bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization models for biorefinery supply chain network design under uncertainty
Authors: Kazemzadeh Narges , Hu Guiping
Published: September 2013

Biofuel industry has attracted much attention due to its potential to reduce dependency on fossil fuels and contribute to the renewable energy. The high levels of uncertainty in feedstock yield, market prices, production costs, and many other parameters are among the major challenges in this industry. This challenge has created an ongoing interest on studies considering different aspects of uncertainty in investment decisions of the biofuel industry. This study aims to determine the optimal design of supply chain for biofuel refineries in order to maximize annual profit considering uncertainties in fuel market price, feedstock yield, and logistic costs. In order to deal with the stochastic nature of parameters in the biofuel supply chain, we develop two-stage stochastic programming models in which Conditional Value at Risk (CVaR) is utilized as a risk measure to control the amount of shortage in demand zones. Two different approaches including the expected value and CVaR of the profit are considered as the objective function. We apply these models and compare the results for a case study of the biomass supply chain network in the state of Iowa to demonstrate the applicability and efficiency of the presented models.
Experimental research on oxygen-enriched gasification of straw in an entrained-flow gasifier
Authors: Yu Haimiao , Li Zeshen , Yang Xianyu , Jiang Linhong , Zhang Ze , Chen Dezhen
Published: September 2013

Biomass (straw) gasification with oxygen-enriched air was studied in a lab-scale entrained-flow gasifier. Effects of oxygen concentration (OC), equivalence ratio (ER), and reactor temperature on the produced gas composition, gasification index and tar yield were investigated. Compared with air, oxygen-enriched air as gasifying agent was beneficial to increase the H2 content, H2/CO ratio, and lower heating value (LHV) of the gas, and decrease the yield of tar contained in the flue gas. The H2/CO reached 1 when OC was 50%, which was an optimal value for dimethyl ether, methanol, and higher alcohol production in the process of alcohols synthesis. A reference value of OC was given approximately to 40% according to economic consideration. A reference value of ER was given around 0.25 when OC was 40%, achieved a relatively high LHV of 8.2 MJ/Nm3 and low tar yield of 2.6 mg/g. In addition, high reaction temperature could improve both gas quality and gasification indexes significantly. The better gasification performance achieved in the paper verified that the oxygen-enriched gasification was a good option for the improvement of direct air gasification.
Satellite/spray suppression in electrohydrodynamic printing with a gated head
Authors: Lee Sukhan , An Kichul , Son Sanguk , Choi Jaeyong
Published: September 2013

During electro-hydrodynamic printing, part of discharged jets may be broken into tiny satellites/sprays, making patterns scattered. This paper presents a method of suppressing these satellites/sprays based on a ring-shaped gate electrode placed in between nozzle and substrate. We discover, by simulation and experimentation, that the maximum satellite/spray suppression can be achieved when the diameter of gate hole and the distance from nozzle to gate are, respectively, about 5, and 2.5 times the outer diameter of nozzle and when the gate voltage applied has a waveform of a negative and positive pulse pair mixed with a fixed gate bias.
The Scale of Scatter: Rethinking Social Topologies via the Anthropology of ‘Residual’ China
Authors: Vasantkumar Chris
Published: September 2013

After the ‘Bamboo Curtain’ closed China to foreign social scientists in 1949, anthropologists shifted their attention to those ‘residues’ of China beyond the control of the People's Republic. In the process, formerly heterodox and out-of-the-way locales such as Taiwan and the New Territories of Hong Kong were made into the exemplars par excellence of Chinese culture. In this paper I argue that the peculiar spatialities of this Cold-War-era anthropology of ‘residual China’ have potentially generative consequences for a rethinking of the after-actor-network-theory (aANT) focus on social topologies. In particular, these spatialities' simultaneous enactment of the presence and absence of Chineseness evinces parallels with and prompts revisions to the notion of a “fire topology”. These revisions in turn suggest the necessity of inventing novel topological models for (more-than-) human realities in order to work against both the creeping naturalization of after-actor-network-theory analytic frames in particular and the routinization of theory more broadly.
A Mild and Convenient Synthesis of 1,2,3-Triiodoarenes via Consecutive Iodination/Diazotization/Iodination Strategy
Authors: Al-Zoubi Raed M. , Futouh Hassan Abul , McDonald Robert
Published: September 2013

A mild and convenient synthesis of 1,2,3-triiodoarenes has been developed. This method consists of two steps which can be performed on multigram scale with moderate to excellent yields. This report discloses a practical synthesis of 1,2,3-triiodoarenes and 1,2,3-trihaloarenes that is general in scope, operationally simple, scalable, and is easy to workup and to purify. We also report the first regioselective transmetalation reaction of 1,2,3-triiodoarenes to provide ortho-diiodoaryl derivatives, which are useful building blocks and indeed are hard to make by other means.
Irx3 and Pax6 establish differential competence for Shh-mediated induction of GABAergic and glutamatergic neurons of the thalamus
Authors: Robertshaw Ellen , Matsumoto Ken , Lumsden Andrew , Kiecker Clemens
Published: September 2013

