bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viterbi training in PRISM
Authors: SATO TAISUKE , KUBOTA KEIICHI 
Published: January 2014

AbstractVT (Viterbi training), or hard expectation maximization (EM), is an efficient way of parameter learning for probabilistic models with hidden variables. Given an observation y, it searches for a state of hidden variables x that maximizes p(x,y | θ) by coordinate ascent on parameters θ and x. In this paper we introduce VT to PRogramming In Statistical Modeling (PRISM), a logic-based probabilistic modeling system for generative models. VT improves PRISM in three ways. First, VT in PRISM converges faster than EM in PRISM due to VT's termination condition. Second, parameters learned by VT often show good prediction performance compared with those learned by EM. We conducted two parsing experiments with probabilistic grammars while learning parameters by a variety of inference methods, i.e. VT, EM, MAP and VB. The result is that VT achieved the best parsing accuracy among them in both experiments. Also, we conducted a similar experiment for classification tasks where a hidden variable is not a prediction target unlike probabilistic grammars. We found that in such a case VT does not necessarily yield superior performance. Third, since VT always deals with a single probability of a single explanation, Viterbi explanation, the exclusiveness condition imposed on PRISM programs is no more required if we learn parameters by VT. Last but not least, we can say that as VT in PRISM is general and applicable to any PRISM program, it largely reduces the need for the user to develop a specific VT algorithm for a specific model. Furthermore, since VT in PRISM can be used just by setting a PRISM flag appropriately, it makes VT easily accessible to (probabilistic) logic programmers.
Maternal tract factors contribute to paternal seminal fluid impact on metabolic phenotype in offspring
Authors: Bromfield John J. , Schjenken John E. , Chin Peck Y. , Care Alison S. , Jasper Melinda J. , Robertson Sarah A. 
Published: January 2014

Significance
Events at conception shape the future growth and health of offspring, to impact life course potential and disease susceptibility. The environment and experiences of both parents contribute to programming offspring phenotype through epigenetic modifications imparted before embryo implantation. How the father transmits this information remains elusive. Possible pathways include the sperm genome and epigenome, postejaculatory effects of seminal fluid on sperm, and indirect actions of seminal fluid on various female factors regulating embryo development. In this study, we provide evidence that seminal fluid acts to influence both sperm integrity and the balance of embryotrophic and embryotoxic signals in the female reproductive tract, in turn affecting embryo development and programming of future adiposity and metabolic phenotype in male offspring.
The Fanconi anemia pathway has a dual function in Dickkopf-1 transcriptional repression
Authors: Huard Caroline C. , Tremblay Cédric S. , Magron Audrey , Lévesque Georges , Carreau Madeleine 
Published: January 2014

Significance
Fanconi anemia (FA) is a devastating disease associated with a progressive bone marrow failure (BMF) and clonal proliferation of primitive hematopoietic cells that leads to leukemia. In an effort to understand the molecular basis of BMF and leukemogenesis in FA, we recently uncovered a unique function of proteins associated with FA in transcriptional regulation that translates into elevated levels of the signaling molecule Dickkopf-1 (DKK1). Overproduction of DKK1 has been shown to alter functions in hematopoiesis and to promote hematologic malignancies. Thus, our findings represent a crucial step in the development of strategies aimed at preventing BMF and/or clonal hematopoiesis in patients with FA.
JAK/STAT1 signaling promotes HMGB1 hyperacetylation and nuclear translocation
Authors: Lu Ben , Antoine Daniel J. , Kwan Kevin , Lundbäck Peter , Wähämaa Heidi , Schierbeck Hanna , Robinson Melissa , Van Zoelen Marieke A. D. , Yang Huan , Li Jianhua , Erlandsson-Harris Helena , Chavan Sangeeta S. , Wang Haichao , Andersson Ulf , Tracey Kevin J. 
Published: January 2014

