bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing
Authors: Baranašić Damir , Zucko Jurica , Diminic Janko , Gacesa Ranko , Long Paul F , Cullum John , Hranueli Daslav , Starcevic Antonio 
Published: October 2013

Abstract
Successful genome mining is dependent on accurate prediction of protein function from sequence. This often involves dividing protein families into functional subtypes (e.g., with different substrates). In many cases, there are only a small number of known functional subtypes, but in the case of the adenylation domains of nonribosomal peptide synthetases (NRPS), there are &gt;500 known substrates. Latent semantic indexing (LSI) was originally developed for text processing but has also been used to assign proteins to families. Proteins are treated as ‘‘documents’’ and it is necessary to encode properties of the amino acid sequence as ‘‘terms’’ in order to construct a term-document matrix, which counts the terms in each document. This matrix is then processed to produce a document-concept matrix, where each protein is represented as a row vector. A standard measure of the closeness of vectors to each other (cosines of the angle between them) provides a measure of protein similarity. Previous work encoded proteins as oligopeptide terms, i.e. counted oligopeptides, but used no information regarding location of oligopeptides in the proteins. A novel tokenization method was developed to analyze information from multiple alignments. LSI successfully distinguished between two functional subtypes in five well-characterized families. Visualization of different ‘‘concept’’ dimensions allows exploration of the structure of protein families. LSI was also used to predict the amino acid substrate of adenylation domains of NRPS. Better results were obtained when selected residues from multiple alignments were used rather than the total sequence of the adenylation domains. Using ten residues from the substrate binding pocket performed better than using 34 residues within 8 Å of the active site. Prediction efficiency was somewhat better than that of the best published method using a support vector machine.
Exposure to life adversity in high school and later work participation: A longitudinal population‐based study
Authors: Strøm Ida Frugård , Thoresen Siri , Wentzel‐Larsen Tore , Hjemdal Ole Kristian , Lien Lars , Dyb Grete 
Published: October 2013

AbstractThis paper investigates whether exposure to violence, sexual abuse, or bullying is associated with later work participation and whether high school completion has a potential mediating role. Self‐reported junior high school questionnaire data were linked for eight consecutive years to prospective registry data for the demographics, educational progress, employment activity, and social benefits of 11,874 individuals. Ordinal regression analysis showed that violence and/or bullying at 15 years of age predicted negative work participation outcomes eight years later, independent of high school completion and other relevant factors. Although increasing educational level may have some preventive effect, these results indicate that prevention efforts should be initiated at an early age and should target adverse life experiences.
Toward coherently representing turbulent wall-flow dynamics
Authors: Klewicki J. C. 
Published: October 2013

AbstractThe complex dynamics of turbulent flow in the vicinity of a solid surface underlie numerous scientifically important processes, and pose persistently daunting challenges in many engineering applications. Since their discovery decades ago, coherent motions have presented a tantalizing prospective opportunity for constructing descriptions of wall-flow dynamics using only a relatively small number of elements. The veracity and reliability of such representations are, however, ultimately tied to their basis in the Navier–Stokes equations. In this regard, the study by Sharma & McKeon (J. Fluid Mech., vol. 728, 2013, pp. 196–238) constitutes an important contribution, as it not only provides insights regarding the mechanisms underlying wall-flow coherent motion formation and evolution, but does so within a Navier–Stokes framework.
Turbulent acidic jets and plumes injected into an alkaline environment
Authors: Ülpre H. , Eames I. , Greig A. 
Published: October 2013

AbstractThe characteristics of an acidic turbulent jet and plume injected into an alkaline environment are examined theoretically and experimentally. Fluid-flow and chemistry models are combined to understand how the concentration of acid in a parcel of fluid changes as it reacts with alkaline fluid entrained from the ambient. The resulting model is tested in an experimental study in which nitric acid jets or plumes are injected into a large tank containing a variety of alkaline substances. A video camera records a pH-sensitive dye in the jet or plume, which changes colour with variations in the pH. The results were time averaged and processed to measure distance from the source to the point of neutralization. The agreement between predictions and observations of neutralization distances is good, confirming that the model captures the salient physics of the problem. Using empirically determined titration curves, a combined fluid flow and chemistry model is applied to discuss the environmental implications of a warm acidic turbulent plume injected into an alkaline river or sea.
Mixing in gravity currents
Authors: Fragoso A. T. , Patterson M. D. , Wettlaufer J. S. 
Published: October 2013