Significance

Classic embryological studies suggested that small groups of cells called organizers change the fate of neighboring tissues through inductive processes. In these studies it was also postulated that the receiving tissue has to be “competent” to respond to the inducer in a specific way. In the posterior forebrain, the signaling factor Sonic hedgehog is released from an organizer called the zona limitans intrathalamica and induces GABAergic and glutamatergic neurons of the thalamus. Here we demonstrate that the differential expression of two transcription factors, Irx3 and Pax6, spatially limits the area of competence for these inductions.
Relationship between dynamical entropy and energy dissipation far from thermodynamic equilibrium
Authors: Green Jason R. , Costa Anthony B. , Grzybowski Bartosz A. , Szleifer Igal
Published: September 2013

Significance

The dissipation of energy occurs naturally in systems as diverse as those in biology and as common as those responsible for the weather. Systems that dissipate energy while self-assembling also show promise as a synthetic route to responsive nanoscale materials. Optimizing the energy efficiency of these syntheses requires reducing the theoretical description to only those variables that are essential to an accurate prediction of the energy lost as heat. Here, with computer simulations and a model of assembly, we establish a methodology for identifying those essential variables. With this minimal description of the system we also find a linear relationship between the dynamical entropy of the self-assembling system and the energy dissipated as heat during assembly.
Unraveling the role of protein dynamics in dihydrofolate reductase catalysis
Authors: Luk Louis Y. P. , Javier Ruiz-Pernía J. , Dawson William M. , Roca Maite , Loveridge E. Joel , Glowacki David R. , Harvey Jeremy N. , Mulholland Adrian J. , Tuñón Iñaki , Moliner Vicent , Allemann Rudolf K.
Published: September 2013

Significance

The role of protein dynamics in enzyme catalysis remains a topic of considerable debate. Here, we use a combination of experimental and computational methods to identify the origins of the observed changes in reactivity on isotopic substitution of dihydrofolate reductase fromEscherichia coli. Isotopic substitution causes differences in environmental coupling to the hydride transfer step and protein dynamics have therefore a small but measurable effect on the chemical reaction rate.
Size homeostasis in adherent cells studied by synthetic phase microscopy
Authors: Sung Yongjin , Tzur Amit , Oh Seungeun , Choi Wonshik , Li Victor , Dasari Ramachandra R. , Yaqoob Zahid , Kirschner Marc W.
Published: September 2013

Significance

Accurate measurement of cell size is critical in studies of cell growth. Optical methods based on interferometry are known to be suitable for attached cells, but the existing techniques were originally designed for thin samples and are not ideal for thick ones, such as mitotic cells. Synthetic phase microscopy (SPM), a new tomographic interferometric method, offers an elegant solution to this problem. This paper demonstrates the ability of SPM to measure the growth of mammalian cells accurately, and it demonstrates a clear requirement for feedback in the growth process.
Sensitivity-enhanced solid-state NMR detection of expansin’s target in plant cell walls
Authors: Wang Tuo , Park Yong Bum , Caporini Marc A. , Rosay Melanie , Zhong Linghao , Cosgrove Daniel J. , Hong Mei
Published: September 2013

Significance

The protein expansin loosens the cell walls of plants for cell growth, but its carbohydrate target of binding has been elusive because of the difficulty of studying the noncrystalline plant cell wall by most structural biology techniques and the trace amount of expansin needed for wall loosening. We have now combined dynamic nuclear polarization sensitivity-enhanced solid-state NMR spectroscopy with
13
C labeling of
Arabidopsis thaliana
plants and
13
C,
15
N labeling of expansin, to determine that expansin binds cellulose microfibrils to loosen the plant cell wall. The expansin binding site is enriched in the hemicellulose xyloglucan and has a different cellulose structure from bulk cellulose, shedding light on the mechanism of wall loosening.
1. Should ideologies be ill-reputed?
Authors: Freeden Michael
Published: September 2013

Ideology is a word that evokes strong emotional responses. ‘Should ideologies be ill-reputed’ examines how ideologies are perceived. For many, ideologies are associated with -isms, such as communism, fascism, or anarchism. Ideology is viewed with suspicion and ‘ism’ as a faintly derogatory term. However, ideologies offer competing interpretations of events and seek to impose a pattern on them. The influence of Karl Marx and Friedrich Engels in shaping and developing the concept of ideology is examined in more detail. Particularly the way in which they linked class and ideology, and how their ideas have influenced non-Marxists.
2. Overcoming illusions: how ideologies came to stay
Authors: Freeden Michael
Published: September 2013

