bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outbreaks attributed to fresh leafy vegetables, United States, 1973–2012
Authors: HERMAN K. M. , HALL A. J. , GOULD L. H. 
Published: February 2015

SUMMARYLeafy vegetables are an essential component of a healthy diet; however, they have been associated with high-profile outbreaks causing severe illnesses. We reviewed leafy vegetable-associated outbreaks reported to the Centers for Disease Control and Prevention between 1973 and 2012. During the study period, 606 leafy vegetable-associated outbreaks, with 20 003 associated illnesses, 1030 hospitalizations, and 19 deaths were reported. On average, leafy vegetable-associated outbreaks were larger than those attributed to other food types. The pathogens that most often caused leafy vegetable-associated outbreaks were norovirus (55% of outbreaks with confirmed aetiology), Shiga toxin-producingEscherichia coli(STEC) (18%), andSalmonella(11%). Most outbreaks were attributed to food prepared in a restaurant or catering facility (85%). An ill food worker was implicated as the source of contamination in 31% of outbreaks. Efforts by local, state, and federal agencies to control leafy vegetable contamination and outbreaks should span from the point of harvest to the point of preparation.
Preferential carriage of class 2 integrons in Acinetobacter baumannii CC113 and novel singletons
Authors: RAMÍREZ M. S. , MONTAÑA S. , CASSINI M. , CENTRÓN D. 
Published: February 2015

SUMMARYOur understanding of the distribution of integrons associated with multidrug resistance in Acinetobacter baumannii isolates around the world remains incomplete. The association between the class 1 and 2 integron A. baumannii-positive isolates (n = 60), recovered since 1982 from 11 Argentinean hospitals, and the circulating lineages, was investigated. While class 2 integrons were highly significantly associated with clonal lineage CC113B/CC79P (P = 0·009) and novel singletons (P = 0·001), class 1 integrons were found not to be associated with CC109B/CC1P or other lineages. The study reveals a differential distribution of class 2 integrons in lineages, and suggests that the prevalence of intI2 in Argentina is related to the emergence of novel singletons in recent years and to the abundance of CC113B/CC79P, which has been the local dominant lineage for several decades.
A Regional and Social Dialectology of the BATH Vowel in South African English
Authors: Mesthrie Rajend , Chevalier Alida , Dunne Timothy 
Published: February 2015

AbstractThis paper provides the beginnings of a pan–South African English dialectology, characterizing five cities (Cape Town, Port Elizabeth, Kimberley, Johannesburg, and Durban) and four ethnicities (Black, Colored, Indian, and White), via a single vowel, BATH (or /ɑ:/). From interviews with 200 selected speakers, 5553 tokens were subjected to acoustic analysis via PRAAT (Boersma & Weenink, 2010), yielding bivariate data on vowel quality. Statistical analysis via analysis of variance focused on sets of five persons in each of 40 city-ethnicity-gender combinations. Overall, no city shows cohesion across all ethnic groups, though Kimberley, the smallest of the cities, and Johannesburg, the largest, come close. Conversely, no ethnicity shows cohesion across all cities, although Black speakers of traditional L2 English background come close. There is a robust regional difference for Colored speakers between Johannesburg and the other cities. Gender effects are notable: women's means are closer to the historically prestige [ɑ:] variant than the historically broader variant [ɔ:] in 6 of 20 possible groupings by city and ethnicity; in none of the cases is the opposite true.
Sociolinguistic Patterns in Seattle English
Authors: Wassink Alicia Beckford 
Published: February 2015

AbstractAlthough it was the focus of several publications by Carroll Reed in the 1950s and early 1960s, English spoken in the Pacific Northwestern United States (PNWE) has received minimal research attention in variationist sociolinguistics. This paper provides the first report from an ongoing sociophonetic study. Data from a single-ethnicity, 25-person subsample of the larger corpus, constituted to explore change in apparent time, clarifies Seattleites' use of key markers of Western speech, including merger of cot /a/ and caught /ɔ/, and the positions of all vowel phonemes in the system. Several heretofore unreported characteristic features are found, including a tendency for PNWE speakers to monophthongize /e:/ bake and to raise prevelar /æ/ bag and /ε/ beg toward /e:/.
A statistical model for grammar mapping
Authors: BASIRAT A. , FAILI H. , NIVRE J. 
Published: February 2015

