed with carbon-based electrodes
Authors: Kim Taekyeong , Liu Zhen-Fei , Lee Chulho , Neaton Jeffrey B. , Venkataraman Latha
Published: July 2014

Significance

Single-molecule circuits represent an ultimate limit of device size and control, where function relates to intrinsic molecular properties. Here, we introduce a new paradigm for such circuits. Instead of using precious metals that have smooth densities of states around the Fermi energy, we introduce a hybrid device structure with the molecule trapped across a gold/graphite gap. These junctions rectify and have among the highest rectification ratios reported for a molecular junction. Using quantitative and predictive calculations, we explain our results as directly emanating from a nonuniform voltage drop and a nonconstant graphite density of states near the Fermi level. This work introduces the electrode as a tunable variable for realizing nonlinear device phenomena in hybrid junctions formed with layered two-dimensional materials.
Absence of lipofuscin in motor neurons of SOD1-linked ALS mice
Authors: Bandyopadhyay Urmi , Nagy Maria , Fenton Wayne A. , Horwich Arthur L.
Published: July 2014

Significance

This is the first report, to our knowledge, of the absence of lipofuscin, “aging pigment,” in a setting of motor neuron neurodegenerative disease, mutant SOD1-linked ALS. Although the initial hypothesis was that this must be due to a block in the autophagy/lysosome pathway, instead studies of autophagy markers and of ALS mice treated with chloroquine suggest the opposite, that there is hyperactivity of the autophagy/lysosome pathway, at least in part mediated through MTORC1.
Impaired excitability of somatostatin- and parvalbumin-expressing cortical interneurons in a mouse model of Dravet syndrome
Authors: Tai Chao , Abe Yasuyuki , Westenbroek Ruth E. , Scheuer Todd , Catterall William A.
Published: July 2014

Significance

Dravet syndrome (DS) is an intractable childhood epilepsy syndrome accompanied by mental disability, behaviors similar to autism, and premature death. DS is caused by dominant loss-of-function mutations in the gene encoding the NaV1.1 sodium channel,SCN1A, which initiates electrical signals in the nerve cells of the brain. The physiological basis for this disease is largely unknown. Here we describe the functional effects of DS mutations on inhibitory neurons in the cerebral cortex in mice. Our results show that two major types of inhibitory neurons are impaired in generation of electrical signals by a DS mutation, whereas excitatory neurons are unaffected. The resulting imbalance of excitatory over inhibitory electrical signaling would contribute in an important way to the symptoms of DS.
Decreased dopamine brain reactivity in marijuana abusers is associated with negative emotionality and addiction severity
Authors: Volkow Nora D. , Wang Gene-Jack , Telang Frank , Fowler Joanna S. , Alexoff David , Logan Jean , Jayne Millard , Wong Christopher , Tomasi Dardo
Published: July 2014

Significance

Marijuana abusers show lower positive and higher negative emotionality scores than controls, which is consistent, on one hand, with lower reward sensitivity and motivation and, on the other hand, with increased stress reactivity and irritability. To investigate this aspect of marijuana’s impact on the human brain, we compared the brain’s reactivity in marijuana abusers vs. controls when challenged with methylphenidate (MP). We found that marijuana abusers display attenuated dopamine (DA) responses to MP, including reduced decreases in striatal distribution volumes. These deficits cannot be unambiguously ascribed to reduced DA release (because decreases in nondisplaceable binding potential were not blunted) but could reflect a downstream postsynaptic effect that in the ventral striatum (brain reward region) might contribute to marijuana’s negative emotionality and addictive behaviors.
Theme and variations
Authors: Berry Margaret , Thompson Geoff , Hillier Hilary
Published: July 2014

There has been a great deal of interest recently in investigating the configurations
of linguistic choices which characterise different registers. This chapter
focuses on the particular area of patterns of thematic choice across registers.
We bring together two traditions in register analysis: Systemic Functional
Linguistics, and Corpus Linguistics as implemented by Biber and colleagues.
We carry out a manual analysis of Theme, using SFL categories, in a small set
of texts designed to mirror the registers which appear at key points on Biber’s
Dimension 1 (“Involved versus Informational Production”). The goal is to see
to what extent variation in thematic patterning accords with the positioning
on Biber’s scale; and we attempt to account for any similarities and differences
that emerge.
“That’s so a construction!”
Authors: Gonzálvez-García Francisco
Published: July 2014