The emergence of the concept of ideology from under the Marxist wing is a complex story. ‘Overcoming illusions: how ideologies came to stay’ traces this story and in particular the contributions of three 20th-century thinkers: Karl Mannheim, Antonio Gramsci, and Louis Althusser. Each of them, in their own way, operating from Marxist premises, contributed to the transformation of the conception of ideology. Their key insights led to the removal of much of the pejorative connotations of ideology and ensured that it became a permanent feature of the political and social landscape.
1. Inventing the Presidency
Authors: Jones Charles O.
Published: September 2013

The creative work involved in writing the Constitution of the United States in Philadelphia in 1787 has been interpreted and analysed in political and policy debate ever since. ‘Inventing the Presidency’ considers how the Founders of the United States tried to create unity in a separated system. Why was the title of president selected? What was the role of president going to look like? How long should the single executive serve? Should the person be term-limited? Providing a legislative or law-making role for the president was the subject of considerable debate at the beginning. Inventors solve problems: they tinker until they have a workable device. The creation of the presidency was a process of trial and error.
5. Connecting to and Leading the Government
Authors: Jones Charles O.
Published: September 2013

The Founders were aware of the need for leadership but wary of the ease of control. Presidents face challenges as they endeavor to meet expectations of leadership beyond given powers. ‘Connecting to and Leading the Government’ shows how the presidency manages the organizations and expenditure of government, a task that has grown in complexity and intensity over time. To whom or what must presidents connect? The federal government is intricately connected to governance in the fifty states and thousands of localities. Bureaucrats learn to serve presidents and their associates. The challenge for presidents is to take advantage of bureaucratic experience in formulating and promoting their programs.
6. Presidents at Work: Making Law and Doing Policy
Authors: Jones Charles O.
Published: September 2013

How powerful ought the president to be? The role of president is one of decision maker. They have to balance what is expected with what can be delivered. The Founders ensure that making decisions was to be a joint enterprise. ‘Presidents at Work: Making Law and Doing Policy’ considers how this joint enterprise works: Congress can pass bills, the president signs them into law; presidents negotiate treaties, but two-thirds of the Senate must approve; the Supreme Court can negotiate a law, but Congress and the president can achieve their purpose by enacting a law that avoids the issue raised by the Court. Despite all this, the president is held accountable for what happens in government.
Contemporary Fiction
Authors: Eaglestone Robert
Published: September 2013

Contemporary Fiction: A Very Short Introduction explores a wide and diverse field, now global in dimension, with an enormous range of novels and writers that continues to grow at a fantastic speed. This VSI provides an exploration of the major themes, patterns, and debates of contemporary fiction. From genre, form, and experimentalism to the legacies of modernism and postmodernism, the relationship between globalization and terrorism, and the impact of technology, it examines how works both reflect the world in which we live and the artistic concerns of writers and readers alike.
Methods and challenges in timing chromosomal abnormalities within cancer samples
Authors: Purdom Elizabeth , Ho Christine , Grasso Catherine S. , Quist Michael J. , Cho Raymond J. , Spellman Paul
Published: September 2013

Motivation: Tumors acquire many chromosomal amplifications, and those acquired early in the lifespan of the tumor may be not only important for tumor growth but also can be used for diagnostic purposes. Many methods infer the order of the accumulation of abnormalities based on their occurrence in a large cohort of patients. Recently, Durinck et al. (2011) and Greenman et al. (2012) developed methods to order a single tumor’s chromosomal amplifications based on the patterns of mutations accumulated within those regions. This method offers an unprecedented opportunity to assess the etiology of a single tumor sample, but has not been widely evaluated.

Results: We show that the model for timing chromosomal amplifications is limited in scope, particularly for regions with high levels of amplification. We also show that the estimation of the order of events can be sensitive for events that occur early in the progression of the tumor and that the partial maximum likelihood method of Greenman et al. (2012) can give biased estimates, particularly for moderate read coverage or normal contamination. We propose a maximum-likelihood estimation procedure that fully accounts for sequencing variability and show that it outperforms the partial maximum-likelihood estimation method. We also propose a Bayesian estimation procedure that stabilizes the estimates in certain settings. We implement these methods on a small number of ovarian tumors, and the results suggest possible differences in how the tumors acquired amplifications.

Availability and implementation: We provide implementation of these methods in an R package cancerTiming, which is available from the Comprehensive R Archive Network (CRAN) at http://CRAN.R-project.org/.

Contact:  epurdom@stat.Berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
BioServices: a common Python package to access biological Web Services programmatically
Authors: Cokelaer Thomas , Pultz Dennis , Harder Lea M. , Serra-Musach Jordi , Saez-Rodriguez Julio
Published: September 2013

Motivation: Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework.

Results: BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming.