SignificanceHigh-mobility group box (HMGB)1 is a nuclear protein that we have identified as a proinflammatory mediator during infection or sterile tissue injury, which importantly orchestrates the innate immune responses. The mechanisms of HMGB1 release require translocation of HMGB1 from nucleus to cytoplasm and release into the extracellular space. We recently reported that the inflammasome and PKR mediates HMGB1 release from the cytoplasm, but the mechanism of HMGB1 translocation from nucleus to cytoplasm was previously unknown. Here, we describe our discovery that JAK/STAT1 is required for LPS- or interferon-induced HMGB1 nuclear translocation. These findings have significant implications for the field, and for designing therapeutics for potential use in inflammatory diseases.
Accounting for inhomogeneous broadening in nano-optics by electromagnetic modeling based on Monte Carlo methods
Authors: Gudjonson Herman , Kats Mikhail A. , Liu Kun , Nie Zhihong , Kumacheva Eugenia , Capasso Federico 
Published: January 2014

SignificanceThe advent of nanotechnology has enabled the study of physical phenomena in structures with nanoscale dimensions. Pushing the limits of fabrication techniques inevitably leads to uncertainties—for example, an array of nanoscale resonators may be designed to be identical, but in fact has a distribution of sizes due to fabrication imperfections, leading to a distribution of responses. In optical experiments involving collections of nanostructures these effects are often acknowledged but rarely quantified. We demonstrate a technique that combines electromagnetic simulations with a Monte Carlo sampling technique to rigorously account for “inhomogeneous broadening” of optical resonances as a result of fabrication or synthesis imperfections. This approach has wide applicability to any experiments involving collections of structures designed to be identical.
A Basis for Scientific and Engineering Translation
Authors: Hann Michael 
Published: January 2014

This CD-rom and the accompanying handbook attack many of the most crucial difficulties encountered by both native and non-native English speakers when translating scientific and engineering material from German.
The CD-rom is like a miniature encyclopaedia dealing with the fundamental conceptual basis of science, engineering and mathematics, with particular regard to terminology. It provides didactically organised dictionaries, thesauri and a wide range of microglossaries highlighting polysemy, homonymy, hyponymy, context, collocation, usage as well as grammatical, lexical and semantic considerations essential to accurate translation. It also supplies a wide variety of reference material and illustrations useful to self-taught professional technical translators, translator trainers at universities, and especially to student translators.
All the main branches of industrial technology are examined, such as mechanical, electrical, electronic, chemical, nuclear engineering, and fundamental terminologies are provided for a broad range of important subfields: automotive engineering, plastics, computer systems, construction technology, aircraft, machine tools.
The handbook provides a useful introduction to the CD-Rom, enabling readers proficient in two languages to acquire the basic skills necessary for technical translation by familiarity with fundamental engineering conceptions themselves.
The Linguistic Structure of Modern English
Authors: Brinton Laurel J. , Brinton Donna M. 
Published: January 2014

This text is for advanced undergraduate and graduate students interested in contemporary English, especially those whose primary area of interest is English as a second language, primary or secondary-school education, English stylistics, theoretical and applied linguistics, or speech pathology. The emphasis is on empirical facts of English rather than any particular theory of linguistics; the text does not assume any background in language or linguistics. In this newly revised edition numerous example sentences are taken from the Corpus of Contemporary American English. A full glossary of key terms, an additional chapter on pedagogy and new sections on cognitive semantics and politeness have been added. Other changes include: completely updated print references; web links to sites of special interest and relevance; and a revised, reader-friendly layout. A companion website that includes a complete workbook with self-testing exercises and a comprehensive list of web links accompanies the book. The website can be found at the following address: https://doi.org/10.1075/z.156.workbook.

Students completing the text and workbook will acquire: a knowledge of the sound system of contemporary English; an understanding of the formation of English words; a comprehension of the structure of both simple and complex sentence in English; a recognition of complexities in the expression of meaning; an understanding of the context and function of use upon the structure of the language; and an appreciation of the importance of linguistic knowledge to the teaching of English to first and second-language learners.
Laurel J. Brinton is Professor of English Language at the University of British Columbia.
Donna M. Brinton is Senior Lecturer in TESOL at the University of Southern California's Rossier School of Education.

