bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate domain identification with structure‐anchored hidden Markov models, saHMMs
Authors: Tångrot Jeanette E. , Kågström Bo , Sauer Uwe H. 
Published: December 2008

AbstractThe ever increasing speed of DNA sequencing widens the discrepancy between the number of known gene products, and the knowledge of their function and structure. Proper annotation of protein sequences is therefore crucial if the missing information is to be deduced from sequence‐based similarity comparisons. These comparisons become exceedingly difficult as the pairwise identities drop to very low values. To improve the accuracy of domain identification, we exploit the fact that the three‐dimensional structures of domains are much more conserved than their sequences. Based on structure‐anchored multiple sequence alignments of low identity homologues we constructed 850 structure‐anchored hidden Markov models (saHMMs), each representing one domain family. Since the saHMMs are highly family specific, they can be used to assign a domain to its correct family and clearly distinguish it from domains belonging to other families, even within the same superfamily. This task is not trivial and becomes particularly difficult if the unknown domain is distantly related to the rest of the domain sequences within the family. In a search with full length protein sequences, harbouring at least one domain as defined by the structural classification of proteins database (SCOP), version 1.71, versus the saHMM database based on SCOP version 1.69, we achieve an accuracy of 99.0%. All of the few hits outside the family fall within the correct superfamily. Compared to Pfam_ls HMMs, the saHMMs obtain about 11% higher coverage. A comparison with BLAST and PSI‐BLAST demonstrates that the saHMMs have consistently fewer errors per query at a given coverage. Within our recommended E‐value range, the same is true for a comparison with SUPERFAMILY. Furthermore, we are able to annotate 232 proteins with 530 nonoverlapping domains belonging to 102 different domain families among human proteins labelled “unknown” in the NCBI protein database. Our results demonstrate that the saHMM database represents a versatile and reliable tool for identification of domains in protein sequences. With the aid of saHMMs, homology on the family level can be assigned, even for distantly related sequences. Due to the construction of the saHMMs, the hits they provide are always associated with high quality crystal structures. The saHMM database can be accessed via the FISH server at http://babel.ucmp.umu.se/fish/. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Action following the discovery of a global association between the whole genome and adverse event risk in a clinical drug‐development programme
Authors: Whitehead John , Kelly Patrick , Zhou Yinghui , Stallard Nigel , Thygesen Helene , Bowman Clive 
Published: December 2008

AbstractObservation of adverse drug reactions during drug development can cause closure of the whole programme. However, if association between the genotype and the risk of an adverse event is discovered, then it might suffice to exclude patients of certain genotypes from future recruitment. Various sequential and non‐sequential procedures are available to identify an association between the whole genome, or at least a portion of it, and the incidence of adverse events. In this paper we start with a suspected association between the genotype and the risk of an adverse event and suppose that the genetic subgroups with elevated risk can be identified. Our focus is determination of whether the patients identified as being at risk should be excluded from further studies of the drug. We propose using a utility function to determine the appropriate action, taking into account the relative costs of suffering an adverse reaction and of failing to alleviate the patient's disease. Two illustrative examples are presented, one comparing patients who suffer from an adverse event with contemporary patients who do not, and the other making use of a reference control group. We also illustrate two classification methods, LASSO and CART, for identifying patients at risk, but we stress that any appropriate classification method could be used in conjunction with the proposed utility function. Our emphasis is on determining the action to take rather than on providing definitive evidence of an association. Copyright © 2008 John Wiley & Sons, Ltd.
Pharmaceutical cleaning validation using non‐proximate large‐area desorption electrospray ionization mass spectrometry
Authors: Soparawalla Santosh , Salazar Gary A. , Perry Richard H. , Nicholas Mark , Cooks R. Graham 
Published: December 2008

