bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaporation Estimation of Rift Valley Lakes: Comparison of Models
Authors: Melesse Assefa M. , Abtew Wossenu , Dessalegne Tibebe
Published: December 2009

Evapotranspiration (ET) accounts for a substantial amount of the water flux in the arid and semi-arid regions of the World. Accurate estimation of ET has been a challenge for hydrologists, mainly because of the spatiotemporal variability of the environmental and physical parameters governing the latent heat flux. In addition, most available ET models depend on intensive meteorological information for ET estimation. Such data are not available at the desired spatial and temporal scales in less developed and remote parts of the world. This limitation has necessitated the development of simple models that are less data intensive and provide ET estimates with acceptable level of accuracy. Remote sensing approach can also be applied to large areas where meteorological data are not available and field scale data collection is costly, time consuming and difficult. In areas like the Rift Valley regions of Ethiopia, the applicability of the Simple Method (Abtew Method) of lake evaporation estimation and surface energy balance approach using remote sensing was studied. The Simple Method and a remote sensing-based lake evaporation estimates were compared to the Penman, Energy balance, Pan, Radiation and Complementary Relationship Lake Evaporation (CRLE) methods applied in the region. Results indicate a good correspondence of the models outputs to that of the above methods. Comparison of the 1986 and 2000 monthly lake ET from the Landsat images to the Simple and Penman Methods show that the remote sensing and surface energy balance approach is promising for large scale applications to understand the spatial variation of the latent heat flux.
Bundle Block Adjustment with 3D Natural Cubic Splines
Authors: Lee Won Hee , Yu Kiyun
Published: December 2009

Point-based methods undertaken by experienced human operators are very effective for traditional photogrammetric activities, but they are not appropriate in the autonomous environment of digital photogrammetry. To develop more reliable and accurate techniques, higher level objects with linear features accommodating elements other than points are alternatively adopted for aerial triangulation. Even though recent advanced algorithms provide accurate and reliable linear feature extraction, the use of such features that can consist of complex curve forms is more difficult than extracting a discrete set of points. Control points that are the initial input data, and break points that are end points of segmented curves, are readily obtained. Employment of high level features increases the feasibility of using geometric information and provides access to appropriate analytical solutions for advanced computer technology.
Data Centric Sensor Stream Reduction for Real-Time Applications in Wireless Sensor Networks
Authors: Aquino Andre Luiz Lins , Nakamura Eduardo Freire
Published: December 2009

This work presents a data-centric strategy to meet deadlines in soft real-time applications in wireless sensor networks. This strategy considers three main aspects: (i) The design of real-time application to obtain the minimum deadlines; (ii) An analytic model to estimate the ideal sample size used by data-reduction algorithms; and (iii) Two data-centric stream-based sampling algorithms to perform data reduction whenever necessary. Simulation results show that our data-centric strategies meet deadlines without loosing data representativeness.
Low Magnetic Field Detection Using a CuPt Nano Structure Made on a SiO2/Si Structure
Authors: Hajghassem Hassan , Banihashemian Seyedeh Maryam , Aliahmadi Majidreza
Published: December 2009

A Si/SiO2/CuPt structure is formed by depositing a very thin SiO2 layer between CuPt and P-type Si layers using e-beam evaporation. SEM images show the formation of CuPt nano clusters with an average size of less than 100 nm. This structure shows high sensitivity to applied magnetic fields at 77K and at low and high dc voltages such that magnetic field as low as 6 mT is detected using I-V and I-B measurements. The variation of current with various magnetic field strength at the constant voltage shows also an oscillatory behavior. The sensitivity of this structure to magnetic fields is believed to be due to small nano size of the platinum–copper structures as well as their discrete energy states and the tunneling of carriers into the insulating layer. Our results indicate that this structure may be a good candidate for small, simple, low cost and sensitive low magnetic field detectors.
HIV-1 Protease: Structural Perspectives on Drug Resistance
Authors: Weber Irene  T. , Agniswamy Johnson
Published: December 2009