The Linguistic Structure of Modern English is a revised edition of The Structure of Modern English by Laurel J. Brinton (2000).
Nonverbal Communication across Disciplines
Authors: Poyatos Fernando 
Published: January 2014

In a progressive and systematic approach to communication, and always through an interdisciplinary and cross-cultural perspective, this first volume presents culture as an intricate grid of sensible and intelligible sign systems in space and time, identifying the semiotic and interactive problems inherent in intercultural and subcultural communication according to verbal-nonverbal cultural fluency. The author lays out fascinating complexity of our direct and synesthesial sensory perception of people and artifactual and environmental elements; and its audible and visual manifestations through our ‘speaking face’, to then acknowledge the triple reality of discourse as ‘verbal language-paralanguage-kinesics’, which is applied through two realistic models: (a)for a verbal-nonverbal comprehensive transcription of interactive speech, and (b)for the implementation of nonverbal communication in foreign-language teaching. The author presents his exhaustive model of ‘nonverbal categories’ for a detailed analysis of normal or pathological behaviors in any interactive or noninteractive manifestation; and, based on all the previous material, his equally exhaustive structural model for the study of conversational encounters, which suggests many applications in different fields, such as the intercultural and multisystem communication situation developed in simultaneous or consecutive interpretating.
956 literary quotations from 103 authors and 194 works illustrate all the points discussed.
The Economics of Information, Deep Capture, and the Obesity Debate
Authors: Smith Trenton G. , Tasnádi Attila 
Published: January 2014

AbstractThe economic theory of regulatory capture predicts that industry groups will attempt to influence their regulators (for example, by lobbying for rules that exclude competition). It has been suggested that the same logic applies to any powerful institution with the ability to affect industry profits. When the aim of industry is to alter the public's perception of its product (for example, by disseminating favorable messages to the news media or via an advertising campaign, or by funding industry‐friendly scientific research), the end result has been dubbed deep capture. We develop a formal model of deep capture, in which consumers have imperfect information about product quality, and a dominant producer is able to increase his profits by altering the parameters of the consumer's search problem. We demonstrate the empirical relevance of the phenomenon with a discussion of the food industry response to the obesity epidemic.
Bio Simulators: a web UI for biological simulation
Authors: Pedersen Michael , Oury Nicolas , Gravill Colin , Phillips Andrew 
Published: January 2014

AbstractSummary: A host of formal, textual languages for modeling cellular processes have recently emerged, but their simulation tools often require an installation process which can pose a barrier for use. Bio Simulators is a framework for easy online deployment of simulators, providing a uniform web-based user interface to a diverse pool of tools. The framework is demonstrated through two plugins based on the KaSim Kappa simulator, one running directly in the browser and another running in the cloud.Availability: Web tool: bsims.azurewebsites.net. KaSim client side simulator: github.com/NicolasOury/KaSimJS. KaSim cloud simulator: github.com/mdpedersen/KaSimCloud.Contact: michael.d.pedersen@gmail.com or Andrew.Phillips@microsoft.comSupplementary information: Supplementary data are available at Bioinformatics online.
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains
Authors: Meslamani Jamel , Smith Steven G. , Sanchez Roberto , Zhou Ming-Ming 
Published: January 2014

AbstractContext: Epigenome reader domains are rapidly emerging as a new class of drug targets for a wide array of human diseases. To facilitate study of structure–activity relationship and small-molecule ligand design for these domains, we have created ChEpiMod. ChEpiMod is a free knowledgebase of chemical modulators with documented modulatory activity for epigenome reader domains.Methods: ChEpiMod organizes information about chemical modulators and their associated binding-affinity data, as well as available structures of epigenome readers from the Protein Data Bank. The data are gathered from the literature and patents. Entries are supplemented by annotation. The current version of ChEpiMod covers six epigenome reader domain families (Bromodomain, PHD finger, Chromodomain, MBT, PWWP and Tudor). The database can be used to browse existing chemical modulators and bioactivity data, as well as, all available structures of readers and their molecular interactions. The database is updated weekly.Availability: ChEpiMod is freely available at http://chepimod.orgContact: ming-ming.zhou@mssm.eduSupplementary information: Supplementary data is available at Bioinformatics online.
Effects of acute and long‐term typical or atypical neuroleptics on morphine‐induced behavioural effects in mice
Authors: Hollais André W , Patti Camilla L , Zanin Karina A , Fukushiro Daniela F , Berro Laís F , Carvalho Rita C , Kameda Sonia R , Frussa‐Filho Roberto 
Published: January 2014

Summary

It has been suggested that the high prevalence of drug abuse in schizophrenics is related to chronic treatment with typical neuroleptics and dopaminergic supersensitivity that develops as a consequence. Within this context, atypical neuroleptics do not seem to induce this phenomenon. In the present study, we investigated the effects of acute administration or withdrawal from long‐term administration of haloperidol and/or ziprasidone on morphine‐induced open‐field behaviour in mice.