This paper provides a fine-grained analysis of the “X is so N(P)” constructionin present-day English, in which the noun in the A slot necessarily involvesmetonymic inferencing and can be determinerless, even if it is countable. Thisconstruction conveys a positive or negative assessment by the speaker/writerof a given person, entity, event or state of affairs, with some interpretationsexhibiting a higher degree of conventionalization than others. From a syntagmaticviewpoint, the construction under scrutiny instantiates a step-wise,gradual transition from noun to adjective in the A slot (e.g. “That’s so applepie”< “That’s so cool”). Our analysis also reveals the existence of paradigmaticsets with other intensifiers (e.g. “very”, “quite”, “totally”, “really”, “too”) in predicativeand attributive contexts.
Individual and Cooperative Management of Invasive Species in Human‐mediated Landscapes
Authors: Epanchin-Niell Rebecca S. , Wilen James E.
Published: July 2014

As a bioinvasion spreads across a landscape from its point of introduction, damages rise roughly with the square of the distance from the original invasion. It is thus generally beneficial, at the landscape scale, to apply eradication or containment controls early if not immediately upon discovery. However, an individual property owner only has incentives to consider the costs and benefits of control on his/her own property rather than potential landscape‐scale damages. Bioinvasions will therefore generally be under‐controlled in a landscape of independent owners operating under a laissez‐faire system. A mechanism is thus needed to induce early cooperative contributions to control costs from beneficiaries who would, without them, be invaded later. We develop a spatially‐explicit, integrated model of invasion spread and human behavior to examine how different degrees of spatial cooperation affect patterns of invasion spread and the total costs and damages imposed. We compare individual laissez‐faire, cooperative control by adjacent neighbors, and cooperative control by groups including more distant but nearby neighbors. As expected, private laissez‐faire control decisions tend to under‐control the invasion relative to socially optimal control under most circumstances. But a reasonably high fraction of first best payoffs can be achieved with only a modest geographical reach of cooperation. We also find that less extensive cooperation is needed to control invasions whose costs and damages otherwise lead to the largest externalities (circumstances with costs that are relatively low compared with damages). This suggests that even small amounts of cooperation to control bioinvasions can provide large social benefits.
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013
Authors: Verspoor Karin , Shatkay Hagit , Hirschman Lynette , Blaschke Christian , Valencia Alfonso
Published: July 2014

The ISMB Special Interest Group on Linking Literature, Information and Knowledge for Biology (BioLINK) organized a one-day workshop at ISMB/ECCB 2013 in Berlin, Germany. The theme of the workshop was ‘Roles for text mining in biomedical knowledge discovery and translational medicine’. This summary reviews the outcomes of the workshop. Meeting themes included concept annotation methods and applications, extraction of biological relationships and the use of text-mined data for biological data analysis.

Availability and implementation: All articles are available at http://biolinksig.org/proceedings-online/ .

Contact:  karin.verspoor@unimelb.edu.au
The Bioinformatics Open Source Conference (BOSC) 2013
Authors: Harris Nomi L. , Cock Peter J. A. , Chapman Brad A. , Goecks Jeremy , Hotz Hans-Rudolf , Lapp Hilmar
Published: July 2014

Contact:  nlharris@lbl.gov
Using a weight-structured oyster population dynamic model to explore top-down control of coastal water quality in a subtropical embayment
Authors: Richards Russell G. , Chaloupka Milani
Published: July 2014

