bluuebunny/crossref_metadata_2025 huggingface dataset:
A biosemiotic note on organisms, animals, machines, cyborgs, and the quasi-autonomy of robots
Authors: Emmeche Claus
Published: February 2013

It is argued in this paper that robots are just quasi-autonomous beings, which must be understood, within an emergent systems view, as intrinsically linked to and presupposing human beings as societal creatures within a technologically mediated world. Biosemiotics is introduced as a perspective on living systems that is based upon contemporary biology but reinterpreted through a qualitative organicist tradition in biology. This allows for emphasizing the differences between (1) an organism as a general semiotic system with vegetative and self-reproductive capacities, (2) an animal body also with sentience and phenomenal states, and (3) higher forms of anthroposemiotic systems such as humans, machines and robots. On all three levels, representations (or sign action) are crucial processes. The “representationalism” invoked by critiques of cognitive science and robotics tends to focus only on simplistic notions of representation, and must be distinguished from a Peircean or biosemiotic notion of representation. Implications for theorizing about the physical, biological, animate, phenomenal and social body and their forms of autonomy are discussed.
Aristotle, autonomy and the explanation of behaviour
Authors: Pérez Carlos Herrera , Ziemke Tom
Published: February 2013

This paper examines Aristotle’s notion of autonomy and its implication for the mechanicism/autonomy debate. We introduce the basic principles of Aristotle’s scientific framework, including his theory of four causes for the explanation of nature. We draw parallels between these notions of autonomy and causation and autopoietic theory, dynamical systems and robotics, suggesting that they may be compatible with Aristotle’s framework. We argue that understanding the problem of design of autonomous robots may benefit from the consideration of integration of Aristotle’s causes, while robotics, in turn, may contribute to the debate providing a common ground for epistemological and ontological notions of autonomy.
An improved constraint filtering technique for inferring hidden states and parameters of a biological model
Authors: Murtuza Baker Syed , Poskar C. Hart , Schreiber Falk , Junker Björn H.
Published: February 2013

Motivation: In systems biology, kinetic models represent the biological system using a set of ordinary differential equations (ODEs). The correct values of the parameters within these ODEs are critical for a reliable study of the dynamic behaviour of such systems. Typically, it is only possible to experimentally measure a fraction of these parameter values. The rest must be indirectly determined from measurements of other quantities. In this article, we propose a novel statistical inference technique to computationally estimate these unknown parameter values. By characterizing the ODEs with non-linear state-space equations, this inference technique models the unknown parameters as hidden states, which can then be estimated from noisy measurement data.

Results: Here we extended the square-root unscented Kalman filter SR-UKF proposed by Merwe and Wan to include constraints with the state estimation process. We developed the constrained square-root unscented Kalman filter (CSUKF) to estimate parameters of non-linear state-space models. This probabilistic inference technique was successfully used to estimate parameters of a glycolysis model in yeast and a gene regulatory network. We showed that our method is numerically stable and can reliably estimate parameters within a biologically meaningful parameter space from noisy observations. When compared with the two common non-linear extensions of Kalman filter in addition to four widely used global optimization algorithms, CSUKF is shown to be both accurate and computationally efficient. With CSUKF, statistical analysis is straightforward, as it directly provides the uncertainty on the estimation result.

Availability and implementation: Matlab code available upon request from the author.

Contact:  baker@ipk-gatersleben.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Asinibacterium
lactis gen. nov., sp. nov., a member of the family

Chitinophagaceae

, isolated from donkey (Equus asinus) milk
Authors: Lee Dong-Geol , Park Ji-Min , Kang Heecheol , Hong So-Young , Lee Kyung Real , Chang Hung-Bae , Trujillo Martha E.
Published: February 2013

A novel bacterial strain, designated LCJ02T, was isolated on R2A agar from donkey (Equus asinus) milk powder and subjected to a taxonomic study using a polyphasic approach. Strain LCJ02T showed a Gram-negative reaction, was non-motile, non-spore-forming and possessed rod-shaped cells and yellow-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate formed a cluster with several uncultured bacterial clones and with cultured members of the genera

Hydrotalea

,

Sediminibacterium

and

Lacibacter

(family

Chitinophagaceae

, phylum

Bacteroidetes

). The gene sequence similarities with respect to the type strains of recognized species from the above genera and other phylogenetic neighbours ranged from 89.3 to 92.9 %. The G+C content of the genomic DNA was 49.2 mol%, the only isoprenoid quinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipids of strain LCJ02T were phosphatidylethanolamine, two unidentified aminophospholipids, one unidentified aminolipid and five unidentified lipids. The results of physiological and biochemical tests allowed phenotypic differentiation of strain LCJ02T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate LCJ02T represents a novel genus and species in the family

Chitinophagaceae

for which the name Asinibacterium lactis gen. nov., sp. nov. is proposed. The type strain is LCJ02T ( = KCCM 90108T = JCM 18484T).
The Arabidopsis Elongator Complex Subunit2 Epigenetically Regulates Plant Immune Responses
Authors: Wang Yongsheng , An Chuanfu , Zhang Xudong , Yao Jiqiang , Zhang Yanping , Sun Yijun , Yu Fahong , Amador David Moraga , Mou Zhonglin
Published: February 2013