AbstractWe study entrainment in lock-release gravity currents using highly spatially resolved optical transmission experiments and quantitative analysis of the available potential energy of the flow. The principal results provide a resolution to the debate regarding the mechanism and degree of mixing in the head of a gravity current during the slumping phase. The nature of the complex internal mixing structure changes as a bore propagates from the tail to the head of the current during the slumping phase and overtakes its leading edge. We use quantitative methods to identify the connection between dynamics and entrainment and show that its manifestation as examined using different methodologies is the cause of previous contradictory experimental findings. Therefore, we conclude that the two main perspectives previously considered at odds are in accord.
Late Visean – early Serpukhovian conodont succession at the Naqing (Nashui) section in Guizhou, South China
Authors: QI YUPING , NEMYROVSKA TAMARA I. , WANG XIANGDONG , CHEN JITAO , WANG ZHIHAO , LANE H. RICHARD , RICHARDS BARRY C. , HU KEYI , WANG QIULAI 
Published: October 2013

AbstractThis study reports the conodont succession across the Visean–Serpukhovian (V/S) boundary interval at the Naqing section, South China. Continuous centimetre-scale sampling of the relatively deep-water section in recent years has provided new data for a more detailed biostratigraphy of conodonts across the Visean–Serpukhovian boundary. Three conodont zones were described in ascending order: the Gnathodus bilineatus, Lochriea nodosa and Lochriea ziegleri zones. The first appearance datum (FAD) of L. ziegleri has been moved down to 60.1 m above the base of the Naqing section. The correlation of the conodont succession across the Visean–Serpukhovian boundary in the Naqing section with other sections in Eurasia is discussed.
Extension and knowledge transfer: adaptive management approaches for timely impact
Authors: KETTERINGS Q. M. 
Published: October 2013

SUMMARYIn recent years, the term ‘adaptive management’ has become integrated in government agriculture and conservation programmes in the United States. Adaptive management is described as ‘a process of developing improved management practices for efficient production and resource conservation by use of participatory learning through continuous systematic assessment’, by the NEERA1002 Coordinating Committee on Adaptive Nutrient Management. Such developments reflect recognition by government agencies of (1) the need for continuous improvement in managing agricultural systems to enhance productivity and environmental protection at farm, state, watershed and federal levels, and (2) the effectiveness of continuous systematic assessment and an outcome-based evaluation in achieving and documenting such progress. Various methods have existed for knowledge development and transfer in the past, some effective, others less successful. The present paper presents and discusses lessons learned from three different adaptive management approaches, implemented at field, whole farm and regional/state levels, which contributed to improvements in field, farm and regional/state balances for nitrogen and phosphorus in New York. These examples show that a combination of governmental regulations and an innovative, outcome-focused adaptive management approach that includes research, extension, and a focus on human dimensions (a people-based approach) will be most effective in obtaining greater sustainability of agriculture in future years.
THE ASSOCIATION BETWEEN ADULT MORTALITY RISK AND FAMILY HISTORY OF LONGEVITY: THE MODERATING EFFECTS OF SOCIOECONOMIC STATUS
Authors: TEMBY OWEN F. , SMITH KEN R. 
Published: October 2013