AbstractDesorption electrospray ionization (DESI) is a droplet‐based ionization method that is applied to samples in the ambient environment with little or no sample preparation. Its utility for industrial applications is explored here for the case of pharmaceutical cleaning validation. A non‐proximate large‐area DESI system was built to examine representative areas of the surfaces of reaction vessels used in active product ingredient (API) manufacturing. A large‐area sprayer capable of sampling an area of ∼2.5 cm2 was coupled with a transport tube to allow sensitive, representative sampling of APIs from a stainless steel surface 1 m away from the mass spectrometer. The system was used to detect the APIs neostigmine, acebutolol, amiloride, amiodarone, ibuprofen, montelukast, potassium clavulanate, and β‐estradiol, at levels as low as 30–10 ng/cm2, easily satisfying the general acceptable limits set by the pharmaceutical industry. These levels were achieved from surfaces resembling the equipment used in API manufacturing processes at a rate of 30 s per analysis. Copyright © 2008 John Wiley & Sons, Ltd.
Kalman filtering over wireless fading channels—How to handle packet drop
Authors: Mostofi Yasamin , Murray Richard M. 
Published: December 2008

AbstractIn this paper we consider estimation of dynamical systems over wireless fading communication channels using a Kalman filter. We show the impact of the stochastic communication noise on the estimation process. We furthermore show how noisy packets should be handled in the receiver. More specifically, we illustrate the impact of the availability of a cross‐layer information path on the optimum receiver design. In the absence of a cross‐layer information path, it was shown that packet drop should be designed to balance information loss and communication noise in order to optimize the performance. In the presence of a cross‐layer path, we show that keeping all the packets will minimize the average estimation error covariance. We also derive the stability condition in the presence of noisy packets and show that it is independent of the shape of the communication noise variance or availability of a cross‐layer information path. Copyright © 2008 John Wiley & Sons, Ltd.
Internationalization of Chinese and Korean firms
Authors: Yang Xiaohua , Lim Yong‐taek , Sakurai Yuka , Seo Su‐yea 
Published: December 2008

AbstractThis article compares and contrasts the growth of Chinese and Korean multinational enterprises (MNEs). The article identifies the similarities and differences between Chinese and Korean MNEs in terms of motivations for internationalization, expansion strategies, and paths. The goal of this article is to contribute to the literature by shifting focus on host‐country conditions to home‐country conditions in explaining the drivers for firms' internationalization. We conclude that firms are motivated to expand abroad when faced with domestic competitive disadvantages resulting from absence or deficiency of one or more of Porter's Diamond attributes in their domestic market. Implications for further studies are also explored. © 2009 Wiley Periodicals, Inc.
Toxic effects of lactational exposure to 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin (TCDD) on development of male reproductive system: Involvement of antioxidants, oxidants, and p53 protein
Authors: Jin Mei Hua , Hong Chang Hee , Lee Hye Young , Kang Hyo Jin , Han Sang Won 
Published: December 2008

Abstract2,3,7,8‐Tetrachlorodibenzo‐p‐dioxin (TCDD) is a potent endocrine disruptor compound and induces multiple organ dysfunctions. The effect of TCDD exposure both in adults and in utero has been well established. However, little is known about the effects of TCDD acquired through mother's milk on the development of the male reproductive system. The aim of this study was to investigate the effects and mechanisms of TCDD from lactational exposure. TCDD (1 μg/kg) was administered to C57BL/6 mouse mothers for 4 days from the day of delivery. On postnatal day 30 (PND 30) and postnatal day 60 (PND 60), body weight, body length, and anogenital distance (AGD) of male offspring were measured. The weights of the testes and epididymides were also measured. Epididymides were used for sperm counts, and testes were used to measure the activity of antioxidant enzymes (SOD, CAT, GPX, GR), the parameters of oxidative stress (hydrogen peroxide, MDA), and testosterone. In addition, expression of p53 and the proapoptotic protein, Bax, were analyzed by Western blot. TCDD exposure decreased body weight, body length, and AGD in both PND 30 and PND 60 groups compared with the control group. The activity of all antioxidant enzymes at PND 60 was decreased after TCDD treatment. TCDD treatment decreased testicular testosterone levels in both the PND 30 and PND 60 groups. The expression of p53 and Bax were also upregulated by TCDD and did not return to normal levels by PND 60. These data suggest that TCDD affects development of male offspring when the mother is exposed to TCDD during lactation. In addition, oxidative stress is a major mediator of TCDD‐induced adverse effects, and p53 may play an important role in this mechanism. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2010.
Femoral neck fracture following intramedullary nailing with misplacement of an end cup: report of two cases
Authors: Grala Paweł , Mańkowski Bartosz , Kierzynka Grzegorz 
Published: December 2008