Availability and implementation: BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.

Contact:  cokelaer@ebi.ac.uk or bioservices@googlegroups.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles
Authors: Zou Lingyun , Nan Chonghan , Hu Fuquan
Published: September 2013

Motivation: Various human pathogens secret effector proteins into hosts cells via the type IV secretion system (T4SS). These proteins play important roles in the interaction between bacteria and hosts. Computational methods for T4SS effector prediction have been developed for screening experimental targets in several isolated bacterial species; however, widely applicable prediction approaches are still unavailable

Results: In this work, four types of distinctive features, namely, amino acid composition, dipeptide composition, .position-specific scoring matrix composition and auto covariance transformation of position-specific scoring matrix, were calculated from primary sequences. A classifier, T4EffPred, was developed using the support vector machine with these features and their different combinations for effector prediction. Various theoretical tests were performed in a newly established dataset, and the results were measured with four indexes. We demonstrated that T4EffPred can discriminate IVA and IVB effectors in benchmark datasets with positive rates of 76.7% and 89.7%, respectively. The overall accuracy of 95.9% shows that the present method is accurate for distinguishing the T4SS effector in unidentified sequences. A classifier ensemble was designed to synthesize all single classifiers. Notable performance improvement was observed using this ensemble system in benchmark tests. To demonstrate the model’s application, a genome-scale prediction of effectors was performed in Bartonella henselae, an important zoonotic pathogen. A number of putative candidates were distinguished.

Availability: A web server implementing the prediction method and the source code are both available at http://bioinfo.tmmu.edu.cn/T4EffPred.

Contact:  hoofuquan@yahoo.com.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Open-ended song learning in a hummingbird
Authors: Araya-Salas Marcelo , Wright Timothy
Published: September 2013

Vocal learning in birds is typically restricted to a sensitive period early in life, with the few exceptions reported in songbirds and parrots. Here, we present evidence of open-ended vocal learning in a hummingbird, the third avian group with vocal learning. We studied vocalizations at four leks of the long-billed hermit
Phaethornis longirostris
during a four-year period. Individuals produce a single song repertoire, although several song-types can coexist at a single lek. We found that nine of 49 birds recorded on multiple days (18%) changed their song-type between consecutive recordings. Three of these birds replaced song-types twice. Moreover, the earliest estimated age when song replacement occurred ranged from 186 to 547 days (mean = 307 days) and all nine birds who replaced song-types produced a crystallized song before replacement. The findings indicate that song-type replacement is distinct from an initial early learning sensitive period. As half of lekking males do not survive past the first year of life in this species, song learning may well extend throughout the lifespan. This behaviour would be convergent to vocal learning programmes found in parrots and songbirds.
The quest for stiff, strong and tough hybrid materials: an exhaustive exploration
Authors: Barthelat F. , Mirkhalaf M.
Published: September 2013

How to arrange soft materials with strong but brittle reinforcements to achieve attractive combinations of stiffness, strength and toughness is an ongoing and fascinating question in engineering and biological materials science. Recent advances in topology optimization and bioinspiration have brought interesting answers to this question, but they provide only small windows into the vast design space associated with this problem. Here, we take a more global approach in which we assess the mechanical performance of thousands of possible microstructures. This exhaustive exploration gives a global picture of structure–property relationships and guarantees that global optima can be found. Landscapes of optimum solutions for different combinations of desired properties can also be created, revealing the robustness of each of the solutions. Interestingly, while some of the major hybrid designs used in engineering are absent from the set of solutions, the microstructures emerging from this process are reminiscent of materials, such as bone, nacre or spider silk.
Effective viscosity of puller-like microswimmers: a renormalization approach
Authors: Gluzman Simon , Karpeev Dmitry A. , Berlyand Leonid V.
Published: September 2013

Effective viscosity (EV) of suspensions of puller-like microswimmers (pullers), for example
Chlamydamonas
algae, is difficult to measure or simulate for all swimmer concentrations. Although there are good reasons to expect that the EV of pullers is similar to that of passive suspensions, analytical determination of the passive EV for all concentrations remains unsatisfactory. At the same time, the EV of bacterial suspensions is closely linked to collective motion in these systems and is biologically significant. We develop an approach for determining analytical EV estimates at all concentrations for suspensions of pullers as well as for passive suspensions. The proposed methods are based on the ideas of renormalization group (RG) theory and construct the EV formula based on the known asymptotics for small concentrations and near the critical point (i.e. approaching dense packing). For passive suspensions, the method is verified by comparison against known theoretical results. We find that the method performs much better than an earlier RG-based technique. For pullers, the validation is done by comparing them to experiments conducted on
Chlamydamonas
suspensions.
A heuristic model on the role of plasticity in adaptive evolution: plasticity increases adaptation, population viability and genetic variation
Authors: Gomez-Mestre Ivan , Jovani Roger
Published: September 2013