SummaryStudies consistently show that increasing levels of socioeconomic status (SES) and having a familial history of longevity reduce the risk of mortality. But do these two variables interact, such that individuals with lower levels of SES, for example, may experience an attenuated longevity penalty by virtue of having long-lived relatives? This article examines this interaction by analysing survival past age 40 based on data from the Utah Population Database on an extinct cohort of men born from the years 1840 to 1909. Cox proportional hazards regression and logistic regression are used to test for the main and interaction mortality effects of SES and familial excess longevity (FEL), a summary measure of an individual's history of longevity among his or her relatives. This research finds that the mortality hazard rate for men in the top 15th percentile of occupational status decreases more as FEL increases than it does among men in the bottom 15th percentile. In addition, the mortality hazard rate among farmers decreases more as FEL increases than it does for non-farmers. With a strong family history of longevity as a proxy for a genetic predisposition, this research suggests that a gene–environment interaction occurs whereby the benefits of familial excess longevity are more available to those who have occupations with more autonomy and greater economic resources and/or opportunities for physical activity.
Urogenital schistosomiasis in women of reproductive age and pregnant mothers in Kwale County, Kenya
Authors: Kihara J.H. , Kutima H.L. , Ouma J. , Churcher T.S. , Changoma J.M. , Mwalisetso M.A. , French M.D. , Mwandawiro C.S. 
Published: October 2013

AbstractGenerally, women residing in areas endemic for urinary schistosomiasis may suffer from female genital schistosomiasis which is acquired during childhood. The objective of this cross-sectional study was to estimate the prevalence and intensity of infection of Schistosoma haematobium in women of reproductive age (16–45 years) and to investigate whether S. haematobium had any effect on kidney function. A total of 394 women of known pregnancy status (158 pregnant and 236 non-pregnant) were recruited from five villages (known for their high prevalence of infection of S. haematobium) in Kwale County. Serum samples were analysed to determine levels of urea and creatinine as proxy indicators of kidney function. Data revealed that pregnant women did not, on average, have a higher prevalence or intensity of infection of urinary schistosomiasis than non-pregnant women. During pregnancy, the level of prevalence and intensity of infection of S. haematobium was highest in the first trimester (0–13 weeks), dropped in the second trimester (14–26 weeks) and rose again in the third trimester (27–40 weeks). In addition, 24.8% of women were infected with hookworm, while none were diagnosed with malaria parasites. Of 250 samples analysed for serum urea and creatinine, none had significant levels of pathology, either in pregnant or non-pregnant women. Despite World Health Organization (WHO) recommendations that pregnant women should be treated with praziquantel after the first trimester, in practice this has not been the case in many countries, including Kenya. In view of this, healthcare providers should be informed to consider treatment of pregnant women infected with schistosomiasis during antenatal visits and whenever there is mass drug administration as recommended by the WHO.
Navigating in a volumetric world: Metric encoding in the vertical axis of space
Authors: de Perera Theresa Burt , Holbrook Robert , Davis Victoria , Kacelnik Alex , Guilford Tim 
Published: October 2013

AbstractAnimals navigate through three-dimensional environments, but we argue that the way they encode three-dimensional spatial information is shaped by how they use the vertical component of space. We agree with Jeffery et al. that the representation of three-dimensional space in vertebrates is probably bicoded (with separation of the plane of locomotion and its orthogonal axis), but we believe that their suggestion that the vertical axis is stored “contextually” (that is, not containing distance or direction metrics usable for novel computations) is unlikely, and as yet unsupported. We describe potential experimental protocols that could clarify these differences in opinion empirically.
Monkeys in space: Primate neural data suggest volumetric representations
Authors: Lehky Sidney R. , Sereno Anne B. , Sereno Margaret E. 
Published: October 2013

AbstractThe target article does not consider neural data on primate spatial representations, which we suggest provide grounds for believing that navigational space may be three-dimensional rather than quasi–two-dimensional. Furthermore, we question the authors' interpretation of rat neurophysiological data as indicating that the vertical dimension may be encoded in a neural structure separate from the two horizontal dimensions.
The problem of conflicting reference frames when investigating three-dimensional space in surface-dwelling animals
Authors: Savelli Francesco , Knierim James J. 
Published: October 2013

AbstractIn a surface-dwelling animal like the rat, experimental strategies for investigating the hippocampal correlates of three-dimensional space appear inevitably complicated by the interplay of global versus local reference frames. We discuss the impact of the resulting confounds on present and future empirical analysis of the “bicoded map” hypothesis by Jeffery and colleagues.
Are all types of vertical information created equal?
Authors: Weisberg Steven M. , Newcombe Nora S. 
Published: October 2013