Abstract
Femoral neck fracture is an unusual complication of intramedullary fixation of a broken femur. We report on two cases of femoral neck fractures attributed to misplacement of an end cup and subsequent invasive maneuvers in an effort to remove it. Iatrogenic fractures of the femoral neck during or after intramedullary nailing are reported in the medical literature. Authors associate it with many possible technical mistakes performed during the procedure, yet no complications after missed end cup placement were noted. We suggest that the fractures described below were a consequence of injury to the vascular supply and bone stock of the initially intact femoral neck.
The use of circular fine wire frames for the treatment of displaced intra-articular calcaneal fractures
Authors: Mauffrey C. , Klutts P. , Seligson D. 
Published: December 2008

AbstractBackgroundThe treatment of displaced intra-articular calcaneal fractures is still controversial.Materials and methodsSixteen consecutive patients admitted at University Hospital with intra-articular fractures were treated with fine wire circular frames and followed up at an average of 160 days from their injuries. We focused on radiological outcome and functional outcome using a patient-based questionnaire.ResultsWe had no secondary reconstruction procedures. With the numbers available, the difference between the preoperative values and the follow-up measurements for Böhler’s angle, Gissane’s angle and posterior subtalar joint space was not statistically significant (P = 0.8,P = 0.2, andP = 0.4, respectively). The standardized AAOS FAS ranged from 42 to 96, with a mean of 80 and a standard deviation of 19.ConclusionsFine wire circular frame is a good alternative to ORIF in displaced intra-articular calcaneal fractures, yielding good patient function, a high return-to-work rate and a low complication rate.
Water supply: Public or private?
Authors: Pérard Edouard 
Published: December 2008

AbstractMost theories on private sector participation in water infrastructure are based on the sole supposed difference of efficiency between the public and the private sector. The review of 22 empirical tests and 51 case studies shows that private sector participation per se in water supply does not systematically have a significant positive effect on efficiency. Thus, the choice between public and private water delivery is probably not only a question of efficiency.We developed a complete theory of the choice between public and private water supply based on four components: difference of cost of funds, transaction costs of outsourcing, difference of efficiency and potential political cost of privatizing. Since determinants of the theory fluctuate over the time and depend on the local context, this theory can explain both privatization and municipalization movements as well as why some local governments outsource water supply, while others opt for direct provision.The tests on 459 US counties in charge of water supply in 45 states provide substantial support for the theory. Significant determinants of the choice of public versus private water delivery include the cost of funds, especially the social cost of taxes, transaction costs, the difference of efficiency and the potential political cost of privatizing.Moreover, we tested other literature's theories, which suggest employment as a motive of public provision and cost of public wages as a cause of privatization. These two arguments seem to be irrelevant.We additionally tested the influence of ownership on the number of drinking water environmental violations and found no significance.
Feasibility of imaging living cells at subnanometer resolutions by ultrafast X-ray diffraction
Authors: Bergh Magnus , Huldt Gösta , Tîmneanu Nicusor , Maia Filipe R. N. C. , Hajdu Janos 
Published: December 2008