An ongoing new synthesis in evolutionary theory is expanding our view of the sources of heritable variation beyond point mutations of fixed phenotypic effects to include environmentally sensitive changes in gene regulation. This expansion of the paradigm is necessary given ample evidence for a heritable ability to alter gene expression in response to environmental cues. In consequence, single genotypes are often capable of adaptively expressing different phenotypes in different environments, i.e. are adaptively plastic. We present an individual-based heuristic model to compare the adaptive dynamics of populations composed of plastic or non-plastic genotypes under a wide range of scenarios where we modify environmental variation, mutation rate and costs of plasticity. The model shows that adaptive plasticity contributes to the maintenance of genetic variation within populations, reduces bottlenecks when facing rapid environmental changes and confers an overall faster rate of adaptation. In fluctuating environments, plasticity is favoured by selection and maintained in the population. However, if the environment stabilizes and costs of plasticity are high, plasticity is reduced by selection, leading to genetic assimilation, which could result in species diversification. More broadly, our model shows that adaptive plasticity is a common consequence of selection under environmental heterogeneity, and hence a potentially common phenomenon in nature. Thus, taking adaptive plasticity into account substantially extends our view of adaptive evolution.
Drifting behaviour as an alternative reproductive strategy for social insect workers
Authors: Blacher Pierre , Yagound Boris , Lecoutey Emmanuel , Devienne Paul , Chameron Stéphane , Châline Nicolas
Published: September 2013

Restricted reproduction is traditionally posited as the defining feature of eusocial insect workers. The discovery of worker reproduction in foreign colonies challenges this view and suggests that workers’ potential to pursue selfish interests may be higher than previously believed. However, whether such reproductive behaviour truly relies on a reproductive decision is still unknown. Workers’ reproductive decisions thus need to be investigated to assess the extent of workers’ reproductive options. Here, we show in the bumblebee
Bombus terrestris
that drifting is a distinct strategy by which fertile workers circumvent competition in their nest and reproduce in foreign colonies. By monitoring workers’ movements between colonies, we show that drifting is a remarkably dynamic behaviour, widely expressed by both fertile and infertile workers. We demonstrate that a high fertility is, however, central in determining the propensity of workers to enter foreign colonies as well as their subsequent reproduction in host colonies. Moreover, our study shows that the drifting of fertile workers reflects complex decision-making processes associated with in-nest reproductive competition. This novel finding therefore adds to our modern conception of cooperation by showing the previously overlooked importance of alternative strategies which enable workers to assert their reproductive interests.
Genetic composition of social groups influences male aggressive behaviour and fitness in natural genotypes ofDrosophila melanogaster
Authors: Saltz Julia B.
Published: September 2013

Indirect genetic effects (IGEs) describe how an individual's behaviour—which is influenced by his or her genotype—can affect the behaviours of interacting individuals. IGE research has focused on dyads. However, insights from social networks research, and other studies of group behaviour, suggest that dyadic interactions are affected by the behaviour of other individuals in the group. To extend IGE inferences to groups of three or more, IGEs must be considered from a group perspective. Here, I introduce the ‘focal interaction’ approach to study IGEs in groups. I illustrate the utility of this approach by studying aggression among natural genotypes ofDrosophila melanogaster.I chose two natural genotypes as ‘focal interactants’: the behavioural interaction between them was the ‘focal interaction’. One male from each focal interactant genotype was present in every group, and I varied the genotype of the third male—the ‘treatment male’. Genetic variation in the treatment male's aggressive behaviour influenced the focal interaction, demonstrating that IGEs in groups are not a straightforward extension of IGEs measured in dyads. Further, the focal interaction influenced male mating success, illustrating the role of IGEs in behavioural evolution. These results represent the first manipulative evidence for IGEs at the group level.
Sustainable, efficient livestock production with high biodiversity and good welfare for animals
Authors: Broom D. M. , Galindo F. A. , Murgueitio E.
Published: September 2013

What is the future for livestock agriculture in the world? Consumers have concerns about sustainability but many widely used livestock production methods do not satisfy consumers' requirements for a sustainable system. However, production can be sustainable, occurring in environments that: supply the needs of the animals resulting in good welfare, allow coexistence with a wide diversity of organisms native to the area, minimize carbon footprint and provide a fair lifestyle for the people working there. Conservation need not just involve tiny islands of natural vegetation in a barren world of agriculture, as there can be great increases in biodiversity in farmed areas. Herbivores, especially ruminants that consume materials inedible by humans, are important for human food in the future. However, their diet should not be just ground-level plants. Silvopastoral systems, pastures with shrubs and trees as well as herbage, are described which are normally more productive than pasture alone. When compared with widely used livestock production systems, silvopastoral systems can provide efficient feed conversion, higher biodiversity, enhanced connectivity between habitat patches and better animal welfare, so they can replace existing systems in many parts of the world and should be further developed.
Cathepsin C is a tissue-specific regulator of squamous carcinogenesis
Authors: Ruffell Brian , Affara Nesrine I. , Cottone Lucia , Junankar Simon , Johansson Magnus , DeNardo David G. , Korets Lidiya , Reinheckel Thomas , Sloane Bonnie F. , Bogyo Mathew , Coussens Lisa M.
Published: September 2013

