bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structure and biochemical properties of putrescine carbamoyltransferase from Enterococcus faecalis: Assembly, active site, and allosteric regulation
Authors: Shi Dashuang , Yu Xiaolin , Zhao Gengxiang , Ho Jeremy , Lu Shennon , Allewell Norma M. , Tuchman Mendel 
Published: January 2012

AbstractPutrescine carbamoyltransferase (PTCase) catalyzes the conversion of carbamoylputrescine to putrescine and carbamoyl phosphate (CP), a substrate of carbamate kinase (CK). The crystal structure of PTCase has been determined and refined at 3.2 Å resolution. The trimeric molecular structure of PTCase is similar to other carbamoyltransferases, including the catalytic subunit of aspartate carbamoyltransferase (ATCase) and ornithine carbamoyltransferase (OTCase). However, in contrast to other trimeric carbamoyltransferases, PTCase binds both CP and putrescine with Hill coefficients at saturating concentrations of the other substrate of 1.53 ± 0.03 and 1.80 ± 0.06, respectively. PTCase also has a unique structural feature: a long C‐terminal helix that interacts with the adjacent subunit to enhance intersubunit interactions in the molecular trimer. The C‐terminal helix appears to be essential for both formation of the functional trimer and catalytic activity, since truncated PTCase without the C‐terminal helix aggregates and has only 3% of native catalytic activity. The active sites of PTCase and OTCase are similar, with the exception of the 240′s loop. PTCase lacks the proline‐rich sequence found in knotted carbamoyltransferases and is unknotted. A Blast search of all available genomes indicates that 35 bacteria, most of which are Gram‐positive, have an agcB gene encoding PTCase located near the genes that encode agmatine deiminase and CK, consistent with the catabolic role of PTCase in the agmatine degradation pathway. Sequence comparisons indicate that the C‐terminal helix identified in this PTCase structure will be found in all other PTCases identified, suggesting that it is the signature feature of the PTCase family of enzymes Proteins 2012; © 2012 Wiley Periodicals, Inc.
Recognition between a short unstructured peptide and a partially folded fragment leads to the thioredoxin fold sharing native‐like dynamics
Authors: Binolfi Andrés , Fernández Claudio O. , Sica Mauricio P. , Delfino José M. , Santos Javier 
Published: January 2012

AbstractThioredoxins (TRXs) constitute attractive α/β scaffolds for investigating molecular recognition. The interaction between the recombinant fragment spanning the sequence 1–93 of full‐length TRX (TRX1‐93) and the synthetic peptide comprising residues 94–108 (TRX94‐108), plus a C‐terminal tyrosine tag (the numbering scheme used in entry pdb 2TRX is used throughout the article, two complementary moieties of E. coli TRX, brings about the consolidation of a native‐like complex. Despite its reduced thermodynamic stability, this complex is able to acquire fine structural features remarkably similar to those characteristic of full‐length TRX, namely, hydrodynamic behavior, assessed by diffusion‐ordered spectroscopy (DOSY)‐NMR; the pattern of secondary structure, as revealed by three‐bond HNHα coupling constants and secondary shifts for Hα/CO/Cα/Cβ; native‐like tertiary structural signatures revealed by near‐UV circular dichroism (CD) spectroscopy. The complex exhibits a relaxation behavior compatible with that expected for a native‐like structure. However, heteronuclear nuclear Overhauser effect (NOE)s reveal an enhanced dynamics for the complex by comparison with full‐length TRX. Furthermore, higher R2 values for residues 43–50 and 74–89 would likely result from an exchange process modulated by the peptide at the interface region. The slow kinetics of the consolidation reaction was followed by CD and real‐time NMR. Equilibrium titration experiments by NMR yield a KD value of 1.4 ± 1.0 μM and a second low‐affinity (>150 μM) binding event in the vicinity of the active site. Molecular dynamics simulations of both the isolated fragment TRX1‐93 and the complex suggest the destabilization of α2 and α3 helical elements and the persistence of β‐structure in the absence of TRX94‐108. Altogether, structural and dynamic evidence presented herein points to the key role played by the C‐terminal helix in establishing the overall fold. This critical switch module endows reduced TRX with the ability to act as a cooperative folding unit. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
The Graphical Analysis for Maintenance Management Method: A Quantitative Graphical Analysis to Support Maintenance Management Decision Making
Authors: Martínez Luis Barberá , Márquez Adolfo Crespo , Gunckel Pablo Viveros , Andreani Adolfo Arata 
Published: January 2012