AbstractThe two main classes of grammars are (a) hand-crafted grammars, which are developed by language experts, and (b) data-driven grammars, which are extracted from annotated corpora. This paper introduces a statistical method for mapping the elementary structures of a data-driven grammar onto the elementary structures of a hand-crafted grammar in order to combine their advantages. The idea is employed in the context of Lexicalized Tree-Adjoining Grammars (LTAG) and tested on two LTAGs of English: the hand-crafted LTAG developed in the XTAG project, and the data-driven LTAG, which is automatically extracted from the Penn Treebank and used by the MICA parser. We propose a statistical model for mapping any elementary tree sequence of the MICA grammar onto a proper elementary tree sequence of the XTAG grammar. The model has been tested on three subsets of the WSJ corpus that have average lengths of 10, 16, and 18 words, respectively. The experimental results show that full-parse trees with average F1-scores of 72.49, 64.80, and 62.30 points could be built from 94.97%, 96.01%, and 90.25% of the XTAG elementary tree sequences assigned to the subsets, respectively. Moreover, by reducing the amount of syntactic lexical ambiguity of sentences, the proposed model significantly improves the efficiency of parsing in the XTAG system.
Limitations of the Trail Making Test Part-B in Assessing Frontal Executive Dysfunction
Authors: Chan Edgar , MacPherson Sarah E. , Robinson Gail , Turner Martha , Lecce Francesca , Shallice Tim , Cipolotti Lisa 
Published: February 2015

AbstractPart B of the Trail Making Test (TMT-B) is one of the most widely used neuropsychological tests of “executive” function. A commonly held assumption is that the TMT-B can be used to detect frontal executive dysfunction. However, so far, research evidence has been limited and somewhat inconclusive. In this retrospective study, performance on the TMT-B of 55 patients with known focal frontal lesions, 27 patients with focal non-frontal lesions and 70 healthy controls was compared. Completion time and the number of errors made were examined. Patients with frontal and non-frontal lesions performed significantly worse than healthy controls for both completion time and the number of errors. However, there was no significant difference for both completion time and the number of errors when patients with frontal and non-frontal lesions were compared. Performance was also not significantly different between patients with focal lesions within different regions of the frontal lobe (orbital, left lateral, right lateral, medial). Our findings suggest that the TMT-B is a robust test for detection of brain dysfunction. However, its capacity for detecting frontal executive dysfunction appears rather limited. Clinicians should be cautious when drawing conclusions from performance on the TMT-B alone. (JINS, 2015, 21, 169–174)
Single-taxon field measurements of bacterial gene regulation controlling DMSP fate
Authors: Varaljay Vanessa A , Robidart Julie , Preston Christina M , Gifford Scott M , Durham Bryndan P , Burns Andrew S , Ryan John P , Marin III Roman , Kiene Ronald P , Zehr Jonathan P , Scholin Christopher A , Ann Moran Mary 
Published: February 2015

Abstract
The ‘bacterial switch’ is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the cleavage pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the demethylation pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.
Consequences of chirality on the dynamics of a water-soluble supramolecular polymer
Authors: Baker Matthew B. , Albertazzi Lorenzo , Voets Ilja K. , Leenders Christianus M.A. , Palmans Anja R.A. , Pavan Giovanni M. , Meijer E.W. 
Published: February 2015