Serine and cysteine cathepsin (Cts) proteases are an important class of intracellular and pericellular enzymes mediating multiple aspects of tumor development. Emblematic of these is CtsB, reported to play functionally significant roles during pancreatic islet and mammary carcinogenesis. CtsC, on the other hand, while up-regulated during pancreatic islet carcinogenesis, lacks functional significance in mediating neoplastic progression in that organ. Given that protein expression and enzymatic activity of both CtsB and CtsC are increased in numerous tumors, we sought to understand how tissue specificity might factor into their functional significance. Thus, whereas others have reported that CtsB regulates metastasis of mammary carcinomas, we found that development of squamous carcinomas occurs independently of CtsB. In contrast to these findings, our studies found no significant role for CtsC during mammary carcinogenesis but revealed squamous carcinogenesis to be functionally dependent on CtsC. In this context, dermal/stromal fibroblasts and bone marrow-derived cells expressed increased levels of enzymatically active CtsC that regulated the complexity of infiltrating immune cells in neoplastic skin, development of angiogenic vasculature, and overt squamous cell carcinoma growth. These studies highlight the important contribution of tissue/microenvironment context to solid tumor development and indicate that tissue specificity defines functional significance for these two members of the cysteine protease family.
Increasing the complexity: new genes and new types of albinism
Authors: Montoliu Lluís , Grønskov Karen , Wei Ai‐Hua , Martínez‐García Mónica , Fernández Almudena , Arveiler Benoît , Morice‐Picard Fanny , Riazuddin Saima , Suzuki Tamio , Ahmed Zubair M. , Rosenberg Thomas , Li Wei
Published: September 2013

Albinism is a rare genetic condition globally characterized by a number of specific deficits in the visual system, resulting in poor vision, in association with a variable hypopigmentation phenotype. This lack or reduction in pigment might affect the eyes, skin, and hair (oculocutaneous albinism, OCA), or only the eyes (ocular albinism, OA). In addition, there are several syndromic forms of albinism (e.g. Hermansky–Pudlak and Chediak–Higashi syndromes, HPS and CHS, respectively) in which the described hypopigmented and visual phenotypes coexist with more severe pathological alterations. Recently, a locus has been mapped to the 4q24 human chromosomal region and thus represents an additional genetic cause of OCA, termed OCA5, while the gene is eventually identified. In addition, two new genes have been identified as causing OCA when mutated: SLC24A5 and C10orf11, and hence designated as OCA6 and OCA7, respectively. This consensus review, involving all laboratories that have reported these new genes, aims to update and agree upon the current gene nomenclature and types of albinism, while providing additional insights from the function of these new genes in pigment cells.
Quality of Life and Mental Health Related to Timing, Frequency and Dose of Hemodialysis
Authors: Cohen Scott D. , Kimmel Paul L.
Published: September 2013

The perceived quality of life (QOL) and mental health of dialysis patients can have a significant impact on clinical outcomes in the end‐stage renal disease (ESRD) population. There is growing interest in increasing dialysis frequency, dose and duration to achieve more adequate dialysis clearance, particularly of middle molecules. Over the past decade, there has been an interest in earlier initiation of dialysis; however, the results of the IDEAL study call this practice into question, and showed no difference in QOL scores between the early‐start and later start dialysis patients. There are inconsistent results regarding the impact of increased dialysis frequency and dose on patients' perceived health‐related QOL (HRQOL). Some studies of daily nocturnal dialysis patients show a positive impact on QOL, while others show no significant difference. The disparate outcomes may be partly related to differences in the demographic characteristics of the study populations and the specific questionnaires used to measure HRQOL. Additional research is necessary to determine whether changes in dialysis frequency, timing, and dose can positively or negatively impact patients' perceptions of their QOL and mental health.
A Global Approach to Turbomachinery Flow Control: Passage Vortex Control
Authors: Bloxham Matthew J. , Bons Jeffrey P.
Published: September 2013