Antiviral inhibitors of HIV-1 protease are a notable success of structure-based drug design and have dramatically improved AIDS therapy. Analysis of the structures and activities of drug resistant protease variants has revealed novel molecular mechanisms of drug resistance and guided the design of tight-binding inhibitors for resistant variants. The plethora of structures reveals distinct molecular mechanisms associated with resistance: mutations that alter the protease interactions with inhibitors or substrates; mutations that alter dimer stability; and distal mutations that transmit changes to the active site. These insights will inform the continuing design of novel antiviral inhibitors targeting resistant strains of HIV.
Premature Aortic Atherosclerosis in Systemic Lupus Erythematosus: A Controlled Transesophageal Echocardiographic Study
Authors: ROLDAN CARLOS A. , JOSON JOSEPH , SHARRAR JANEEN , QUALLS CLIFFORD R. , SIBBITT WILMER L.
Published: December 2009

Objective.

Premature carotid and coronary atherosclerosis are common in systemic lupus erythematosus (SLE), but data on aortic atherosclerosis (AA) are limited. Thus, using multiplane transesophageal echocardiography (TEE), we sought to determine the prevalence and clinical correlates of AA in patients with SLE.

Methods.

Forty-seven patients with SLE (44 women, age 38 ± 12 years) and 21 healthy controls (19 women, age 34 ± 12 years) underwent clinical and laboratory evaluations and TEE to assess AA defined as aortic intima media thickness (IMT) > 0.86 mm or plaques as > 50% focal IMT as compared with surrounding walls. TEE studies were interpreted by an experienced observer unaware of subjects’ clinical data.

Results.

The prevalence of abnormal aortic IMT, plaques, or both lesions was higher in patients as compared to controls (37%, 23%, and 43% vs 14%, 0%, and 14%, respectively, all p ≤ 0.02). In patients, age at diagnosis of SLE was the only positive independent predictor of AA [OR 1.12 per year from diagnosis of SLE, 95% confidence interval (CI) 1.04–1.19, p = 0.001] and cyclophosphamide therapy was the only negative independent predictor of AA (OR 0.186, 95% CI 0.153–0.95, p = 0.04, equivalent to 5.4 times less likely to develop AA).

Conclusion.

AA is common in young patients with SLE and is predicted by a later age at diagnosis of SLE, but is negatively correlated with cyclophosphamide therapy. Thus, early diagnosis and more aggressive immunosuppressive therapy may be required to decrease the development and progression of atherosclerosis in patients with SLE.
Observational Study of Treatment Outcome in Early Diffuse Cutaneous Systemic Sclerosis
Authors: HERRICK ARIANE L. , LUNT MARK , WHIDBY NINA , ENNIS HOLLY , SILMAN ALAN , McHUGH NEIL , DENTON CHRISTOPHER P.
Published: December 2009

Objective.

Randomized clinical trials in early diffuse cutaneous systemic sclerosis (dcSSc) are challenging. We used an observational approach to estimate the relative effectiveness of different current treatment approaches, capturing entry and outcome data in a standardized way.

Methods.

Patients with dcSSc within 3 years of the onset of skin thickening were included. Standardized entry and followup data were collected in relation to the first disease-modifying treatment at baseline and 4–6 weeks, then 3, 6, 12, 18, 24, 30, and 36 months. The 5 different protocols were (1) intravenous cyclophosphamide followed by mycophenolate mofetil (MMF); (2) antithymocyte globulin followed by MMF; (3) MMF alone; (4) no disease-modifying treatment; (5) other immunosuppressant treatment. The primary outcome measure was the modified Rodnan skin score (mRSS). Inverse probability of treatment weights were used to allow for differing patient characteristics between groups.

Results.