AbstractThe rational design of supramolecular polymers in water is imperative for their widespread use, but the design principles for these systems are not well understood. Herein, we employ a multi-scale (spatial and temporal) approach to differentiate two analogous water-soluble supramolecular polymers: one with and one without a stereogenic methyl. Initially aiming simply to understand the molecular behaviour of these systems in water, we find that while the fibres may look identical, the introduction of homochirality imparts a higher level of internal order to the supramolecular polymer. Although this increased order does not seem to affect the basic dimensions of the supramolecular fibres, the equilibrium dynamics of the polymers differ by almost an order of magnitude. This report represents the first observation of a structure/property relationship with regard to equilibrium dynamics in water-soluble supramolecular polymers.
Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis
Authors: Srivastava Monika , Duan Guowen , Kershaw Nadia J. , Athanasopoulos Vicki , Yeo Janet H. C. , Ose Toyoyuki , Hu Desheng , Brown Simon H. J. , Jergic Slobodan , Patel Hardip R. , Pratama Alvin , Richards Sashika , Verma Anil , Jones E. Yvonne , Heissmeyer Vigo , Preiss Thomas , Dixon Nicholas E. , Chong Mark M. W. , Babon Jeffrey J. , Vinuesa Carola G. 
Published: February 2015

AbstractRoquin is an RNA-binding protein that prevents autoimmunity and inflammation via repression of bound target mRNAs such as inducible costimulator (Icos). When Roquin is absent or mutated (Roquinsan), Icos is overexpressed in T cells. Here we show that Roquin enhances Dicer-mediated processing of pre-miR-146a. Roquin also directly binds Argonaute2, a central component of the RNA-induced silencing complex, and miR-146a, a microRNA that targets Icos mRNA. In the absence of functional Roquin, miR-146a accumulates in T cells. Its accumulation is not due to increased transcription or processing, rather due to enhanced stability of mature miR-146a. This is associated with decreased 3′ end uridylation of the miRNA. Crystallographic studies reveal that Roquin contains a unique HEPN domain and identify the structural basis of the ‘san’ mutation and Roquin’s ability to bind multiple RNAs. Roquin emerges as a protein that can bind Ago2, miRNAs and target mRNAs, to control homeostasis of both RNA species.
An octave-spanning mid-infrared frequency comb generated in a silicon nanophotonic wire waveguide
Authors: Kuyken Bart , Ideguchi Takuro , Holzner Simon , Yan Ming , Hänsch Theodor W. , Van Campenhout Joris , Verheyen Peter , Coen Stéphane , Leo Francois , Baets Roel , Roelkens Gunther , Picqué Nathalie 
Published: February 2015

AbstractLaser frequency combs, sources with a spectrum consisting of hundred thousands evenly spaced narrow lines, have an exhilarating potential for new approaches to molecular spectroscopy and sensing in the mid-infrared region. The generation of such broadband coherent sources is presently under active exploration. Technical challenges have slowed down such developments. Identifying a versatile highly nonlinear medium for significantly broadening a mid-infrared comb spectrum remains challenging. Here we take a different approach to spectral broadening of mid-infrared frequency combs and investigate CMOS-compatible highly nonlinear dispersion-engineered silicon nanophotonic waveguides on a silicon-on-insulator chip. We record octave-spanning (1,500–3,300 nm) spectra with a coupled input pulse energy as low as 16 pJ. We demonstrate phase-coherent comb spectra broadened on a room-temperature-operating CMOS-compatible chip.
Phagocyte NADPH oxidase and specific immunity
Authors: Cachat Julien , Deffert Christine , Hugues Stephanie , Krause Karl-Heinz 
Published: February 2015