A flow control scheme was implemented in a low-pressure turbine cascade that simultaneously mitigated profile and endwall losses using midspan vortex generator jets (VGJs) and endwall suction. The combined system had an approximate zero-net mass flux. During the design, a theoretical model was used that effectively predicted the trajectory of the passage vortex using inviscid results obtained from two-dimensional computational fluid dynamics (CFD). The model was used in the design of two flow control approaches: the removal and redirection approaches. The emphasis of the removal approach was the direct application of flow control along the passage vortex (PV) trajectory. The redirection approach attempted to alter the trajectory of the PV with the judicious placement of suction holes. A potential flow model was created to aid in the design of the redirection approach. The model results were validated using flow visualization and particle image velocimetry (PIV) in a linear turbine cascade. Detailed total pressure loss wake surveys were measured while matching the suction and VGJ mass flow rates for the removal and redirection approaches at ReCx = 25,000 and blowing ratio, B, of 2. When compared with the no control results, the addition of VGJs and endwall suction reduced the wake losses by 69% (removal) and 68% (redirection). The majority of the total pressure loss reduction resulted from the spanwise VGJs, while the suction schemes provided modest additional reductions (<2%). At ReCx = 50,000, the endwall control effectiveness was assessed for a range of suction rates without midspan VGJs. Area-averaged total pressure loss reductions of up to 28% were measured in the wake at ReCx = 50,000, B = 0, with applied endwall suction (compared to no suction at ReCx = 50,000), at which point the loss core of the PV was almost completely eliminated.
Application of Flow Control in a Novel Sector Test Rig
Authors: Simpson Alexander , Aalburg Christian , Schmitz Michael B. , Pannekeet Robbert , Michelassi Vittorio , Larisch Florian
Published: September 2013

An experimental and numerical study has been performed to evaluate the effectiveness of steady injection flow control for the reduction of losses in the return channel of a radial compressor. This investigation formed part of an overall attempt to develop a strategy for reducing the diffusion ratio of radial compressors. It is envisaged that this flow control would be activated at off-design conditions, where separation levels on the return channel vanes are considerable. A novel radial compressor sector test rig, supported by a blow-down facility and equipped with a range of instrumentation, was used for the experimental portion of the study. This allowed multiple flow control configurations to be studied in a simplified environment. A set of exchangeable, inlet guide vanes provide the test vanes with the correct inlet three-dimensional flow-field, while airfoil static pressure taps allowed the blade loading to be assessed. The numerical portion of the study was conducted using 3D-computational fluid dynamics (CFD) and involved simulations of both the sector test rig and a “substitute system”. In this paper, the rationale for the inclusion of flow control in a radial compressor return channel is discussed. The sector test rig is then described, including the implementation of flow control. The results of the matrix of flow control experiments are then discussed with comparison to the numerical results.
Influence of Purge Flow Injection Angle on the Aerothermal Performance of a Rotor Blade Cascade
Authors: Barigozzi G. , Franchini G. , Perdichizzi A. , Maritano M. , Abram R.
Published: September 2013

This paper is focused on the influence of stator-rotor purge flow injection angle on the aerodynamic and thermal performance of a rotor blade cascade. Tests were performed in a seven-blade cascade of a high-pressure gas turbine rotor at low Mach number (Ma2is = 0.3) under different blowing conditions. A number of fins were installed inside the upstream slot to simulate the effect of rotation on the seal flow exiting the gap in a linear cascade environment. The resulting coolant flow is ejected with the correct angle in the tangential direction. Purge flow injection angle and blowing conditions were changed in order to identify the best configuration in terms of end wall thermal protection and secondary flows reduction. The 3D flow field was surveyed by traversing a five-hole miniaturized pressure probe in a downstream plane. Secondary flow velocities, loss coefficient, and vorticity distributions are presented for the most significant test conditions. Film cooling effectiveness distributions on the platform were obtained by thermochromic liquid crystals (TLC) technique. Results show that purge flow injection angle has an impact on secondary flows development and, thus, on the end wall thermal protection, especially at high injection rates. Passage vortex is enhanced by a negative injection angle, which simulates the real counter rotating purge flow direction.
Small Wind Turbines in the Built Environment: Influence of Flow Inclination on the Potential Energy Yield
Authors: Bianchi Serena , Bianchini Alessandro , Ferrara Giovanni , Ferrari Lorenzo
Published: September 2013

Increasing interest is being paid by architects, project developers and local governments to understanding where small wind turbines can effectively be exploited to provide delocalized power in the built environment. The wind conditions in the rooftop area of buildings in urban locations are, however, very complex and the real adaptability of wind turbines to these environments is not yet tested both in terms of real producibility and of structural compatibility with the building themselves. In these installations, in particular, the flow that incomes on the rotor is often inclined with respect to the horizontal direction due to the interaction with the building façade and the roof. A correct estimation of the impact of an inclined flow on the performance of horizontal-axis wind turbines, therefore, becomes a very relevant issue to correctly predict the potential energy yield of a machine. To this purpose, a simulation code based on a blade element momentum (BEM) approach was developed and validated by means of experimental data found in the literature. The code was then used to evaluate the energetic suitability of a small-size wind turbine installation in the rooftop of a building in a conventional European city. A numerical computational fluid dynamics (CFD) analysis was carried out to characterize the flow field in the rooftop area of different buildings. The flow velocity modulus and direction were calculated for several oncoming wind profiles: The results were projected into an available wind power curve in the rooftop of the building. The effective energy-yield capabilities were then corrected using the model for the flow inclination as a function of the specific flow conditions in the rooftop area. The results were finally exploited to analyze the energy-oriented feasibility of an installation in a similar context.
Time-Action Analysis of Catheter Manipulation During Navigation Tasks in Bifurcations
Authors: Clogenson H. C. M. , Dankelman J. , van den Dobbelsteen J. J.
Published: September 2013