In the first experiment, mice were given a single injection of haloperidol (1 mg/kg, i.p.) or several doses of ziprasidone (2, 4 or 6 mg/kg, i.p.) and motor activity was quantified by the open‐field test. The aim of the second experiment was to verify the effects of an acute injection of haloperidol (1 mg/kg) or ziprasidone (6 mg/kg) on 20 mg/kg morphine‐induced behaviours in the open‐field test. In the third experiment, mice were treated with 1 mg/kg haloperidol and/or 2, 4 or 6 mg/kg ziprasidone for 20 days. Seventy‐two hours after the last injection, mice were injected with 20 mg/kg, i.p., morphine and then subjected to the open‐field test. Acute haloperidol or ziprasidone decreased spontaneous general activity and abolished morphine‐induced locomotor stimulation.

Withdrawal from haloperidol or ziprasidone did not modify morphine‐elicited behaviours in the open‐field test. The results suggest that withdrawal from neuroleptic treatments does not contribute to the acute effect of morphine in schizophrenic patients.
Microbial ecology of arsenic‐mobilizing Cambodian sediments: lithological controls uncovered by stable‐isotope probing
Authors: Héry Marina , Rizoulis Athanasios , Sanguin Hervé , Cooke David A. , Pancost Richard D. , Polya David A. , Lloyd Jonathan R. 
Published: January 2014

SummaryMicrobially mediated arsenic release from Holocene and Pleistocene Cambodian aquifer sediments was investigated using microcosm experiments and substrate amendments. In the Holocene sediment, the metabolically active bacteria, including arsenate‐respiring bacteria, were determined by DNA stable‐isotope probing. After incubation with 13C‐acetate and 13C‐lactate, active bacterial community in the Holocene sediment was dominated by different Geobacter spp.‐related 16S rRNA sequences. Substrate addition also resulted in the enrichment of sequences related to the arsenate‐respiring Sulfurospirillum spp. 13C‐acetate selected for ArrA related to Geobacter spp. whereas 13C‐lactate selected for ArrA which were not closely related to any cultivated organism. Incubation of the Pleistocene sediment with lactate favoured a 16S rRNA‐phylotype related to the sulphate‐reducing Desulfovibrio oxamicus DSM1925, whereas the ArrA sequences clustered with environmental sequences distinct from those identified in the Holocene sediment. Whereas limited As(III) release was observed in Pleistocene sediment after lactate addition, no arsenic mobilization occurred from Holocene sediments, probably because of the initial reduced state of As, as determined by X‐ray Absorption Near Edge Structure. Our findings demonstrate that in the presence of reactive organic carbon, As(III) mobilization can occur in Pleistocene sediments, having implications for future strategies that aim to reduce arsenic contamination in drinking waters by using aquifers containing Pleistocene sediments.
Interleukin‐17 and interleukin‐23: importance in the pathogenesis of lung impairment in patients with systemic sclerosis
Authors: Olewicz‐Gawlik Anna , Danczak‐Pazdrowska Aleksandra , Kuznar‐Kaminska Barbara , Gornowicz‐Porowska Justyna , Katulska Katarzyna , Trzybulska Dorota , Batura‐Gabryel Halina , Silny Wojciech , Poplawski Dariusz , Hrycaj Pawel 
Published: January 2014