This article proposes a logical support tool for maintenance management decision making. This tool is called the Graphical Analysis for Maintenance Management (GAMM), a method to visualize and analyze equipment dependability data in a graphical form. The method helps for a quick and clear analysis and interpretation of equipment maintenance (corrective and preventive) and operational stoppages. Then, opportunities can be identified to improve both operations and maintenance management (short–medium term) and potential investments (medium–long term). The method allows an easy visualization of parameters, such as the number of corrective actions between preventive maintenance, the accumulation of failures in short periods of time, and the duration of maintenance activities and sequence of stops of short duration. In addition, this tool allows identifying, a priori, anomalous behavior of equipment, whether derived from its own function, maintenance activities, misuse, or even equipment designs errors.In this method, we used a nonparametric estimator of the reliability function as a basis for the analysis. This estimator takes into account equipment historical data (total or partial) and can provide valuable insights to the analyst even with few available data. Copyright © 2012 John Wiley & Sons, Ltd.
Making skeletal muscle from progenitor and stem cells: development versus regeneration
Authors: Fan Chen‐Ming , Li Lydia , Rozo Michelle E. , Lepper Christoph 
Published: January 2012

AbstractFor locomotion, vertebrate animals use the force generated by contractile skeletal muscles. These muscles form an actin/myosin‐based biomachinery that is attached to skeletal elements to affect body movement and maintain posture. The mechanics, physiology, and homeostasis of skeletal muscles in normal and disease states are of significant clinical interest. How muscles originate from progenitors during embryogenesis has attracted considerable attention from developmental biologists. How skeletal muscles regenerate and repair themselves after injury by the use of stem cells is an important process to maintain muscle homeostasis throughout lifetime. In recent years, much progress has been made toward uncovering the origins of myogenic progenitors and stem cells as well as the regulation of these cells during development and regeneration. WIREs Dev Biol 2012, 1:315–327. doi: 10.1002/wdev.30This article is categorized under:

Signaling Pathways > Cell Fate Signaling
Vertebrate Organogenesis > Musculoskeletal and Vascular
Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches
Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration
An approach to enrich users’ personomy using the recommendation of semantic tags
Authors: da Silva Sérgio R. P. , Borth Marcelo R. , Ferreira Josiane M. P. , Feltrim Valéria D. 
Published: January 2012

Abstract
Tagging-based systems are a popular and convenient way to organize information on the Web. Despite the alleged advantage of the free choice of words used to categorize Web resources in this kind of systems, it also brings some disadvantages due to the difficulty to remember freely chosen tags when users need to retrieve tagged resources. This paper presents a new approach to improve the quality of the categorizations performed by users in tagging-based systems by means of the recommendation of semantic tags. Our approach combines three sources of information for selecting the recommended tags: the Web resource been categorized, the tagging-based system folksonomy and the user personomy. By using these sources, we combine some features of the context of the categorization, the social opinion about the resource been categorized and the users’ vocabulary preferences. The use of the Web resource helps to solve the cold start problem, and the recommendation of more contextualized and personalized tags helps to develop a better personomy for the user, which could relieve the users’ cognitive effort when retrieving tagged resources.
Self‐Reported Issues With Driving in Patients With Chronic Pain
Authors: Fan Anita , Wilson Keith G. , Acharya Meena , Cranney Anne , Buenger Usha , Marshall Shawn 
Published: January 2012