Endovascular intervention is a form of minimally invasive intervention that allows catheters to be placed in practically any location of the vascular tree. However, to provide access to all these remote locations, an extensive array of catheters is needed. A specific catheter is choose based on experience, without any objective indication of its suitability during the actual procedure (Bakker, N. H., Tanase, D., Reekers, J. A., and Grimbergen, C. A., 2002, “Evaluation of Vascular and Interventional Procedures with Time—Action Analysis: A Pilot Study,” J. Vasc. Intervent. Radiol., 13(5), pp. 483–488). The aim of this study is to evaluate several catheters using time-action analysis during a navigation task in bifurcations of various geometries. The relation between the geometry of bifurcations, the catheters, and the time taken to perform specific actions is investigated. Nine novices manipulated five widely used selective catheters with a 0.035” guidewire in a model. In the model, four bifurcations of various diameters and angles were selected. Each bifurcation was cannulated six times with two different yet suitable catheters. The participants had no direct vision of the model but navigated the instruments using the images that were captured by a camera and displayed on a screen. All images presented to the participant were recorded and used for detailed time-action analysis of the various actions to cannulate a branch (e.g., catheter or guidewire retracted, rotated, and advanced). On average, the participants needed 28.3 s to cannulate a branch. When the ratio between the diameter of the main and side branch was high, the average time per task increased significantly, as did the number of attempts to navigate into a branch. However, neither the choice between the two suitable catheters for each bifurcation, nor the angles of the bifurcation made a significant difference in navigation time. Time-action analysis enabled objective measurement of the time spent on various actions to cannulate a branch. The results revealed that most time was spent on retracting and rotating the catheter. This was comparable for all catheters and branches, showing that all the instruments were manipulated in a similar way and presented the same difficulties.
Product Design Retrieval by Matching Bills of Materials
Authors: Kashkoush M. , ElMaraghy H.
Published: September 2013

A new automatic design retrieval method that identifies the legacy product design most similar to a new one is proposed. Matching phylogenetic trees has been utilized in biological science for decades and is referred to as “tree reconciliation.” A new application of this approach in manufacturing is presented where legacy designs are retrieved based on reconciliation of trees representing products bill of materials (BOM). A product BOM is a structured tree, which represents its components and their hierarchal relationships; hence, it captures the contents and structure of assembled products. Making use of data associated with the retrieved designs also helps speed-up other downstream planning activities such as process planning, hence improving planning efficiency. A chemical processing centrifugal pump is used as a case study for illustration. The results obtained using the proposed method is compared with those recently published on BOM trees matching for further analysis and verification. This novel method is less computationally complex than available state-of-the-art algorithms.
Development of a Multistage Reliability-Based Design Optimization Method
Authors: Paulson Eric J. , Starkey Ryan P.
Published: September 2013

Complex system acquisition and its associated technology development have a troubled recent history. The modern acquisition timeline consists of conceptual, preliminary, and detailed design followed by system test and production. The evolving nature of the estimates of system performance, cost, and schedule during this extended process may be a significant contribution to recent issues. The recently proposed multistage reliability-based design optimization (MSRBDO) method promises improvements over reliability-based design optimization (RBDO) in achieved objective function value. In addition, its problem formulation more closely resembles the evolutionary nature of epistemic design uncertainties inherent in system design during early system acquisition. Our goal is to establish the modeling basis necessary for applying this new method to the engineering of early conceptual/preliminary design. We present corrections in the derivation and solutions to the single numerical example problem published by the original authors, Nam and Mavris, and examine the error introduced under the reduced-order reliability sampling used in the original publication. MSRBDO improvements over the RBDO solution of 10–36% for the objective function after first-stage optimization are shown for the original second-stage example problem. A larger 26–40% improvement over the RBDO solution is shown when an alternative comparison method is used than in the original. The specific implications of extending the method to arbitrary m-stage problems are presented, together with a solution for a three-stage numerical example. Several approaches are demonstrated to mitigate the computational cost increase of MSRBDO over RBDO, resulting in a net decrease in calculation time of 94% from an initial MSRBDO baseline algorithm.