The phagocyte NADPH oxidase NOX2 produces reactive oxygen species (ROS) and is a well-known player in host defence. However, there is also increasing evidence for a regulatory role of NOX2 in adaptive immunity. Deficiency in phagocyte NADPH oxidase causes chronic granulomatous disease (CGD) in humans, a condition that can also be studied in CGD mice. Clinical observations in CGD patients suggest a higher susceptibility to autoimmune diseases, in particular lupus, idiopathic thrombocytopenic purpura and rheumatoid arthritis. In mice, a strong correlation exists between a polymorphism in a NOX2 subunit and the development of autoimmune arthritis. NOX2 deficiency in mice also favours lupus development. Both CGD patients and CGD mice exhibit increased levels of immunoglobulins, including autoantibodies. Despite these phenotypes suggesting a role for NOX2 in specific immunity, mechanistic explanations for the typical increase of CGD in autoimmune disease and antibody levels are still preliminary. NOX2-dependent ROS generation is well documented for dendritic cells and B-lymphocytes. It is unclear whether T-lymphocytes produce ROS themselves or whether they are exposed to ROS derived from dendritic cells during the process of antigen presentation. ROS are signalling molecules in virtually any cell type, including T- and B-lymphocytes. However, knowledge about the impact of ROS-dependent signalling on T- and B-lymphocyte phenotype and response is still limited. ROS might contribute to Th1/Th2/Th17 cell fate decisions during T-lymphocyte activation and might enhance immunoglobulin production by B-lymphocytes. In dendritic cells, NOX2-derived ROS might be important for antigen processing and cell activation.
Impact of transient hypotension on regional cerebral blood flow in humans
Authors: Lewis Nia C.S. , Smith Kurt J. , Bain Anthony R. , Wildfong Kevin W. , Numan Tianne , Ainslie Philip N. 
Published: February 2015

We examined the impact of progressive hypotension with and without hypocapnia on regional extracranial cerebral blood flow (CBF) and intracranial velocities. Participants underwent progressive lower-body negative pressure (LBNP) until pre-syncope to inflict hypotension. End-tidal carbon dioxide was clamped at baseline levels (isocapnic trial) or uncontrolled (poikilocapnic trial). Middle cerebral artery (MCA) and posterior cerebral artery (PCA) blood velocities (transcranial Doppler; TCD), heart rate, blood pressure and end-tidal carbon dioxide were obtained continuously. Measurements of internal carotid artery (ICA) and vertebral artery (VA) blood flow (ICABF and VABF respectively) were also obtained. Overall, blood pressure was reduced by ∼20% from baseline in both trials (P&lt;0.001). In the isocapnic trial, end-tidal carbon dioxide was successfully clamped at baseline with hypotension, whereas in the poikilocapnic trial it was reduced by 11.1 mmHg (P&lt;0.001) with hypotension. The decline in the ICABF with hypotension was comparable between trials (−139±82 ml; ∼30%; P&lt;0.0001); however, the decline in the VABF was −28±22 ml/min (∼21%) greater in the poikilocapnic trial compared with the isocapnic trial (P=0.002). Regardless of trial, the blood flow reductions in ICA (−26±14%) and VA (−27±14%) were greater than the decline in MCA (−21±15%) and PCA (−19±10%) velocities respectively (P≤0.01). Significant reductions in the diameter of both the ICA (∼5%) and the VA (∼7%) contributed to the decline in cerebral perfusion with systemic hypotension, independent of hypocapnia. In summary, our findings indicate that blood flow in the VA, unlike the ICA, is sensitive to changes hypotension and hypocapnia. We show for the first time that the decline in global CBF with hypotension is influenced by arterial constriction in the ICA and VA. Additionally, our findings suggest TCD measures of blood flow velocity may modestly underestimate changes in CBF during hypotension with and without hypocapnia, particularly in the posterior circulation.
Sambamba: fast processing of NGS alignment formats
Authors: Tarasov Artem , Vilella Albert J. , Cuppen Edwin , Nijman Isaac J. , Prins Pjotr 
Published: February 2015

Abstract
Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability.
Availability and implementation: Sambamba is free and open source software, available under a GPLv2 license. Sambamba can be downloaded and installed from http://www.open-bio.org/wiki/Sambamba.
Sambamba v0.5.0 was released with doi:10.5281/zenodo.13200.
Contact: j.c.p.prins@umcutrecht.nl
Extending P450 site-of-metabolism models with region-resolution data
Authors: Zaretzki Jed M. , Browning Michael R. , Hughes Tyler B. , Swamidass S. Joshua 
Published: February 2015