AbstractDetailed structural investigations on living cells are problematic because existing structural methods cannot reach high resolutions on non-reproducible objects. Illumination with an ultrashort and extremely bright X-ray pulse can outrun key damage processes over a very short period. This can be exploited to extend the diffraction signal to the highest possible resolution in flash diffraction experiments. Here we present an analysis of the interaction of a very intense and very short X-ray pulse with a living cell, using a non-equilibrium population kinetics plasma code with radiation transfer. Each element in the evolving plasma is modeled by numerous states to monitor changes in the atomic populations as a function of pulse length, wavelength, and fluence. The model treats photoionization, impact ionization, Auger decay, recombination, and inverse bremsstrahlung by solving rate equations in a self-consistent manner and describes hydrodynamic expansion through the ion sound speed. The results show that subnanometer resolutions could be reached on micron-sized cells in a diffraction-limited geometry at wavelengths between 0·75 and 1·5 nm and at fluences of 1011–1012 photons μm−2in less than 10 fs. Subnanometer resolutions could also be achieved with harder X-rays at higher fluences. We discuss experimental and computational strategies to obtain depth information about the object in flash diffraction experiments.
From numerical concepts to concepts of number
Authors: Rips Lance J. , Bloomfield Amber , Asmuth Jennifer 
Published: December 2008

AbstractMany experiments with infants suggest that they possess quantitative abilities, and many experimentalists believe that these abilities set the stage for later mathematics: natural numbers and arithmetic. However, the connection between these early and later skills is far from obvious. We evaluate two possible routes to mathematics and argue that neither is sufficient: (1) We first sketch what we think is the most likely model for infant abilities in this domain, and we examine proposals for extrapolating the natural number concept from these beginnings. Proposals for arriving at natural number by (empirical) induction presuppose the mathematical concepts they seek to explain. Moreover, standard experimental tests for children's understanding of number terms do not necessarily tap these concepts. (2) True concepts of number do appear, however, when children are able to understand generalizations over all numbers; for example, the principle of additive commutativity (a+b=b+a). Theories of how children learn such principles usually rely on a process of mapping from physical object groupings. But both experimental results and theoretical considerations imply that direct mapping is insufficient for acquiring these principles. We suggest instead that children may arrive at natural numbers and arithmetic in a more top-down way, by constructing mathematical schemas.
Do mental magnitudes form part of the foundation for natural number concepts? Don't count them out yet
Authors: Barth Hilary 
Published: December 2008

AbstractThe current consensus among most researchers is that natural number is not built solely upon a foundation of mental magnitudes. On their way to the conclusion that magnitudes do not form any part of that foundation, Rips et al. pass rather quickly by theories suggesting that mental magnitudes might play some role. These theories deserve a closer look.
Not all basic number representations are analog: Place coding as a precursor of the natural number system
Authors: Fias Wim , Verguts Tom 
Published: December 2008

AbstractRips et al.'s arguments for rejecting basic number representations as a precursor of the natural number system are exclusively based on analog number coding. We argue that these arguments do not apply to place coding, a type of basic number representation that is not considered by Rips et al.
Recursive reminding and children's concepts of number
Authors: Hintzman Douglas L. 
Published: December 2008

AbstractAccording to the recursive reminding hypothesis, repetition interacts with episodic memory to produce memory representations that encode – and recursively embed – experiences of reminding. These representations provide the rememberer with a basis for differentiating among the first time something happens, the second time it happens, and so on. I argue that such representations could mediate children's understanding of natural number.
Early numerical representations and the natural numbers: Is there really a complete disconnect?
Authors: Lourenco Stella F. , Levine Susan C. 
Published: December 2008

AbstractThe proposal of Rips et al. is motivated by discontinuity and input claims. The discontinuity claim is that no continuity exists between early (nonverbal) numerical representations and natural number. The input claim is that particular experiences (e.g., cardinality-related talk and object-based activities) do not aid in natural number construction. We discuss reasons to doubt both claims in their strongest forms.
Learning natural numbers is conceptually different than learning counting numbers
Authors: Read Dwight 
Published: December 2008