ObjectiveTo assess the driving habits, driving patterns, and barriers to driving reported by patients with chronic pain.DesignCross‐sectional mail survey with self‐administered questionnaires.SettingUniversity‐affiliated hospital.ParticipantsA sample of 223 patients seen in consultation by a physiatrist through the Chronic Pain Rehabilitation Service.InterventionsNot applicable.Main Outcome MeasurementsPercentage of subjects who were current drivers, percentage of subjects experiencing difficulty with driving, and driving characteristics.ResultsResponse rate was 48.9%. Of the subjects, 79% were current drivers; of the nondrivers, 56% reported stopping driving because of chronic pain. A significantly greater percentage of nondrivers (80%) than drivers (62.9%) were women (P = .039). Nondrivers reported greater levels of pain than drivers (P = .027). The mean Pain Disability Index total score was significantly lower for drivers (42.3) than for nondrivers (48.7; P = .006). Of all subjects, 70% indicated that pain limited their driving in some manner; 41% of this group indicated that they experienced quite a bit or a great deal of difficulty driving. Factors that limited driving included pain (88.9%), fatigue (50.6%), limited joint mobility/stiffness (48.3%), and weakness (19.4%). The most frequently reported difficulties related to driving were sitting for any length of time (79.6%) and getting into the driver's seat (66.5%). Only 2.4% of current drivers had been referred for a driving assessment.ConclusionsMost people with chronic pain continue to drive and overall appear to have better functioning than those who cannot continue driving because of chronic pain. Despite being able to drive, a significant proportion of drivers with chronic pain are facing challenges not only with driving the vehicle but also with entering and positioning themselves within the vehicle. Our results suggest that chronic pain does have an impact on driving. However, it appears to be generally unrecognized as a factor for driving other than when the implications of opioid use are considered.
SALAFI TRANSFORMATIONS: ADEN AND THE CHANGING VOICES OF RELIGIOUS REFORM IN THE INTERWAR INDIAN OCEAN
Authors: Reese Scott S. 
Published: January 2012

AbstractThe Islamic reformist movement known as Salafism is generally portrayed as a relentlessly literalist and rigid school of religious thought. This article pursues a more nuanced picture of a historical Salafism that is less a movement with a single, linear origin than a dynamic intellectual milieu continually shaped by local contexts. Using 1930s Aden as a case study, the article examines how a transregional reformist discourse could be vulnerable to local interpretation and begins to unpack the transformation of Salafi activism from a broad, doctrinaire, and, above all, foreign ideology to an integral part of local religious discourse. It situates reform within an evolving Islamic discursive tradition that in part developed as a result of its own theological logic but was equally shaped by local and historically contingent institutions, social practices, and power structures. It thus explores Salafism as a dynamic tradition that could be adapted by local intellectuals to engage the problems facing their own communities.
Darwin, Concepción, and the Geological Sublime
Authors: White Paul 
Published: January 2012

ArgumentDarwin's narrative of the earthquake at Concepción, set within the frameworks of Lyellian uniformitarianism, romantic aesthetics, and the emergence of geology as a popular science, is suggestive of the role of the sublime in geological enquiry and theory in the early nineteenth century. Darwin'sBeaglediary and later notebooks and publications show that the aesthetic of the sublime was both a form of representing geology to a popular audience, and a crucial structure for the observation and recording of the event from the beginning. The awesome spectacle of the earthquake proved in turn the magnitude of the forces at stake in earth history, and helped to make geology an epic conjoining the history of civilization with the history of the earth.
The Nature of Emergency: The Great Kanto Earthquake and the Crisis of Reason in Late Imperial Japan
Authors: Orihara Minami , Clancey Gregory 
Published: January 2012

ArgumentHijōji(emergency) was an important keyword in the militarist Japan of the 1930s. Previous scholarship has assumed that such language sprung from the global financial crisis of 1929, and subsequent diplomatic events. Our article demonstrates, however, that a full-bodied language of emergency was crafted well before the collapse of the global economy, and against the backdrop of the Great Kanto Earthquake of 1923, which destroyed the Japanese capital. While previous “great earthquakes” had been opportunities to strengthen Japanese participation in the global project of science, this one led more dramatically to a crisis of reason, and indirectly contributed to the spiritual, anti-western, and anti-rational rhetoric of what became the “Showa Restoration.” This and other post-disaster landscapes, we argue, should be examined as compelling sites for the crafting of political language – sites of opportunity and meaning as well as trial. While the phrase “state of emergency” was coined under very different circumstances in post-war Britain, it gained power and charisma in Japan, and likely other places around the world, by its association with natural catastrophe. Thus did modern politics establish a new connection with the traditional realm of the sublime, and in the case of Japan, the supernatural. Emergency's ability to associate politics with nature would never disappear, and has perhaps even strengthened in the early twenty-first century.
“Collective Monitoring, Collective Defense”: Science, Earthquakes, and Politics in Communist China
Authors: Fan Fa-ti 
Published: January 2012