AbstractMotivation: Cytochrome P450s are a family of enzymes responsible for the metabolism of approximately 90% of FDA-approved drugs. Medicinal chemists often want to know which atoms of a molecule—its metabolized sites—are oxidized by Cytochrome P450s in order to modify their metabolism. Consequently, there are several methods that use literature-derived, atom-resolution data to train models that can predict a molecule’s sites of metabolism. There is, however, much more data available at a lower resolution, where the exact site of metabolism is not known, but the region of the molecule that is oxidized is known. Until now, no site-of-metabolism models made use of region-resolution data.Results: Here, we describe XenoSite-Region, the first reported method for training site-of-metabolism models with region-resolution data. Our approach uses the Expectation Maximization algorithm to train a site-of-metabolism model. Region-resolution metabolism data was simulated from a large site-of-metabolism dataset, containing 2000 molecules with 3400 metabolized and 30 000 un-metabolized sites and covering nine Cytochrome P450 isozymes. When training on the same molecules (but with only region-level information), we find that this approach yields models almost as accurate as models trained with atom-resolution data. Moreover, we find that atom-resolution trained models are more accurate when also trained with region-resolution data from additional molecules. Our approach, therefore, opens up a way to extend the applicable domain of site-of-metabolism models into larger regions of chemical space. This meets a critical need in drug development by tapping into underutilized data commonly available in most large drug companies.Availability and implementation: The algorithm, data and a web server are available at http://swami.wustl.edu/xregion.Contact: swamidass@wustl.edu
The GPMDB REST interface
Authors: Fenyö David , Beavis Ronald C. 
Published: February 2015

Abstract
Summary: The Global Proteome Machine and Database (GPMDB) representational state transfer (REST) service was designed to provide simplified access to the proteomics information in GPMDB using a stable set of methods and parameters. Version 1 of this interface gives access to 25 methods for retrieving experimental information about protein post-translational modifications, amino acid variants, alternate splicing variants and protein cleavage patterns.
Availability and implementation: GPMDB data and database tables are freely available for commercial and non-commercial use. All software is also freely available, under the Artistic License. http://rest.thegpm.org/1 (GPMDB REST Service), http://wiki.thegpm.org/wiki/GPMDB_REST (Service description and help), and http://www.thegpm.org (GPM main project description and documentation). The code for the interface and an example REST client is available at ftp://ftp.thegpm.org/repos/gpmdb_rest
Contact: rbeavis@thegpm.org or david@fenyolab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Acoustic biomass estimation of mesopelagic fish: backscattering from individuals, populations, and communities
Authors: Davison Peter C. , Koslow J. Anthony , Kloser Rudy J. 
Published: February 2015

Abstract
Acoustic survey methods are useful to estimate the distribution, abundance, and biomass of mesopelagic fish, a key component of open ocean ecosystems. However, mesopelagic fish pose several challenges for acoustic biomass estimation based on their small size, wide depth range, mixed aggregations, and length-dependent acoustic reflectance, which differentiate them from the larger epipelagic and neritic fish for which these methods were developed. Foremost, there is a strong effect of depth on swimbladder resonance, so acoustic surveys of mesopelagic fish must incorporate depth-stratification. Additionally, the 1–3 cm juveniles of many species are not only more abundant, but can also be stronger acoustic backscatterers than the larger adults that comprise most of the biomass. The dominant species in terms of biomass may thus be weak acoustic backscatters. Failure to properly incorporate depth, the full size distribution, and certain less-abundant species into mesopelagic acoustic analyses could lead to errors in estimated biomass of up to three orders of magnitude. Thus, thorough validation, or “ground-truthing ”, of the species composition, depth structure, population size distribution, capture efficiency of the sampling device, and acoustic properties of the fish present is critical for credible acoustic estimates of mesopelagic fish biomass. This is not insurmountable, but requires more ancillary data than is usually collected.