The Arabidopsis thaliana Elongator complex subunit2 (ELP2) genetically interacts with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1), a key transcription coactivator of plant immunity, and regulates the induction kinetics of defense genes. However, the mechanistic relationship between ELP2 and NPR1 and how ELP2 regulates the kinetics of defense gene induction are unclear. Here, we demonstrate that ELP2 is an epigenetic regulator required for pathogen-induced rapid transcriptome reprogramming. We show that ELP2 functions in a transcriptional feed-forward loop regulating both NPR1 and its target genes. An elp2 mutation increases the total methylcytosine number, reduces the average methylation levels of methylcytosines, and alters (increases or decreases) methylation levels of specific methylcytosines. Interestingly, infection of plants with the avirulent bacterial pathogen Pseudomonas syringae pv tomato DC3000/avrRpt2 induces biphasic changes in DNA methylation levels of NPR1 and PHYTOALEXIN DEFICIENT4 (PAD4), which encodes another key regulator of plant immunity. These dynamic changes are blocked by the elp2 mutation, which is correlated with delayed induction of NPR1 and PAD4. The elp2 mutation also reduces basal histone acetylation levels in the coding regions of several defense genes. Together, our data demonstrate a new role for Elongator in somatic DNA demethylation/methylation and suggest a function for Elongator-mediated chromatin regulation in pathogen-induced transcriptome reprogramming.
CD8+ Effector T Cells at the Fetal–Maternal Interface, Balancing Fetal Tolerance and Antiviral Immunity
Authors: Tilburgs Tamara , Strominger Jack L.
Published: February 2013

During pregnancy CD8+ effector T cells need optimal immune regulation to prevent a detrimental response to allogeneic fetal cells while providing immune protection to infections. A significant proportion of (prospective) mothers carry naïve or memory CD8+ T cells with a TCR that can directly bind to paternal MHC molecules. In addition, a high percentage of pregnant women develop specific T cell responses to fetal minor histocompatibility antigens (mHags). Under normal conditions, fetal–maternal MHC and mHag mismatches lead to elevated lymphocyte activation but do not induce pregnancy failure. Furthermore, viral infections alter the maternal CD8+ T cell response by changing the CD8+ T cell repertoire and increasing the influx of CD8+ T cells to decidual tissue. The normally high T cell activation threshold at the fetal–maternal interface may prevent efficient clearance of viral infections. Conversely, the increased inflammatory response due to viral infections may break fetal–maternal tolerance and lead to pregnancy complications. The aim of this review is to discuss the recent studies of CD8+ T cells in pregnancy, identify potential mechanisms for antigen‐specific immune recognition of fetal extravillous trophoblast (EVT) cells by CD8+ T cells, and discuss the impact of viral infections and virus‐specific CD8+ T cells during pregnancy.
Von Willebrand disease‐associated angiodysplasia: a few answers, still many questions
Authors: Franchini Massimo , Mannucci Pier Mannuccio
Published: February 2013

The association between angiodysplasia and von Willebrand disease (VWD) has been known for more than 40 years. Bleeding in the gastrointestinal tract associated with angiodysplasia worsens the clinical course of this inherited haemorrhagic disorder and management may become difficult and challenging. Angiodysplasia associated with acquired defects or dysfunctions of von Willebrand factor (VWF) has also been reported in a variety of conditions such as monoclonal gammopathies, Heyde syndrome and in carriers of ventricular assist devices. The most recent advances concerning the mechanistic, clinical and therapeutic aspects of VWD‐associated angiodysplasia are summarized in this review, together with the limitations of our knowledge that warrant further research in the frame of international cooperation.
Priming motivation through unattended speech
Authors: Radel Rémi , Sarrazin Philippe , Jehu Marie , Pelletier Luc
Published: February 2013

This study examines whether motivation can be primed through unattended speech. Study 1 used a dichotic‐listening paradigm and repeated strength measures. In comparison to the baseline condition, in which the unattended channel was only composed by neutral words, the presence of words related to high (low) intensity of motivation led participants to exert more (less) strength when squeezing a hand dynamometer. In a second study, a barely audible conversation was played while participants' attention was mobilized on a demanding task. Participants who were exposed to a conversation depicting intrinsic motivation performed better and persevered longer in a subsequent word‐fragment completion task than those exposed to the same conversation made unintelligible. These findings suggest that motivation can be primed without attention.
Cut Loose in the Caribbean: Neoliberalism and the Demise of the Commonwealth Sugar Trade
Authors: RICHARDSON BEN , NGWENYA PAMELA RICHARDSON
Published: February 2013