The natural filtering capacity of oysters and other suspension filter-feeders has seen them put forward as a potential water quality management option. However, the specifics of how many oysters would be required to clean a system are not necessarily straightforward to evaluate because of the size-dependence of oyster physiological rates along with the dynamic coupling that exists between the oysters and the environment. We use a weight-structured shellfish population model and a nutrient–phytoplankton–detritus model to answer the question of how many oysters it would take to clean a large estuary located in Queensland, Australia. Modelling results indicate that improvements in the water quality are not seen until the stocking density of oysters exceeds 0.09 ind. m−3 and that local water quality guidelines are not fully met until the density exceeds 1.80 ind. m−3. At these densities, the corresponding times to filter the entire volume of the study area are 52–38 d (0.09 ind. m−3) and 1.80–1.35 d (1.80 ind. m−3), respectively. This research highlights that regulatory feedback pathways exist between a shellfish population and the water quality constituents that they control through filtration. While the use of oysters and other filter-feeders may be an appealing approach to nutrient management and top-down control of phytoplankton, the practicalities of deploying oysters at a system-scale may be the greatest barrier to this option.
Cohort Profile: The Nicotine Dependence in Teens (NDIT) Study
Authors: O’Loughlin Jennifer , Dugas Erika N , Brunet Jennifer , DiFranza Joseph , Engert James C , Gervais Andre , Gray-Donald Katherine , Karp Igor , Low Nancy C , Sabiston Catherine , Sylvestre Marie-Pierre , Tyndale Rachel F , Auger Nathalie , Auger Nathalie , Mathieu Belanger , Tracie Barnett , Chaiton Michael , Chenoweth Meghan J , Constantin Evelyn , Contreras Gisèle , Kakinami Lisa , Labbe Aurelie , Maximova Katerina , McMillan Elizabeth , O’Loughlin Erin K , Pabayo Roman , Roy-Gagnon Marie-Hélène , Tremblay Michèle , Wellman Robert J , Hulst Andraeavan , Paradis Gilles
Published: July 2014

The Nicotine Dependence in Teens (NDIT) study is a prospective cohort investigation of 1294 students recruited in 1999–2000 from all grade 7 classes in a convenience sample of 10 high schools in Montreal, Canada. Its primary objectives were to study the natural course and determinants of cigarette smoking and nicotine dependence in novice smokers. The main source of data was self-report questionnaires administered in class at school every 3 months from grade 7 to grade 11 (1999–2005), for a total of 20 survey cycles during high school education. Questionnaires were also completed after graduation from high school in 2007–08 and 2011–12 (survey cycles 21 and 22, respectively) when participants were aged 20 and 24 years on average, respectively. In addition to its primary objectives, NDIT has embedded studies on obesity, blood pressure, physical activity, team sports, sedentary behaviour, diet, genetics, alcohol use, use of illicit drugs, second-hand smoke, gambling, sleep and mental health. Results to date are described in 58 publications, 20 manuscripts in preparation, 13 MSc and PhD theses and 111 conference presentations. Access to NDIT data is open to university-appointed or affiliated investigators and to masters, doctoral and postdoctoral students, through their primary supervisor ( www.nditstudy.ca ).
Inheritance of Prehaustorial Resistance to Puccinia graminis f. sp. avenae in Barley (Hordeum vulgare L.)
Authors: Dracatos Peter M. , Ayliffe Michael , Khatkar Mehar S. , Fetch Tom , Singh Davinder , Park Robert F.
Published: July 2014

Rust pathogens within the genus Puccinia cause some of the most economically significant diseases of crops. Different formae speciales of P. graminis have co-evolved to mainly infect specific grass hosts; however, some genotypes of other closely related cereals can also be infected. This study investigated the inheritance of resistance to three diverse pathotypes of the oat stem rust pathogen (P. graminis f. sp. avenae) in the ‘Yerong’ ✕ ‘Franklin’ (Y/F) barley doubled haploid (DH) population, a host with which it is not normally associated. Both parents, ‘Yerong’ and ‘Franklin’, were immune to all P. graminis f. sp. avenae pathotypes; however. there was transgressive segregation within the Y/F population, in which infection types (IT) ranged from complete immunity to mesothetic susceptibility, suggesting the presence of heritable resistance. Both QTL and marker-trait association (MTA) analysis was performed on the Y/F population to map resistance loci in response to P. graminis f. sp. avenae. QTL on chromosome 1H (‘Yerong’ Rpga1 and Rpga2) were identified using all forms of analysis, while QTL detected on 5H (‘Franklin’ Rpga3 and Rpga4) and 7H (Rpga5) were only detected using MTA or composite interval mapping–single marker regression analysis respectively. Rpga1 to Rpga5 were effective in response to all P. graminis f. sp. avenae pathotypes used in this study, suggesting resistance is not pathotype specific. Rpga1 co-located to previously mapped QTL in the Y/F population for adult plant resistance to the barley leaf scald pathogen (Rhynchosporium secalis) on chromosome 1H. Histological evidence suggests that the resistance observed within parental and immune DH lines in the population was prehaustorial and caused by callose deposition within the walls of the mesophyll cells, preventing hyphal penetration.
Detection, Diversity, and Population Dynamics of WaterbornePhytophthora ramorumPopulations
Authors: Eyre C. A. , Garbelotto M.
Published: July 2014