The study included 147 patients from 12 centers. Numbers of patients starting on Protocols 1 to 5 were 29, 25, 61, 19, and 13, respectively. mRSS decreased over time from 24 (IQ 19–32) at baseline to 15.5 (IQ 9–24.5) at 3 years. Although there were differences in the magnitude of the change for different protocols, there were no significant differences between protocols in the rate of change of mRSS over time (p = 0.43). When inverse probability weights were applied, the results remained nonsignificant (p = 0.41).

Conclusion.

Using this observational approach, there were no obvious differences in outcome between groups after allowing as far as possible for baseline differences in treatment allocations.
Demographic and Clinical Features Related to a Symptomatic Onset of Paget’s Disease of Bone
Authors: VARENNA MASSIMO , ZUCCHI FRANCESCA , GALLI LAURA , MANARA MARIA , DE MARCO GABRIELE , SINIGAGLIA LUIGI
Published: December 2009

Objective.

Paget’s disease of bone (PDB) is a focal disorder of skeletal remodeling that can lead to bone pain, deformity, and fractures, but it can often be asymptomatic for a long time. This study investigated which factors may distinguish patients with clinical manifestations from asymptomatic patients.

Methods.

The study group consisted of 224 patients with PDB referred to our Bone Disease Unit. For all patients, data were collected about clinical and demographic variables and diagnostic procedures. Logistic regression analyses were used to assess the role of recorded variables on the odds of being diagnosed clinically rather than by chance.

Results.

Among the 124 patients with clinical manifestations leading to the diagnosis (55.4%), 36 subjects complained of bone pain, 32 articular pain, 42 back pain, 2 headache; 9 had fractures in Paget bone, and 3 had bone deformity. In 100 patients (44.6%) PDB was diagnosed by chance. At the multivariate analysis, only the number of bones involved (OR for 1 site increment = 1.18, 95% CI: 1.007–1.402; p = 0.04) acted as an independent predictor for a clinical diagnosis. Some skeletal localizations were associated with a clinical diagnosis: the involvement of lumbar spine (OR = 2.085, 95% CI: 1.024–4.224; p = 0.043) was more likely in symptomatic patients; pelvis and tibia showed a borderline statistical significance. The skull was predictive for asymptomatic PDB.

Conclusion.

A systematic laboratory screening including serum alkaline phosphatase of an older subject complaining of bone pain, articular pain, or back pain is the sole strategy to improve the diagnostic sensitivity for PDB.
Developing a Successful Nursing Objective Structured Clinical Examination
Authors: McWilliam Paula , Botwinski Carol
Published: December 2009

The evaluation of nursing students' clinical competencies is essential to the educational process. The Objective Structured Clinical Examination (OSCE) program was designed to assess students in a variety of health topics that may not be experienced during the assigned clinical rotation. Building on prior work, the purpose of this study was to examine specific aspects of the nursing OSCE toward developing a reliable and valid tool for evaluating selected students' clinical competencies.

The following areas were investigated using an assessment design: the development of case scenarios and updates, the role and training of the standardized patient, and students' perceptions of the nursing OSCE experience. Recommendations are made for the variety of case scenarios, frequency of updates, methods by which standardized patients should be trained, remediation, and program requirements. Students were overwhelmingly favorable to perceived benefits of participation in OSCEs during their nursing education.
Camp BONES: A Partnership Initiative to Engage Underrepresented Adolescents in a Career in Nursing at the Baccalaureate Level
Authors: Pollard Deborah L. , Kuiper RuthAnne , Meredith Cynthia M.
Published: December 2009