This article focuses on the way the Anglophone Caribbean succumbed to the overhaul of the European Union sugar trade and how these countries have attempted to restructure their economies in its wake. We show how the protagonists of reform gave a sense of inevitability to the demise of the Commonwealth trade system and conveyed (unrealistic) strategies for how this should be managed for the benefit of the Caribbean. In this way we detail the hegemony of neoliberalism in contemporary trade politics and the need for alternative strategies for rural development in the Caribbean region.
Hypopigmented onychocytic matricoma as a clinical mimic of onychomatricoma: clinical, intraoperative and histopathologic correlations
Authors: Spaccarelli Natalie , Wanat Karolyn A. , Miller Christopher J. , Rubin Adam I.
Published: February 2013

Onychocytic matricoma is a newly described matrical tumor of the nail unit that clinically presents with localized thickening of the nail plate and melanonychia and represents a benign acanthoma of onychocytes. Onychocytic matricoma can be classified according to its histopathologic type (acanthotic, papillomatous or keratogenous with retarded maturation) and pigmentation (pigmented, melanocytic or non‐pigmented). However, there are no published reports of non‐pigmented onychocytic matricoma. We report a case of hypopigmented onychocytic matricoma that presented with a thickened nail plate, xanthonychia and histopathologic features of acanthosis, prekeratogenous zone and keratogenous zone cells forming pseudosquamous eddies, and minimal pigmentation with Fontana staining. We also provide detailed clinical, intraoperative and histopathologic correlations of this rare tumor. Both clinicians and dermatopathologists should be aware that onychocytic matricoma can present with xanthonychia, thickening of the nail plate and mimic an onychomatricoma.
A comparison of rural and urban Indian children's visual detection of threatening and nonthreatening animals
Authors: Penkunas Michael J. , Coss Richard G.
Published: February 2013

Recent studies indicate that young children preferentially attend to snakes, spiders, and lions compared with nondangerous species, but these results have yet to be replicated in populations that actually experience dangerous animals in nature. This multi‐site study investigated the visual‐detection biases of southern Indian children towards two potentially dangerous taxa, snakes and lions, that constituted major threats during human evolution. Three‐ to 8‐year‐old children from two distinct populations were presented with visual‐search tasks containing one target image embedded in matrices of eight distractor images. Children living in Bangalore city, an urban setting in which exposure to dangerous animals would only occur occasionally during family outings to zoos and forest areas, were compared with children living in and around National Parks where exposure to dangerous species is frequent. In the first two experiments, children from both locations detected snake and lion images more rapidly than nonthreatening lizard and antelope images, respectively. Neither urban nor rural children displayed a bias for detecting horses versus cows, the latter constituting a familiar animal with strong religious significance. For all three experiments, the reaction times of urban and rural children were very similar, indicating that periodic exposure to dangerous animals early in life, coupled with adult cautioning, did not facilitate better snake and lion detection. This consistency of urban and rural children with different exposure to dangerous animals suggests that detection of some dangerous species may reflect both experience in nature and visual biases shaped by natural selection.
A preliminary study suggests that nicotine and prefrontal dopamine affect cortico‐striatal areas in smokers with performance feedback
Authors: Lee M. R. , Gallen C. L. , Ross T. J. , Kurup P. , Salmeron B. J. , Hodgkinson C. A. , Goldman D. , Stein E. A. , Enoch M. A.
Published: February 2013

Nicotine and tonic dopamine (DA) levels [as inferred by catechol‐O‐methyl tranferase (COMT) Val158Met genotype] interact to affect prefrontal processing. Prefrontal cortical areas are involved in response to performance feedback, which is impaired in smokers. We investigated whether there is a nicotine × COMT genotype interaction in brain circuitry during performance feedback of a reward task. We scanned 23 healthy smokers (10 Val/Val homozygotes, 13 Met allele carriers) during two fMRI sessions while subjects were wearing a nicotine or placebo patch. A significant nicotine × COMT genotype interaction for BOLD signal during performance feedback in cortico‐striatal areas was seen. Activation in these areas during the nicotine patch condition was greater in Val/Val homozygotes and reduced in Met allele carriers. During negative performance feedback, the change in activation in error detection areas such as anterior cingulate cortex (ACC)/superior frontal gyrus on nicotine compared to placebo was greater in Val/Val homozygotes compared to Met allele carriers. With transdermal nicotine administration, Val/Val homozygotes showed greater activation with performance feedback in the dorsal striatum, area associated with habitual responding. In response to negative feedback, Val/Val homozygotes had greater activation in error detection areas, including the ACC, suggesting increased sensitivity to loss with nicotine exposure. Although these results are preliminary due to small sample size, they suggest a possible neurobiological mechanism underlying the clinical observation that Val/Val homozygotes, presumably with elevated COMT activity compared to Met allele carriers and therefore reduced prefrontal DA levels, have poorer outcomes with nicotine replacement therapy.
The ability of the Reciproc R25 instrument to reach the full root canal working length without a glide path
Authors: De‐Deus G. , Arruda T. E. P. , Souza E. M. , Neves A. , Magalhães K. , Thuanne E. , Fidel R. A. S.
Published: February 2013

Aim

To assess the frequency in which the Reciproc instrument reaches the full working length (FWL) of mandibular molar canals without a glide path.