Sudden oak death, the tree disease caused by Phytophthora ramorum, has significant environmental and economic impacts on natural forests on the U.S. west coast, plantations in the United Kingdom, and in the worldwide nursery trade. Stream baiting is vital for monitoring and early detection of the pathogen in high-risk areas and is performed routinely; however, little is known about the nature of water-borne P. ramorum populations. Two drainages in an infested California forest were monitored intensively using stream-baiting for 2 years between 2009 and 2011. Pathogen presence was determined both by isolation and polymerase chain reaction (PCR) from symptomatic bait leaves. Isolates were analyzed using simple sequence repeats to study population dynamics and genetic structure through time. Isolation was successful primarily only during spring conditions, while PCR extended the period of pathogen detection to most of the year. Water populations were extremely diverse, and changed between seasons and years. A few abundant genotypes dominated the water during conditions considered optimal for aerial populations, and matched those dominant in aerial populations. Temporal patterns of genotypic diversification and evenness were identical among aerial, soil, and water populations, indicating that all three substrates are part of the same epidemiological cycle, strongly influenced by rainfall and sporulation on leaves. However, there was structuring between substrates, likely arising due to reduced selection pressure in the water. Additionally, water populations showed wholesale mixing of genotypes without the evident spatial autocorrelation present in leaf and soil populations.
Comparison of Open Versus Percutaneous Pedicle Screw Fixation Using the Sextant System in the Treatment of Traumatic Thoracolumbar Fractures
Authors: Wang Hongwei , Zhou Yue , Li Changqing , Liu Jun , Xiang Liangbi
Published: July 2014

Study Design:

We retrospectively reviewed 100 patients who were posterior stabilized without graft fusion. Using the Sextant system, 22 patients underwent minimally invasive short-segment 4-pedicle screw fixation (MIF4) and 39 patients underwent minimally invasive short-segment combined with intermediate screws fixation, that is, 6-pedicle screw fixation (MIF6). The conventional open posterior short-segment 4-pedicle screw fixation (OPF4) technique was used in 39 patients.

Objective:

To evaluate the feasibility, safety, and efficacy of percutaneous pedicle screw fixation using the Sextant system in the treatment of traumatic thoracolumbar fractures compared with the conventional open posterior short-segment pedicle screw fixation technique.

Summary of Background Data:

To the best of our knowledge, the clinical and radiographic outcomes of MIF4, MIF6 with polyaxial pedicle screws, and OPF4 with monoaxial pedicle screws have not been compared in the treatment of thoracolumbar fractures.

Methods:

Visual analogue scores (VAS), Oswestry disability index (ODI) scores, clinical outcomes including surgical blood loss, operation time, and postoperative hospital stay, sagittal Cobb angle, vertebral body angle, and anterior height of the fractured vertebrae were compared among the 3 groups.

Results:

Significant postoperative improvements, relative to baseline, were observed in the VAS and ODI scores (P<0.05 each). There were no significant differences between the MIF4 and MIF6 groups in clinical outcomes, including surgical blood loss, operation time, postoperative hospital stay, VAS, and ODI scores (P>0.05 each). However, there were significant differences between both MIF groups and the OPF group (P<0.05 each). Significant improvements were observed in the sagittal Cobb angle, vertebral body angle, and anterior height of the fractured vertebrae (P<0.05 each). During follow-up, however, the correction loss of the sagittal Cobb angle was smallest in the MIF6 group (P<0.05).