ArgumentThis paper examines the earthquake monitoring and prediction program, called “collective monitoring, collective defense,” in communist China during the Cultural Revolution, a period of political upheavals and natural disasters. Guided by their scientific and political ideas, the Chinese developed approaches to earthquake monitoring and prediction that emphasized mass participation, everyday knowledge, and observations of macro-seismic phenomena. The paper explains the ideas, practices, and epistemology of the program within the political context of the Cultural Revolution. It also suggests possibilities for comparative analysis of science, state, and natural disasters. The paper redefines the concept of “citizen science” and argues that the concept provides a useful comparative perspective on the intimate relationship between science and the macropolitics of modern state and society.
Prevalence and antimicrobial susceptibility of Salmonella in Japanese broiler flocks
Authors: SASAKI Y. , IKEDA A. , ISHIKAWA K. , MURAKAMI M. , KUSUKAWA M. , ASAI T. , YAMADA Y. 
Published: January 2012

SUMMARYThis study determined the prevalence and antimicrobial susceptibility of Salmonella isolated from broiler flocks in Japan. Caecal dropping samples were collected from 288 broiler flocks between November 2007 and February 2010. Salmonella was prevalent in 248 (86·1%) broiler flocks. The top three serovars were S. Infantis, S. Manhattan and S. Schwarzengrund. S. Infantis was found in all regions tested in this study. However, S. Manhattan and S. Schwarzengrund were frequently found only in the western part of Japan. High antimicrobial resistance rates were observed against oxytetracycline (90·2%), dihydrostreptomycin (86·7%) and ampicillin (36·5%), and 258 (90·5%) of 285 isolates were resistant to two or more antimicrobial agents. Interestingly, 26·3% of isolates were resistant to ceftiofur, especially 38·1% of S. Infantis isolates, although its use in broilers has not been approved in Japan. This study showed that Salmonella is highly prevalent (86·1%) in Japanese broiler flocks, that 90·5% of Salmonella isolates were multidrug-resistant, and that S. Infantis frequently exhibited resistance to cephalosporin antimicrobial agents.
Triage in Mass-Casualty Events: The Haitian Experience
Authors: Merin Ofer , Miskin Ian N. , Lin Guy , Wiser Itay , Kreiss Yitshak 
Published: January 2012

AbstractIntroduction: Mass-casualty triage is implemented when available resources are insufficient to meet the needs of all patients in a disaster situation. The basic principle is to do the maximum good for the most casualties with the least amount of resources. There are limited data to support the applicability of this principle in massive disasters such as the January 2010 earthquake in Haiti, in which the number of patients seeking medical attention overwhelmed the local resources.Objective: To analyze the application of a triage system developed for use in a mass-casualty setting with limited resources. The system was designed to admit only those patients who had medical conditions requiring urgent treatment that were within the capabilities of the hospital and had a good chance of survival after discharge. Priority was given to those whose treatment could be administered within a short hospital stay.Method: A retrospective, observational review of computerized registration forms of Haitian earthquake victims who sought medical care at a 72-bed field hospital within four to 14 days after the event. An analysis of the efficacy of the triage protocol that was used followed, using length of hospital stay to measure consumption of resources.Results: A total of 1,111 patients were triaged for treatment in the field hospital within 14 days of the earthquake. The median length of stay for all patients for whom data was available was 16 hours (mean = 29.7 hours). The majority of patients (n = 620, 65%) were discharged within 24 hours. Two hundred five patients underwent surgery and were discharged within a median of 39 hours (mean = 52.6 hours); of these, 124 (62%) were discharged within 48 hours. The total mortality of the treated patients was 1.5% (n = 17).Conclusions: Currently accepted triage principles for the most part are appropriate for efficiently providing medical care in a disaster area with extremely limited resources, but require extensive adaptation to local conditions.
Effects of alternative label formats on choice of high- and low-sodium products in a New Zealand population sample
Authors: McLean Rachael , Hoek Janet , Hedderley Duncan 
Published: January 2012