Methodology

From a pool of mandibular molars, 253 root canals were classified as straight (G1) and, 249 root canals as moderately curved (G2) following Schneider's method. A R25 Reciproc instrument (VDW, Munich, Germany) was advanced in the canals without any previous glide path. All cases where Reciproc instruments reached the FWL were classified as ‘Reaching the FWL’ (RFWL). When the FWL was not reached by the R25, the root canals were classified as ‘Not Reaching the FWL’ (NRFWL). Pearson's χ2 test compared (i) the frequency distributions of root canals classified as RFWL and NRFWL for each group and (ii) the frequency distributions of NRFWL canals between the groups.

Results

In G1, 9 cases (3.56%) and in G2, 23 canals (9.34%) were classified as NRFWL. The difference between NRFWL and RFWL was significant in both groups (P = 0.00, χ 2 = 217.2 for G1; P = 0.00, χ 2 = 167.8 for G2). The frequency of NRFWL was significantly higher for G2 (P = 0.02, χ 2 = 5.452).

Conclusion

The R25 Reciproc instrument is able to reach the FWL of straight‐ and moderate‐curved mandibular molar canals without a glide path in a large proportion of cases.
Susceptibility of kiwifruit (Actinidia spp.) cultivars to Ceratitis capitata (Diptera: Tephritidae) infestation
Authors: Papachristos D. P. , Papadopoulos N. T. , Maglaras E. , Michaelakis A. , Antonatos S. Α.
Published: February 2013

Laboratory no‐choice tests were conducted to determine whether the kiwifruit cultivars Hayward, Tsechelidis (Actinidia deliciosa) and Soreli (A. chinensis) are hosts of the Mediterranean fruit fly, Ceratitis capitata. Kiwifruits were exposed to gravid females for 24 h, and the number of eggs laid as well as larval developmental rates and survival rates of immatures' was determined. Moreover, oviposition and survival rates were recorded for adults obtained from the above three cultivars. Similar experimental procedures were followed using nectarines (Prunus persica), a favourable host for C. capitata. Furthermore, using McPhail‐type traps loaded with food attractants, we compared adult population densities in four kiwifruits and adjacent citrus orchards. Infestation rates were also determined in kiwifruits collected from the above kiwifruit orchards. The results demonstrate that C. capitata, under laboratory conditions, oviposit on all three kiwifruit cultivars tested. The numbers of eggs laid and survival rates of immatures were significantly lower for the two cultivars of A. deliciosa compared with nectarines. On the other hand, oviposition rates were much higher in the cultivar Soreli (A. chinensis) compared with nectarines; however, none of the immatures reached adulthood. Adults obtained from the Hayward and Tsechelidis cultivars had shorter longevity and females were less fecund than those obtained from nectarines. Adult Mediterranean fruit flies were captured in all four kiwifruit orchards, but at significantly lower numbers compared with citrus orchards. Fruit sampling from the Hayward and Tsechelidis cultivars indicated a minimal infestation of the Hayward fruits only (0.41%), which, however, resulted in no adult emergence. Removal of the fruit surface hairs of Hayward cultivar increased dramatically the oviposition rates of C. capitata in laboratory conditions, suggesting significant oviposition‐deterrent properties. The importance of our findings for determining a non‐host status for kiwifruits is discussed.
Morphological and functional events associated to weaning in rabbits
Authors: Bivolarski B. L. , Vachkova E. G.
Published: February 2013

It is acknowledged that the most critical period of rabbit post natal development comprises the first 10–15 days after weaning, when the animals are most susceptible to gastrointestinal infections and at greatest risk of a fatal outcome. Detailed information on rabbits' weaning is provided. The advantages and disadvantages of early weaning (under 23 days of age) are summarised. Regardless of the numerous reports, the effects of early weaning on the growth and development of bunnies and the physiological status of rabbit does are contradictory. The morphological changes in rabbit digestive tract related to weaning – development of intestinal mucosa, height of villi, crypt depth and villus height to crypt depth ratio – are described in detail. The review also goes over several functional changes in rabbits' organism during weaning: blood cholesterol, triglycerides, α‐amylase, lysozyme, complement, triiodothyronine and thyroxine concentrations, and the time course of epidermal growth factor in the milk of lactating does. Based on published research reports, both ours and of other authors, we suggest that from a physiological point of view, the early weaning of rabbits is not fully justified at present. Nevertheless, the increasing market demand for rabbit meat makes early weaning an attractive alternative for farmers and necessitates further studies on the optimisation of weaning in this species.
Rural Considerations in Establishing Network Adequacy Standards for Qualified Health Plans in State and Regional Health Insurance Exchanges
Authors: Talbot Jean A. , Coburn Andrew , Croll Zach , Ziller Erika
Published: February 2013

Purpose

The Affordable Care Act (ACA) requires Health Insurance Exchanges (HIEs) to specify network adequacy standards for the Qualified Health Plans (QHPs) they offer to consumers. This article examines rural issues surrounding network adequacy standards, and offers recommendations for crafting standards that optimize rural access.