Conclusions:

Minimally invasive posterior stabilization using the Sextant system resulted in reduced injury compared with the open surgery, during both the internal fixation surgery and the implant removal surgery. Percutaneous screw fixation through the pedicle of the fractured vertebra is superior to the conventional OPF4 technique in correcting kyphotic deformities, and can be performed without any extra procedures.
Tick Infestation of the Eyelid With Histopathologic Characterization
Authors: Rai Ruju , Yoon Michael K. , Stacy Rebecca C.
Published: July 2014

Ocular tick infestation is a rare occurrence. The authors report a case that is unique for being the first published example from New England, for its chronic presentation, and for the inclusion of histopathologic analysis in its diagnostic workup. A 75-year-old man was evaluated for a persistent eyelid growth secondary to an incompletely removed tick that had attached 6 months earlier. The lesion was completely excised, and a partially destroyed arthropod was observed embedded within the tissue. Light microscopy demonstrated a mixed granulomatous reaction. Given the disruption of the tick’s anatomy, speciation could not be performed. The patient had an uneventful recovery. A corresponding review of tick bites to the eye is provided.
Using Natural Language Processing to Extract Abnormal Results From Cancer Screening Reports
Authors: Moore Carlton R. , Farrag Ashraf , Ashkin Evan
Published: July 2014

Objectives

Numerous studies show that follow-up of abnormal cancer screening results, such as mammography and Papanicolaou (Pap) smears, is frequently not performed in a timely manner. A contributing factor is that abnormal results may go unrecognized because they are buried in free-text documents in electronic medical records (EMRs), and, as a result, patients are lost to follow-up. By identifying abnormal results from free-text reports in EMRs and generating alerts to clinicians, natural language processing (NLP) technology has the potential for improving patient care. The goal of the current study was to evaluate the performance of NLP software for extracting abnormal results from free-text mammography and Pap smear reports stored in an EMR.

Methods

A sample of 421 and 500 free-text mammography and Pap reports, respectively, were manually reviewed by a physician, and the results were categorized for each report. We tested the performance of NLP to extract results from the reports. The 2 assessments (criterion standard versus NLP) were compared to determine the precision, recall, and accuracy of NLP.

Results

When NLP was compared with manual review for mammography reports, the results were as follows: precision, 98% (96%–99%); recall, 100% (98%–100%); and accuracy, 98% (96%–99%). For Pap smear reports, the precision, recall, and accuracy of NLP were all 100%.

Conclusions

Our study developed NLP models that accurately extract abnormal results from mammography and Pap smear reports. Plans include using NLP technology to generate real-time alerts and reminders for providers to facilitate timely follow-up of abnormal results.
Trends in high-performance computing for engineering calculations
Authors: Giles M. B. , Reguly I.
Published: July 2014

High-performance computing has evolved remarkably over the past 20 years, and that progress is likely to continue. However, in recent years, this progress has been achieved through greatly increased hardware complexity with the rise of multicore and manycore processors, and this is affecting the ability of application developers to achieve the full potential of these systems. This article outlines the key developments on the hardware side, both in the recent past and in the near future, with a focus on two key issues: energy efficiency and the cost of moving data. It then discusses the much slower evolution of system software, and the implications of all of this for application developers.
Large eddy simulations in 2030 and beyond
Authors: Piomelli U
Published: July 2014

Since its introduction, in the early 1970s, large eddy simulations (LES) have advanced considerably, and their application is transitioning from the academic environment to industry. Several landmark developments can be identified over the past 40 years, such as the wall-resolved simulations of wall-bounded flows, the development of advanced models for the unresolved scales that adapt to the local flow conditions and the hybridization of LES with the solution of the Reynolds-averaged Navier–Stokes equations. Thanks to these advancements, LES is now in widespread use in the academic community and is an option available in most commercial flow-solvers. This paper will try to predict what algorithmic and modelling advancements are needed to make it even more robust and inexpensive, and which areas show the most promise.
Advancing predictive models for particulate formation in turbulent flames via massively parallel direct numerical simulations
Authors: Bisetti Fabrizio , Attili Antonio , Pitsch Heinz
Published: July 2014