AbstractHow children learn number concepts reflects the conceptual and logical distinction between counting numbers, based on a same-size concept for collections of objects, and natural numbers, constructed as an algebra defined by the Peano axioms for arithmetic. Cross-cultural research illustrates the cultural specificity of counting number systems, and hence the cultural context must be taken into account.
Precursors to number: Equivalence relations, less-than and greater-than relations, and units
Authors: Sophian Catherine 
Published: December 2008

AbstractInfants' knowledge need not have the same structure as the mature knowledge that develops from it. Fundamental to an understanding of number are concepts of equivalence and less-than and greater-than relations. These concepts, together with the concept of unit, are posited to be the starting points for the development of numerical knowledge.
Dissonances in theories of number understanding
Authors: Rips Lance J. , Bloomfield Amber , Asmuth Jennifer 
Published: December 2008

AbstractTraditional theories of how children learn the positive integers start from infants' abilities in detecting the quantity of physical objects. Our target article examined this view and found no plausible accounts of such development. Most of our commentators appear to agree that no adequate developmental theory is presently available, but they attempt to hold onto a role for early enumeration. Although some defend the traditional theories, others introduce new basic quantitative abilities, new methods of transformation, or new types of end states. A survey of these proposals, however, shows that they do not succeed in bridging the gap to knowledge of the integers. We suggest that a better theory depends on starting with primitives that are inherently structural and mathematical.
Semantic cognition or data mining?
Authors: Borsboom Denny , Visser Ingmar 
Published: December 2008

AbstractWe argue that neural networks for semantic cognition, as proposed by Rogers & McClelland (R&M), do not acquire semantics and therefore cannot be the basis for a theory of semantic cognition. The reason is that the neural networks simply perform statistical categorization procedures, and these do not require any semantics for their successful operation. We conclude that this has severe consequences for the semantic cognition views of R&M.
A crosslinguistic perspective on semantic cognition
Authors: Majid Asifa , Huettig Falk 
Published: December 2008

AbstractCoherent covariation appears to be a powerful explanatory factor accounting for a range of phenomena in semantic cognition. But its role in accounting for the crosslinguistic facts is less clear. Variation in naming, within the same semantic domain, raises vexing questions about the necessary parameters needed to account for the basic facts underlying categorization.
On the semantics of infant categorization and why infants perceive horses as humans
Authors: Quinn Paul C. 
Published: December 2008

AbstractThis commentary considers the issues of what should be taken as evidence for semantic categorization in infants and why infants display a surprising asymmetry in the categorization of humans versus nonhuman animals. It is argued that perceptual knowledge should be viewed as a potent source of information for semantic categorization, and that the asymmetrical categorization behavior arises as a consequence of the frequency and similarity structure of experience.
A simple model from a powerful framework that spans levels of analysis
Authors: Rogers Timothy T. , McClelland James L. 
Published: December 2008

AbstractThe commentaries reflect three core themes that pertain not just to our theory, but to the enterprise of connectionist modeling more generally. The first concerns the relationship between a cognitive theory and an implemented computer model. Specifically, how does one determine, when a model departs from the theory it exemplifies, whether the departure is a useful simplification or a critical flaw? We argue that the answer to this question depends partially upon the model's intended function, and we suggest that connectionist models have important functions beyond the commonly accepted goals of fitting data and making predictions. The second theme concerns perceived in-principle limitations of the connectionist approach to cognition, and the specific concerns these perceived limitations raise for our theory. We argue that the approach is not in fact limited in the ways our critics suggest. One common misconception, that connectionist models cannot address abstract or relational structure, is corrected through new simulations showing directly that such structure can be captured. The third theme concerns the relationship between parallel distributed processing (PDP) models and structured probabilistic approaches. In this case we argue that there the difference between the approaches is not merely one of levels. Our PDP approach differs from structured statistical approaches at all of Marr's levels, including the characterization of the goals of cognitive computations, and of the representations and algorithms used.