Method

This policy analysis reviews ACA requirements for QHP network adequacy standards, considering Medicaid managed care and Medicare Advantage (MA) standards as models. We analyze the implications of stringent vs flexible access standards in terms of how choices might affect health plans' participation in rural markets and rural enrollees' access to care. Finally, we propose strategies for designing standards with the degree of flexibility most likely to benefit rural consumers.

Findings

A traditional approach to safeguarding rural access is to impose strict network adequacy standards on plans in rural areas. However, if strict standards prove difficult to meet due to rural provider scarcity, they might diminish QHPs' willingness to serve rural areas. Thus, they could exacerbate rather than alleviate rural access problems.

Conclusions

To benefit rural communities, network adequacy standards must be strong enough to provide real protections for beneficiaries, yet flexible enough to accommodate rural delivery system constraints and remain attainable for QHPs. Useful strategies to achieve this balance might include: adjusting standards according to degrees of rurality and rural utilization norms; counting midlevel clinicians toward fulfillment of patient‐provider ratios; and allowing plans to ensure rural access through delivery system innovations such as telehealth.
A Chemotactic Model for Interaction of Antagonistic Microflora Colonies: Front Asymptotics and Numerical Simulations
Authors: Málaga C. , Minzoni A. , Plaza R. G. , Simeoni C.
Published: February 2013

This paper studies a two‐dimensional chemotactic model for two species in which one of them produces a chemo‐repellent for the other. It is shown asymptotically and numerically how the chemical inhibits the invasion of a moving front for the second species and how stable steady states, which depend on the chemical concentration, can be reached. The results qualitatively explain experimental observations by Swain and Ray [1] showing that colonies of bacteria produce metabolite agents which prevent the invasion of fungi.
Is All Punishment Local? The Effects of Jurisdictional Context on Sentence Length*
Authors: Chen Elsa Y.
Published: February 2013

Objectives

This article investigates the extent to which contextual and individual factors influence the length of prison sentences in California.

Methods

The analysis applies a hierarchical linear model to individual and county‐level data.

Results

Some characteristics of the racial, organizational, and public safety environments are found to influence the length of prison terms.

Conclusions

The findings support the organizational maintenance perspective and the idea of minority incarceration as a response to a perceived crime threat. Political environment is not found to have a significant effect on sentence lengths, and the findings do not support the racial threat hypothesis. The effects of contextual factors are more modest than those of individual attributes, including legally relevant variables, such as offense severity, prior record, parole status, and three strikes eligibility. African‐American and younger offenders receive longer sentences, but this effect is not found for Latinos. Substantive, methodological, and policy implications are discussed.
Values, Beliefs, Attitudes: An Empirical Study on the Structure of Environmental Concern and Recycling Participation
Authors: Best Henning , Mayerl Jochen
Published: February 2013

Objectives

Empirical studies on environmental behavior have been using a multitude of different operationalizations of environmental concern, which complicates cumulative research. In this article, we empirically explore the dimensionality of four environmental scales of different specificity, their interrelatedness, and their partial contribution to the explanation of recycling behavior. To facilitate the comparison of different studies, we integrate the scales into a hierarchical model.

Methods

In a German mail survey (n= 1,330), we queried participation in household waste recycling, Inglehart's postmaterialism scale, the new environmental paradigm scale, and a general and specific attitude scale. Using traditional path analysis and latent structural equation modeling, we test the hierarchical structure of environmental values, beliefs, and attitudes and their contribution to explaining recycling behavior.

Results

We find direct effects of specific attitudes on behavior, but no direct effects of higher‐level cognitions. Rather, values and primitive beliefs influence general attitudes, which in turn determine specific attitudes. The empirical analyses confirm the proposed hierarchical structure.

Conclusions

Our research reaffirms Ajzen and Fishbein's postulate of correspondence. Comparison of different studies is only meaningful when the hierarchical position of the respective scales is taken into account properly. To facilitate cumulative research, we propose to use standardized general scales such as the NEP in addition to more specific operationalizations.
Ancient Greek Infinitives and Phases
Authors: Sevdali Christina
Published: February 2013

Abstract. This paper is about infinitival clauses and their subjects in Ancient Greek. Ancient Greek has a tripartite paradigm that involves: (a) infinitives with overt accusative subjects (distinct from main‐clause subjects and also coreferential but emphatic), (b) infinitives with null controlled subjects that copy the case of their controller (resulting in the operation of case agreement across copula [CAAC]), and (c) infinitives with null accusative subjects that are referential and arbitrary. To account for this, I first argue that all infinitival clauses are CPs. Arguments for this include the modal distinctions among Ancient Greek infinitival clauses, the coordination of infinitival clauses with finite embedded clauses, the existence of infinitival clauses with overt complementizers, evidence from binding of infinitival subjects as well as enclitic focus particles in Ancient Greek infinitives. Although all infinitives are CPs, I argue that there is a further distinction between strong‐ and weak‐phase CPs, with phasehood being related to features in the left periphery of the clause. Infinitives with overt and null accusative subjects are strong phases, C*Ps, whereas control infinitives are weak phases—CPs that are transparent domains and can therefore allow case agreement to operate across a clause boundary. I also compare Ancient Greek to Latin and argue that the distinction between strong‐ and weak‐phase CPs is also found in the finite domain. The main implication of this proposal is that the availability of a subject is only a property of a clause, defined as a strong‐phase CP.
Aeromechanical Control of High-Speed Axial Compressor Stall and Engine Performance— Part I: Control-Theoretic Models
Authors: McGee O. G. , Coleman K. L.
Published: February 2013