Combustion of fossil fuels is likely to continue for the near future due to the growing trends in energy consumption worldwide. The increase in efficiency and the reduction of pollutant emissions from combustion devices are pivotal to achieving meaningful levels of carbon abatement as part of the ongoing climate change efforts. Computational fluid dynamics featuring adequate combustion models will play an increasingly important role in the design of more efficient and cleaner industrial burners, internal combustion engines, and combustors for stationary power generation and aircraft propulsion. Today, turbulent combustion modelling is hindered severely by the lack of data that are accurate and sufficiently complete to assess and remedy model deficiencies effectively. In particular, the formation of pollutants is a complex, nonlinear and multi-scale process characterized by the interaction of molecular and turbulent mixing with a multitude of chemical reactions with disparate time scales. The use of direct numerical simulation (DNS) featuring a state of the art description of the underlying chemistry and physical processes has contributed greatly to combustion model development in recent years. In this paper, the analysis of the intricate evolution of soot formation in turbulent flames demonstrates how DNS databases are used to illuminate relevant physico-chemical mechanisms and to identify modelling needs.
Benchmark Analysis of Algorithms for Determining and Quantifying Full-length mRNA Splice Forms from RNA-Seq Data
Authors: Hayer K. , Pizzaro A. , Lahens N. L. , Hogenesch J. B. , Grant G. R.
Published: July 2014

The advantages of RNA sequencing (RNA-Seq) suggest it will replace microarrays for highly parallel gene expression analysis. For example, in contrast to arrays, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length transcripts. A number of methods have been developed for this purpose, but short error prone reads makes it a difficult problem in practice. It is essential to determine which algorithms perform best, and where and why they fail. However, there is a dearth of independent and unbiased benchmarking studies of these algorithms. Here we take an approach using both simulated and experimental benchmark data to evaluate their accuracy. We conclude that most methods are inaccurate even using idealized data, and that no is method sufficiently accurate once complicating factors such as polymorphisms, intron signal, sequencing error, and multiple splice forms are present. These results point to the pressing need for further algorithm development.
T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
Authors: Madi Asaf , Shifrut Eric , Reich-Zeliger Shlomit , Gal Hilah , Best Katharine , Ndifon Wilfred , Chain Benjamin , Cohen Irun R. , Friedman Nir
Published: July 2014

The T-cell receptor (TCR) repertoire is formed by random recombinations of genomic precursor elements; the resulting combinatorial diversity renders unlikely extensive TCR sharing between individuals. Here, we studied CDR3β amino acid sequence sharing in a repertoire-wide manner, using high-throughput TCR-seq in 28 healthy mice. We uncovered hundreds of public sequences shared by most mice. Public CDR3 sequences, relative to private sequences, are two orders of magnitude more abundant on average, express restricted V/J segments, and feature high convergent nucleic acid recombination. Functionally, public sequences are enriched for MHC-diverse CDR3 sequences that were previously associated with autoimmune, allograft, and tumor-related reactions, but not with anti-pathogen-related reactions. Public CDR3 sequences are shared between mice of different MHC haplotypes, but are associated with different, MHC-dependent, V genes. Thus, despite their random generation process, TCR repertoires express a degree of uniformity in their post-genomic organization. These results, together with numerical simulations of TCR genomic rearrangements, suggest that biases and convergence in TCR recombination combine with ongoing selection to generate a restricted subset of self-associated, public CDR3 TCR sequences, and invite reexamination of the basic mechanisms of T-cell repertoire formation.
Does Intra‐African Trade Reduce Youth Unemployment in Africa?
Authors: Anyanwu John C.
Published: July 2014