AbstractThe vertical component of space occurs in two distinct fashions in natural environments. One kind of verticality is orthogonal-to-horizontal (as in climbing trees, operating in volumetric spaces such as water or air, or taking elevators in multilevel buildings). Another kind of verticality, which might be functionally distinct, comes from navigating on sloped terrain (as in traversing hills or ramps).
Land Politics and Local State Capacities: The Political Economy of Urban Change in China
Authors: Rithmire Meg 
Published: October 2013

AbstractDespite common national institutions and incentives to remake urban landscapes to anchor growth, generate land-lease revenues and display a capacious administration, Chinese urban governments exhibit varying levels of control over land. This article uses a paired comparison of Dalian and Harbin in China's north-east to link differences in local political economies to land politics. Dalian, benefiting from early access to foreign capital, consolidated its control over urban territory through the designation of a development zone, which realigned local economic interests and introduced dual pressures for enterprises to restructure and relocate. Harbin, facing capital shortages, distributed urban territory to assuage the losers of reform and promote economic growth. The findings suggest that 1) growth strategies, and the territorial politics they produce, are products of the post-Mao urban hierarchy rather than of socialist legacies, and 2), perhaps surprisingly, local governments exercise the greatest control over urban land in cities that adopted market reforms earliest.
A Troposphere Constraint Method To Improve PPP Ambiguity-Resolved Height Solution
Authors: Shi Junbo , Gao Yang 
Published: October 2013

Integer ambiguity resolution is able to improve positioning accuracy and reduce convergence time in Precise Point Positioning (PPP). Although significantly improved horizontal positioning accuracy has been demonstrated, the height solution improvement is found to be less significant, and improving this requires further investigation. In this paper, a troposphere constraint method using precise troposphere corrections is proposed to improve the PPP ambiguity-resolved height solution. This is different from the conventional approach that typically applies meteorological data to calculate the a priori troposphere delay and estimates the residual troposphere delay. The effects of the troposphere delay on PPP ambiguity-resolved height solutions are first studied. Numerical analysis is conducted to ambiguity-resolved positioning results based on the decoupled clock model and hourly Global Positioning System (GPS) observations from a Canadian PPP-inferred troposphere precipitable water vapour system. The results show that by using the proposed method the PPP ambiguity-resolved height accuracy can be further improved to 3·86 cm compared to 5·32 cm using the conventional approach.
Congenital heart disease in 37,294 births in Tunisia: birth prevalence and mortality rate
Authors: Abid Dorra , Elloumi Anis , Abid Leila , Mallek Souad , Aloulou Hajer , Chabchoub Imen , Bouraoui Amira , Thabet Afef , Gargouri Lamia , Zribi Malek , Yaich Sourour , Hachicha Mongia , Gargouri Abdellatif , Mahfoudh Abdelmajid , Maatoug Samir , Dammak Jamel , Kammoun Samir 
Published: October 2013

AbstractAim: To investigate the previously unknown birth incidence, treatment, and mortality of children with congenital heart disease in Tunisia. Methods: We undertook a retrospective review of medical records of all patients who were born in 2010 and 2011, and were diagnosed in Sfax (Tunisia) with congenital heart defect. Results: Among 37,294 births, 255 children were detected to have congenital heart disease, yielding a birth incidence of 6.8 per 1000. The most frequently occurring conditions were ventricular septal defects (31%), ostium secundum atrial septal defects (12.9%), and pulmonary valve abnormalities (12%). Coarctation of the aorta, tetralogy of Fallot, univentricular physiology, pulmonary atresia with ventricular septal defect, and transposition of the great arteries were found in 4.3%, 6.2%, 3.4%, 2.7%, and 2.7%, respectively. During the follow-up of 1 year, 23% of the children died. About three-quarters of those deaths happened before surgery. Conclusion: The present study is in line with the general estimates in the world. It has revealed a high case of mortality among the patients awaiting corrective surgery. These children need more facilities.
Pathophysiology of paradoxical embolism: evaluation of the role of interatrial septum anatomy based on the intracardiac echocardiography assessment of patients with right-to-left shunting
Authors: Rigatelli Gianluca , Dell’Avvocata Fabio , Vassiliev Dobrin , Daggubati Ramesh , Buch Ashesh , Nanjiundappa Aravinda , Giordan Massimo , Oliva Laura , Adami Dario , Cardaioli Paolo 
Published: October 2013