General methodologies are proposed in this two-part paper that further phenomenological understanding of compressible stall inception and aeromechanical control of high-speed axial compressors and engine performance. Developed in Part I are strategies for passive stabilization of compressible rotating stall, using tailored structural design and aeromechanical feedback control, implemented in certain classes of high-speed axial compressors used in research laboratories and by industry. Fundamentals of the stability of various dynamically-compensated, high-speed compressors was set down from linearized, compressible structural-hydrodynamic equations of modal stall inception extended further in this study from previous work. A dimensionless framework for performance-based design of aeromechanically-controlled compression system stall mitigation and engine performance is established, linking specified design flow and work-transfer (pressure) operability to model stages or local blade components, velocity triangle environment, optimum efficiency, extended stall margin and operability loci, and aeromechanical detailed design. A systematic evaluation was made in Part II (Coleman and McGee, 2013, “Aeromechanical Control of High-Speed Axial Compressor Stall and Engine Performance—Part II: Assessments of Methodology,” ASME J. Fluids Eng. (to be published)) on the performance of ten aeromechanical feedback controller schemes to increase the predicted range of stable operation of two laboratory compressor characteristics assumed, using static pressure sensing and local structural actuation to rudimentary postpone high-speed modal stall inception. The maximum flow operating range for each of the ten dynamically-compensated, high-speed compression systems was determined using optimized or “tailored” structural controllers, and the results described in Part II of the companion paper are compared to maximum operating ranges achieved in corresponding low-speed compression systems.
Numerical Simulation for the Motion of the Flexible Floating Collision-Prevention System
Authors: Chen Xu-jun , Huang Guang-yuan , Wu Guang-huai , Tang Xue-feng
Published: February 2013

The flexible floating collision-prevention system (FFSCS) is a valuable floating engineering structure that can be used to prevent the uncontrolled ships to collide with the non-navigational bridge of a large sea-crossing bridge. The system is composed of buoys, block chains, mooring chains and gravity anchors. The deformation of the system under the acting of an uncontrolled ship as well as the movement distance of the gravity anchors are important factors that should be considered by the system designers. Based on the analysis of the relationship between the forces and the deformation of each part of the system, the approximately static equations are solved by a new numerical iterative calculation method. The position changes of the buoys, the movements of the anchors and the history of the inner forces of the block chains when a ship collides with the FFSCS are obtained by iterative calculation. The good agreement between the numerical value and the results of the model test indicate that the small balance method is a validation on the motion response simulation of the FFSCS under the acting of the uncontrolled ship. The results validate that FFSCS can stop the uncontrolled ship before it arrives at the place of the bridge.
Airlift Pump With a Gradually Enlarged Segment in the Riser Tube
Authors: Mahrous A.-F.
Published: February 2013

Airlift pump is a type of deep well pumps. Sometimes, it is used for removing water from mines or pumping slurry of sand and water or other solutions. The performance of airlift pump is affected by two sets of parameters; the geometrical and operational parameters. This work suggests a way to reduce the acceleration loss followed the expansion of air phase in the riser tube of the airlift pump, and consequently minimize transition to annular flow regime that is characterized by poor pumping performance. The method is to gradually enlarge the riser tube at some points after the air injection zone. Enlarging the riser tube can be considered as an alternative way in the cases where increasing airlift tube diameter is restricted by, e.g., the design of air injection system. A numerical model of the airlift pump based on the concept of momentum balance was developed and validated against available experimental data. Parametric predictive studies on model airlift pumps with different riser tube configurations, based on position, degree of expansion ratio and length of tube graduation section, were carried out. The numerical results showed that gradually enlarging the riser tube diameter at a position near the air injection zone would significantly improve the airlift pump discharge rate. Having the enlarged section set at a certain position and increasing the degree of expansion of the gradually enlarged tube section, the predicted results illustrated an improvement in the pump discharge rate but limited by the value of tube expansion ratio. The length of the enlarged tube section is shown not to considerably contribute to the improvement in the pump output rate when gradually enlarging the riser tube.
Cavitation Inception and Head Loss Due to Liquid Flow Through Perforated Plates of Varying Thickness
Authors: Maynes D. , Holt G. J. , Blotter J.
Published: February 2013