AbstractAimT cell abnormalities with a focus on Th17 cells have been associated with the pathogenesis of systemic sclerosis (SSc) and interstitial lung disease (ILD). The aim of this study was to evaluate serum levels of interleukin (IL)‐17, IL‐21 and IL‐23 in SSc patients and to assess their relationship with ILD‐SSc.MethodsThirty‐eight patients with SSc and 39 healthy controls were recruited. Serum IL‐17, IL‐21 and IL‐23 levels were examined using enzyme‐linked immunosorbent assay (ELISA). Lung involvement of SSc patients was assessed functionally (diffusing capacity of the lung for carbon monoxide [DLCO], body plethysmography) and radiologically (using average disease extent on high resolution computed tomography [HRCT] of the lungs according to the percentage of interstitial changes and quantified with a 30‐point Warrick score) in 29 SSc patients.ResultsSerum IL‐17 and IL‐23 levels were significantly decreased and IL‐21 levels were elevated in SSc patients when compared with controls (P < 0.001, P < 0.001, P < 0.01, respectively). The level of IL‐17 was negatively associated with disease duration (P = 0.01) and positively with HRCT Warrick score (P = 0.03). IL‐23 concentration negatively correlated with DLCO (P = 0.04), total lung capacity (TLC) (P = 0.01) and the 6‐min walk test distance (P = 0.03). No associations were found between the cytokine levels and the average extent of the disease on HRCT.ConclusionWhile the relationship between Th17‐associated cytokines and ILD‐SSc needs to be verified in a larger cohort of patients, the changes in concentrations of IL‐17, IL‐21 and IL‐23 support the hypothesis that these cytokines may play a role in the pathogenesis of SSc.
Extinction is the Dream of Modern Powers: Bearing Witness to the Return to Life of the Sinixt Peoples?
Authors: Robertson Sean 
Published: January 2014

AbstractThe Arrow Lakes Band was the only form of legal recognition ever made available to the Sinixt nation by Canada before they were declared extinct. The Oatscott reserve and the state were cartographies that both summoned and willed away the Sinixt. I attempt a “politics of witnessing” of recent Sinixt activities as they push back against these colonial enframings and displacements. I then contextualize biopower within settler society to chart the production of the state through a cultural economy of racialization and erasure, and through a clearing of the land based on more explicit imaginative geographies. The declaration of the extinction of the Sinixt illustrates Indian reserves less as a disciplinary and more a sovereign technology. And yet it is quintessentially modern owing to the absence of instrumental violence. Finally, the limitations of witnessing and the space Indigenous peoples make for alliances are examined.
Tenofovir is superior to entecavir for achieving complete viral suppression in HBeAg‐positive chronic hepatitis B patients with high HBV DNA
Authors: Gao L. , Trinh H. N. , Li J. , Nguyen M. H. 
Published: January 2014

SummaryBackgroundEntecavir (ETV) and tenofovir disoproxil fumarate (TDF) are the two first‐line anti‐viral therapies for chronic hepatitis B (CHB); however, there are limited studies directly comparing their effectiveness.AimTo compare the effectiveness of ETV and TDF in nucleos(t)ide‐naïve CHB patients with high hepatitis B virus (HBV) DNA levels, defined as serum HBV DNA greater than 6 log10 IU/mL.MethodsWe performed a retrospective multicentre cohort study of adult CHB patients who were seen between 2009 and 2012 at four Northern California community gastroenterology and hepatology clinics.ResultsWe identified 59 consecutive patients treated with TDF and 216 patients treated with ETV. Pre‐treatment characteristics were similar between the two groups. Among HBeAg‐negative patients, there was no significant difference in viral suppression rates between ETV and TDF (P = 0.72). In contrast, among HBeAg‐positive patients, those treated with TDF achieved viral suppression significantly more rapidly than those treated with ETV (P < 0.0001); the Kaplan–Meier estimated probability of complete suppression was 18% vs. 11% at 6 months, 51% vs. 28% at 12 months and 72% vs. 39% at 18 months respectively. Multivariate Cox proportional hazards analysis indicated that treatment with TDF compared to ETV was a significant predictor of viral suppression, but only for HBeAg‐positive patients (HR = 2.59; 95% CI 1.58–4.22; P < 0.001).ConclusionTenofovir is significantly more effective than entecavir for achieving complete viral suppression in HBeAg‐positive, nucleos(t)ide‐naïve chronic hepatitis B patients with HBV DNA greater than 6 log10 IU/mL.