AbstractBackground: Detailed anatomic variants of the interatrial septum in patients with right-to-left shunt and contribution of specific anatomies to the risk of ischaemic recurrences has not yet been comprehensively classified. Objective: To report a classification of the anatomic variants of the interatrial septum as observed by intracardiac echocardiography and its correlation with clinical and functional characteristics. Methods: We retrospectively reviewed the medical and instrumental data of 520 consecutive patients (mean age 44±15. 5 years, 355 women) who had over a 10-year period undergone intracardiac echocardiography and right-to-left shunt catheter-based closure. The four main features used to analyse were: (a) diameter of the oval fossa, (b) presence and length of the channel, (c) presence and degree of atrial septal aneurysm, and (d) rim thickness. The presence of Eustachian valve was also tabulated. Results: The combinations of interatrial septum anatomical features were classified into six main anatomical subgroups. Recurrent embolism, multiple ischaemic foci on brain magnetic resonance imaging, high grade shunt, and permanent shunt before transcatheter closure procedure were associated with type 2, type 4, and type 6. Type 4 anatomical subtype (OR 4.1, 1.5–8 [95% CI], p<0.001) and type 2+presence of Eustachian valve (OR 4.3, 1.6–9 [95% CI], p<0.001) were the strongest predictors of recurrent ischaemic events before transcatheter closure. Conclusion: Our study showed that interatrial septum anatomy greatly differs among patients with right-to-left shunt, as well as the risk of ischaemic recurrences in different anatomies.
Authorship analysis of aliases: Does topic influence accuracy?
Authors: LAYTON ROBERT , WATTERS PAUL A. , DAZELEY RICHARD 
Published: October 2013

AbstractAliasesplay an important role in online environments by facilitating anonymity, but also can be used to hide the identity of cybercriminals. Previous studies have investigated this alias matching problem in an attempt to identify whether two aliases are shared by an author, which can assist with identifying users. Those studies create their training data by randomly splitting the documents associated with an alias into two sub-aliases. Models have been built that can regularly achieve over 90% accuracy for recovering the linkage between these ‘random sub-aliases’. In this paper, random sub-alias generation is shown to enable these high accuracies, and thus does not adequately model the real-world problem. In contrast, creating sub-aliases using topic-based splitting drastically reduces the accuracy of all authorship methods tested. We then present a methodology that can be performed on non-topic controlled datasets, to produce topic-based sub-aliases that are more difficult to match. Finally, we present an experimental comparison between many authorship methods to see which methods better match aliases under these conditions, finding that localn-gram methods perform better than others.
NIH EXAMINER: Conceptualization and Development of an Executive Function Battery
Authors: Kramer Joel H. , Mungas Dan , Possin Katherine L. , Rankin Katherine P. , Boxer Adam L. , Rosen Howard J. , Bostrom Alan , Sinha Lena , Berhel Ashley , Widmeyer Mary 
Published: October 2013

AbstractExecutive functioning is widely targeted when human cognition is assessed, but there is little consensus on how it should be operationalized and measured. Recognizing the difficulties associated with establishing standard operational definitions of executive functioning, the National Institute of Neurological Disorders and Stroke entered into a contract with the University of California-San Francisco to develop psychometrically robust executive measurement tools that would be accepted by the neurology clinical trials and clinical research communities. This effort, entitled Executive Abilities: Measures and Instruments for Neurobehavioral Evaluation and Research (EXAMINER), resulted in a series of tasks targeting working memory, inhibition, set shifting, fluency, insight, planning, social cognition and behavior. We describe battery conceptualization and development, data collection, scale construction based on item response theory, and lay the foundation for studying the battery's utility and validity for specific assessment and research goals. (JINS, 2013, 19, 1–9)