This paper reports results of an experimental investigation of the loss coefficient and onset of cavitation caused by water flow through perforated plates of varying thickness and flow area to pipe area ratio at high speeds. The overall plate loss coefficient, point of cavitation inception, and point where critical cavitation occurs are functions of perforation hole size, number of holes, and plate thickness. Sixteen total plates were considered in the study with the total perforation hole area to pipe area ratio ranging from 0.11 and 0.6, the plate thickness to perforation hole diameter ranging from 0.25 to 3.3, and the number of perforation holes ranging from 4 to 1800. The plates were mounted in the test section of a closed water flow loop. The results reveal a complex dependency between the plate loss coefficient with total free-area ratio and the plate thickness to perforation hole diameter ratio. In general, the loss coefficient decreases with increasing free-area ratio and increasing thickness-to-hole diameter ratio. A model based on the data is presented that predicts the loss coefficient for multiholed perforated plates with nonrounded holes. Furthermore, the data show that the cavitation number at the points of cavitation inception and critical cavitation increases with increasing free-area ratio. However, with regard to the thickness-to-hole diameter ratio, the cavitation number at inception exhibits a local maximum at a ratio between 0.5 and 1.0. Empirical models to allow prediction of the point of cavitation inception and the point where critical cavitation begins are presented and compared to single hole orifice plate behavior.
Surface chemistry controlled diameter-modulated semiconductor nanowire superstructures
Authors: Musin Ildar R. , Boyuk Dmitriy S. , Filler Michael A.
Published: February 2013

The authors demonstrate that semiconductor nanowire diameter can be rationally controlled as a function of axial position during vapor–liquid–solid synthesis. Such nanoscale structural tuning is achieved with a “molecular resist,” specifically tetramethyltin, that adsorbs on the nanowire sidewall and restricts radial deposition without destabilizing the growth front. The temporal modulation of tetramethyltin delivery during Ge nanowire growth yields user-programmable diameter-modulated superstructures with sub-100 nm periodicities. The authors also investigate the effect of Sn accumulation in the growth catalyst and propose a second-order kinetic rate law that accurately predicts changes to nanowire axial growth rate.
Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales
Authors: Shanks Orin C. , Newton Ryan J. , Kelty Catherine A. , Huse Susan M. , Sogin Mitchell L. , McLellan Sandra L.
Published: February 2013

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within
Firmicutes
,
Bacteroidetes
,
Actinobacteria
, and
Proteobacteria
. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States.
No Protective Effects of High-Dosage Dietary Zinc Oxide on Weaned Pigs Infected with Salmonella enterica Serovar Typhimurium DT104
Authors: Janczyk Pawel , Kreuzer Susanne , Assmus Jens , Nöckler Karsten , Brockmann Gudrun A.
Published: February 2013

Twenty-eight-day-old weaned pigs were fed diets with a low (LZn), medium (MZn), or high (MZn) Zn concentration (50 to 80, 150, or 2,500 mg Zn/kg of diet, respectively) provided as zinc oxide (ZnO)(24 pigs per group). They were infected orally with
Salmonella enterica
serovar Typhimurium DT104 on day 32. Salmonellae were cultivated from feces (up to 42 days postinfection [dpi]) and organs (2 and 42 dpi). Activation of the adaptive systemic and mucosal immune systems was investigated by recording anti-
Salmonella
IgG levels and levels of B and T lymphocyte subpopulations in blood and gut-associated lymphatic tissue. Growth performance was recorded as well. Salmonellae were shed at higher levels and for longer periods in the HZn group (
P
< 0.05), with no differences in the tissues. At 2 dpi, the relative percentages of CD4
+
T helper cells (
P
< 0.01) and of CD2
+
T and NK cells (
P
< 0.01) in blood were reduced from the relative cell counts obtained at 0 dpi, irrespective of the Zn group. The lowest percentage of cytotoxic T cells was found 14 dpi in the HZn group relative to the MZn (
P
< 0.05) and LZn (
P
< 0.01) groups. Supplementation of the feed with 2,500 mg Zn/kg of diet immediately after weaning could positively affect the immune responses of piglets infected with
Salmonella
Typhimurium, but for a short period only. After 2 weeks, all positive effects disappeared, and rather negative effects, such as higher shedding of salmonellae, lower T cell frequencies, and worse performance, occurred. Thus, supplementation with ZnO at high levels in the pig industry should be limited to 2 to 3 weeks.
Development of a Transferable Bimolecular Fluorescence Complementation System for the Investigation of Interactions between Poly(3-Hydroxybutyrate) Granule-Associated Proteins in Gram-Negative Bacteria
Authors: Pfeiffer Daniel , Jendrossek Dieter
Published: February 2013