AbstractObjectiveDietary sodium reduction is a cost-effective public health intervention to reduce chronic disease. In response to calls for further research into front-of-pack labelling systems, we examined how alternative sodium nutrition label formats and nutrition claims influenced consumers’ choice behaviour and whether consumers with or without a diagnosis of hypertension differed in their choice patterns.DesignAn anonymous online experiment in which participants viewed ten choice sets featuring three fictitious brands of baked beans with varied label formats and nutritional profiles (high and low sodium) and indicated which brand in each set they would purchase if shopping for this product.SettingParticipants were recruited from New Zealand's largest online nationwide research panel.SubjectsFive hundred people with self-reported hypertension and 191 people without hypertension aged 18 to 79 years.ResultsThe addition of a front-of-pack label increased both groups’ ability to discriminate between products with high and low sodium, while the Traffic Light label enabled better identification of the high-sodium product. Both front-of-pack formats enhanced discrimination in the presence of a reduced salt claim, but the Traffic Light label also performed better than the Percentage Daily Intake label in moderating the effect of the claim for the high-sodium product.ConclusionsFront-of-pack labels, particularly those with simple visual cues, enhance consumers’ ability to discriminate between high- and low-sodium products, even when those products feature nutrition claims.
Validation of a general nutrition knowledge questionnaire in a Turkish student sample
Authors: Alsaffar A Aylin 
Published: January 2012

AbstractObjectiveTo validate the general nutrition knowledge questionnaire developed by Parmenter and Wardle (1999) in a Turkish student sample.DesignThe original questionnaire of Parmenter and Wardle (1999) was modified and translated into Turkish. The modified questionnaire was administered to second year undergraduate students. Some students completed the questionnaire twice for the measurement of test–retest reliability. Statistical analysis was performed on the responses to measure the internal reliability, test–retest reliability and construct validity.SettingStudents completed the questionnaire under supervision. The questionnaire was completed at the end of lectures. Retest was carried out two weeks after first administration of the test.SubjectsA total of 195 undergraduate students studying either nutrition and dietetics (n 90) or engineering (n 105) participated in the study. Of these, 125 students completed the questionnaire on two occasions.ResultsOverall internal reliability (Cronbach's α = 0·89) and test–retest reliability (0·86) were high. Significant differences between the scores of the two groups of students indicated that the questionnaire had satisfactory construct validity.ConclusionsThe modified version of the general nutrition knowledge questionnaire can be used as a tool to examine the nutrition knowledge of adults in Turkey. In the next stage of the study, some adjustments need to be made to the items that led to low reliability values so that these items will be more applicable to the eating habits and patterns of Turkish people.
Transcendental Idealism and Ontological Agnosticism
Authors: McWherter Dustin 
Published: January 2012

AbstractSince the initial reception of theCritique of Pure Reasontranscendental idealism has been perceived and criticized as a form of subjective idealism regarding space, time, and the objects within them, despite Kant's protestations to the contrary. In recent years, some commentators have attempted to counter this interpretation by presenting transcendental idealism as a primarily epistemological doctrine rather than a metaphysical one. Others have insisted on the metaphysical character of transcendental idealism. Within these debates, Kant's rejection ofontology(of the kind exemplified by Wolff and Baumgarten) has received comparatively little treatment, although it is often acknowledged. The present essay seeks to contribute to the secondary literature on Kant by offering an analysis of this claim and elaborating its consequences for transcendental idealism. This will take the form of a critical examination of transcendental idealism's supposedontological agnosticism—that is, its disavowal of any ontological claims. The overall conclusion is that Kant's rejection of ontology is deeply problematic, and to such an extent that it may be necessary to reconsider the possibilities of defending transcendental idealism as a purely epistemological, non-ontological doctrine.