This study empirically estimates the effect of Africa's intra‐regional trade on the burgeoning youth unemployment in the continent. This is necessary since very few studies have been undertaken in the particular context of African countries. To the best of our knowledge there are no studies exploring the intra‐African trade–youth unemployment nexus in Africa. We investigate both the aggregate and gender‐specific impacts. Our empirical estimates, using available cross‐sectional time series data over the period 1980 to 2010, suggest that higher levels of intra‐African trade reduce both the aggregate, female and male youth unemployment in Africa. In addition, our results show that domestic investment rate, institutionalized democracy, secondary education, inflation, economic growth, and higher urbanization tend to reduce youth unemployment both on the aggregate and gender‐differentiated and therefore are good for youth unemployment reduction in the continent. On the other hand, higher real per capita GDP and to a lesser extent credit to the private sector have a significant positive effect on youth unemployment in Africa. Government consumption expenditure and foreign direct investment have an insignificant effect on both the aggregate level and the gendered level of youth unemployment in Africa. Based on these results, some policy recommendations are proffered.
Biraderi, Bloc Votes and Bradford: Investigating the Respect Party's Campaign Strategy
Authors: Peace Timothy , Akhtar Parveen
Published: July 2014

Research Highlights and Abstract

This article

Contributes to theoretical debates on minority political participation in the UK, with specific reference to inter-generational variations within the South Asian Muslim community; Contributes to the scholarly literature on the impact and effectiveness of new political parties within the British political system, through a case study of the Respect Party; Adds to empirical primary data on strategies adopted by political parties in courting specific sections of the ethnic minority vote in the UK; Offers an empirically-led demonstration of the changes taking place within the political sphere of South Asian Muslim diasporas in Britain.

In March 2012, the Respect Party won an unexpected by-election in the British city of Bradford, previously regarded as a safe Labour seat. This article examines the party's campaign strategy and in particular how it courted South Asian Muslim voters. A dominant feature of South Asian Muslim politics in the UK has been community bloc voting along lines of kinship (biraderi). The use of kinship networks for political gain effectively disenfranchised many young people and women. We demonstrate how Respect used their experience of campaigning in constituencies with significant numbers of South Asian Muslim voters to achieve an unlikely victory in Bradford. A key strategy was to mobilise otherwise politically marginalised sections of the South Asian Muslim community by offering an alternative to the culture of patronage in Bradford whilst at the same time utilising certain community structures in order to gain their own bloc votes.
The Early Effects of Medicare's Mandatory Hospital Pay‐for‐Performance Program
Authors: Ryan Andrew M. , Burgess James F. , Pesko Michael F. , Borden William B. , Dimick Justin B.
Published: July 2014

Objective

To evaluate the impact of hospital value‐based purchasing (HVBP) on clinical quality and patient experience during its initial implementation period (July 2011–March 2012).

Data Sources

Hospital‐level clinical quality and patient experience data from Hospital Compare from up to 5 years before and three quarters after HVBP was initiated.

Study Design

Acute care hospitals were exposed to HVBP by mandate while critical access hospitals and hospitals located in Maryland were not exposed. We performed a difference‐in‐differences analysis, comparing performance on 12 incentivized clinical process and 8 incentivized patient experience measures between hospitals exposed to the program and a matched comparison group of nonexposed hospitals. We also evaluated whether hospitals that were ultimately exposed to HVBP may have anticipated the program by improving quality in advance of its introduction.

Principal Findings

Difference‐in‐differences estimates indicated that hospitals that were exposed to HVBP did not show greater improvement for either the clinical process or patient experience measures during the program's first implementation period. Estimates from our preferred specification showed that HVBP was associated with a 0.51 percentage point reduction in composite quality for the clinical process measures (p > .10, 95 percent CI: −1.37, 0.34) and a 0.30 percentage point reduction in composite quality for the patient experience measures (p > .10, 95 percent CI: −0.79, 0.19). We found some evidence that hospitals improved performance on clinical process measures prior to the start of HVBP, but no evidence of this phenomenon for the patient experience measures.

Conclusions

The timing of the financial incentives in HVBP was not associated with improved quality of care. It is unclear whether improvement for the clinical process measures prior to the start of HVBP was driven by the expectation of the program or was the result of other factors.
Busted! Management of paediatric upper limb fractures: Not all that it's cracked up to be
Authors: Mills Erin , Craig Simon , Oakley Ed
Published: July 2014

Objective

The primary objective was to assess use of splinting prior to X‐ray in paediatric ED patients with deformed upper limb fractures. Secondary objectives were to evaluate pharmaceutical analgesia use and the impact of demographic, hospital and clinical variables on splint and analgesia provision.