Poly(3-hydroxybutyrate) (PHB) granules are organelle-like multienzyme-polymer complexes (carbonosomes) and are widespread storage compounds in prokaryotes. The interaction of three PHB granule-bound proteins (PHB synthase PhaC1, phasin PhaP5, and PHB/DNA binding protein PhaM) was studiedin vivoby bimolecular fluorescence complementation (BiFC) microscopy inRalstonia eutropha. To this end, a mobilizable 2-plasmid system for arabinose-controlled expression of protein fusions with the N-terminal (YN) and C-terminal (YC) parts of the enhanced yellow fluorescent protein (eYfp) in Gram-negative bacteria was developed. Both plasmids were stably expressed inEscherichia coliand in transconjugants ofR. eutropha. Homo-oligomerization of PhaC1, PhaP5, and PhaM and interactions between PhaC1 and PhaM and between PhaM and PhaP5 were detected inR. eutrophaand colocalized with PHB granules under PHB-permissive conditions. PhaM-PhaC1 complexes were detected near the midcell/nucleoid region in the absence of PHB. Expression of BiFC complexes inR. eutrophawith PhaM (PhaM homo-oligomers or PhaM-PhaC1 or PhaM-PhaP5 complexes) resulted in substantial cell elongation compared to wild-type cells and in BiFC signals that were generally located near the midcell/nucleoid region. Western blot analysis of wild-type cell extracts and proteome analysis of PHB granule-bound proteins revealed that PhaM and PhaP5 are expressed inR. eutrophaand that PhaM is constitutively expressed independently of the presence or absence of PHB. Size exclusion chromatography analysis in combination with cross-linking experiments of purified PhaP5-His6and PhaM-His6showed that PhaP5 forms dimers and that PhaM is present in oligomeric (dodecamer) form. Implications of this finding for subcellular PHB localization and initiation of PHB granule formation inR. eutrophawill be discussed.
Roles of Predicted Glycosyltransferases in the Biosynthesis of the Rhizobium etli CE3 O Antigen
Authors: Ojeda Kristylea J. , Simonds Laurie , Noel K. Dale
Published: February 2013

The
Rhizobium etli
CE3 O antigen is a fixed-length heteropolymer. The genetic regions required for its synthesis have been identified, and the nucleotide sequences are known. The structure of the O antigen has been determined, but the roles of specific genes in synthesizing this structure are relatively unclear. Within the known O-antigen genetic clusters of this strain, nine open reading frames (ORFs) were found to contain a conserved glycosyltransferase domain. Each ORF was mutated, and the resulting mutant lipopolysaccharide (LPS) was analyzed. Tricine SDS-PAGE revealed stepwise truncations of the O antigen that were consistent with differences in mutant LPS sugar compositions and reactivity with O-antigen-specific monoclonal antibodies. Based on these results and current theories of O-antigen synthesis, specific roles were deduced for each of the nine glycosyltransferases, and a model for biosynthesis of the
R. etli
CE3 O antigen was proposed. In this model, O-antigen biosynthesis is initiated with the addition of
N
-acetyl-quinovosamine-phosphate (QuiNAc-P) to bactoprenol-phosphate by glycosyltransferase WreU. Glycosyltransferases WreG, WreE, WreS, and WreT would each act once to attach mannose, fucose, a second fucose, and 3-
O
-methyl-6-deoxytalose (3OMe6dTal), respectively. WreH would then catalyze the addition of methyl glucuronate (MeGlcA) to complete the first instance of the O-antigen repeat unit. Four subsequent repeats of this unit composed of fucose, 3OMe6dTal, and MeGlcA would be assembled by a cycle of reactions catalyzed by two additional glycosyltransferases, WreM and WreL, along with WreH. Finally, the O antigen would be capped by attachment of di- or tri-
O
-methylated fucose as catalyzed by glycosyltransferase WreB.
Requirement of the Lipopolysaccharide O-Chain Biosynthesis Gene
wxocB
for Type III Secretion and Virulence of Xanthomonas oryzae pv. Oryzicola
Authors: Wang Li , Vinogradov Evgeny V. , Bogdanove Adam J.
Published: February 2013

Xanthomonas oryzae
pv. oryzicola causes bacterial leaf streak of rice. A mutant disrupted in
wxocB
, predicted to encode an enzyme for lipopolysaccharide (LPS) synthesis, was previously shown to suffer reduced virulence. Here, we confirm a role for
wxocB
in virulence and demonstrate its requirement for LPS O-chain assembly. Structure analysis indicated that wild-type LPS contains a polyrhamnose O chain with irregular, variant residues and a core oligosaccharide identical to that of other
Xanthomonas
spp. and that the
wxocB
mutant lacks the O chain. The mutant also showed moderate impairment in exopolysaccharide (EPS) production, but comparison with an EPS-deficient mutant demonstrated that this impairment could not account entirely for the reduced virulence. The
wxocB
mutant was not detectably different from the wild type in its induction of pathogenesis-related rice genes, type II secretion competence, flagellar motility, or resistance to two phytoalexins or resveratrol, and it was more, not less, resistant to oxidative stress and a third phytoalexin, indicating that none of these properties is involved. The mutant was more sensitive to SDS and to novobiocin, so increased sensitivity to some host-derived antimicrobials cannot be ruled out. However, the mutant showed a marked decrease in type III secretion into plant cells. This was not associated with any change in expression of genes for type III secretion or the ability to attach to plant cells in suspension. Thus, virulence of the
wxocB
mutant is likely reduced due primarily to a direct, possibly structural, effect of the loss of the O chain on type III delivery of effector proteins.