Methods

A retrospective study of 1407 paediatric ED patients who received upper limb X‐rays. The records of those with fractures requiring manipulation were identified, and reviewed for data on demographics, mode of arrival, triage category, site of fracture, clinician seniority, pain scoring, splint application and analgesic use.

Results

Two hundred and twelve patients had fractures requiring manipulation. Of these, 47 (22%) had a splint applied prior to X‐ray and 161 (76%) of patients were prescribed analgesia in the first hour after presentation. A triage category 1 or 2 and arrival by ambulance predicted for splint application. Children with higher recorded pain scores were more likely to receive any analgesia in the first hour (91% with a pain score ≥7 compared with 62% with pain score of ≤6, P < 0.001), and more likely to receive strong analgesia (59% vs 13%, P < 0.001). Those triaged to category 1 or 2 were more likely to receive analgesia in the first hour (P < 0.001).

Conclusions

This study identified significant shortcomings in ED management of children with deformed upper limb fractures. Only a minority were splinted prior to X‐ray, and a quarter did not receive any analgesia in the first hour after presentation. Future study should investigate methods to improve ED management of these patients.
Fucosylated Chondroitin Sulfate from Sea Cucumber Improves Insulin Sensitivity via Activation of PI3K/PKB Pathway
Authors: Hu Shiwei , Chang Yaoguang , He Min , Wang Jingfeng , Wang Yuming , Xue Changhu
Published: July 2014

This study was to investigate the effects of fucosylated chondroitin sulfate (CHS) from sea cucumber on insulin sensitivity in skeletal muscle of type 2 diabetic mice induced by a high‐fat high‐sucrose diet (HFSD). CHS supplementation for 19 wk significantly improved insulin sensitivity by 20%, and reduced blood glucose and insulin levels. Western blotting assay showed that CHS significantly increased insulin‐stimulated glucose transporter 4 (GLUT4) translocation to 1.7‐fold, phosphorylation of phosphoinositide 3‐kinase (PI3K) at p85 to 5.0‐fold, protein kinase B (PKB) at Ser473 to 1.5‐fold, and Thr308 to 1.6‐fold in skeletal muscle. However, PI3K, PKB, and GLUT4 total proteins expression were unchangeable. In addition, qRT‐PCR analysis proved that the insulin signaling was activated by CHS treatment, showing the increased mRNA expressions of glucose uptake‐related key genes. It indicated that CHS improved insulin sensitivity by activation of PI3K/PKB signaling in skeletal muscle of type 2 diabetic mice. Identification of potential mechanism by which CHS increased insulin sensitivity might provide a new functional food or pharmaceutical application of sea cucumber.
Sensory Characterization of Young South American Red Wines Classified by Varietal and Origin
Authors: Llobodanin Laura Garcia , Barroso Lucia Pereira , Castro Inar Alves
Published: July 2014

Typicality is the set of sensory characteristics that identify a distinctive type of wine. Thus, the aim of this research was to identify the sensory characteristics that contribute to define typicality of young South American red wines based on their varietal and origin, and to evaluate the effect of the vintage on this identification. To achieve this objective, visual appearance, odor, and taste of 138 wines from 2 vintages were submitted to a sensory evaluation using a descriptive analysis complemented with the frequency of citation method, performed by wine experts. The intensity of 17 odor and taste attributes was evaluated using a 5 points rating structured scale. The panel performance evaluation demonstrated its high level of expertise and reproducibility. The wines were separated into 3 clusters by multivariate analyses. Cluster 1 was primarily composed of Carménère, Malbec, and Syrah wines from Chile. Cluster 2 was predominantly composed of Tannat wines from Uruguay and Brazil, while Cluster 3 contained a higher proportion of Malbec and Merlot wines from Argentina and Brazil. Cabernet Sauvignon was equally distributed into all clusters. Wine experts were able to identify the wines according to their varietal and origin, suggesting that there is typicality in young South American red wines. The combination of descriptive analysis with the frequency of citation was useful in characterizing most of the wines, but the typicality perceived by the panelists was not achieved by multivariate analysis. Vintage did not alter the sensory characterization of the wines, and this result could be due the new viticulture or oenological practices used by the winemakers to compensate the environmental variation.