The nursing profession is confronted with significant challenges related to the ever-increasing shortage and lack of diversity in the workforce. To address these challenges, a program for underrepresented middle school students was developed collaboratively between local school districts, academia, and health care partners. The program, Camp BONES, included a 2-week summer camp and follow-up weekend and summer camp experiences for students. Experiences were provided to explore critical thinking skills in the simulated laboratories at the university, as well as at clinical practice areas in nursing. The program was guided by the Theory of Planned Behavior and self-efficacy theory. Early evaluation of the program revealed positive accolades and students' increasing interest in pursuing nursing as a career. Collaborative programs between academia and practice areas, such as Camp BONES, provide important opportunities for middle school students to explore and engage in the nursing profession during the formative years.
The Meaning of Occupational Gaps in Everyday Life in the First Year after Stroke
Authors: Eriksson Gunilla , Tham Kerstin
Published: December 2009

This longitudinal study identified how occupational gaps were characterized in people's lived experiences of performing everyday occupations during the first year after stroke. Four participants were interviewed four times during the year after stroke. The data were collected and analyzed using the Empirical, Phenomenological, Psychological method. Five main characteristics were identified: (1) encountering occupational gaps in formerly taken-for-granted activities, (2) striving to narrow gaps in desired occupations, (3) recognizing oneself in doing, (4) searching for a new sense of self through doing, and (5) creating strategies to enable doing. The findings show the importance of being able to preserve some sense of self in everyday doings after a life course disruption caused by stroke. Important implications for clinical practice include sensitivity to clients' experiences during this process, enablement of experiences in occupations promoting recognition, and support of clients in recapturing desired occupations.
La Habana escultórica: de La Giraldilla a Lennon
Authors: Pereira María de los Ángeles
Published: December 2009

La escultura pública acompañó al desarrollo arquitectónico y urbanístico de La Habana desde su surgimiento hasta su cabal consolidación como ciudad moderna hacia finales del siglo XIX y primeras décadas del XX, contribuyendo de modo sustancial a la configuración de sus perfiles y a la monumentalidad que la caracteriza como capital de Cuba. El desarrollo del arte monumentario conmemorativo, además de reflejar el repertorio icónico de la nación cubana a lo largo de su proceso histórico, constituye un reflejo de la evolución de los derroteros estéticos en el tránsito hacia una renovación formal y conceptual que, finalmente, coloca a esta manifestación en un lugar protagonista entre de las diferentes expresiones de su cultura artística cubana.
Influencia de diferentes productos inoculantes sobre el poder de nucleación y la tendencia a la contracción de la fundición con grafito esferoidal
Authors: Suárez R. , Gutiérrez J. M. , Loizaga A. , Larrañaga P. , Sertucha J.
Published: December 2009

La utilización de sistemas de control metalúrgico, basados en el análisis de las curvas de solidificación, permite examinar las características del metal a lo largo de todo el proceso de fabricación. En este trabajo, dichos sistemas se han utilizado con el fin de estudiar la eficacia de la etapa de inoculación del metal, determinar qué substratos ofrecen mejores resultados a la hora de nuclear el grafito esferoidal, minimizar la tendencia a la formación de cementita y reducir al máximo la tendencia a la contracción de la aleación en la etapa final de la solidificación. Con este objeto, se han seleccionado 10 inoculantes comerciales, con diferencias en su composición química, con el propósito de obtener información sobre la eficacia de los elementos químicos utilizados comercialmente para germinar núcleos grafíticos en la fundición esferoidal. El estudio se completa con pruebas sobre pieza real, donde se verifican los resultados obtenidos con los inoculantes seleccionados.
An Architecture for Interactive Target-Oriented e/m-Learning Systems
Authors: De Castro Cristina , Leonardi Giacomo , Toppan Paolo
Published: December 2009

In this paper, an architecture is proposed for the development of an e/m-Learning system with the following features: (1) learning paths can be tailored to the userâ??s aims and, during the learning process, dynamically modified in order to meet his needs; (2) in context of m-Learning facilities, contents can be scaled and adapted to the userâ??s device and connection technology. As far as learning paths are concerned, each learner is allowed to specify his initial target and, if he decides to deepen some issues, is authorised to redefine such target over time. This process is guided by a â??Path Decision Module
Students' Decisions to Use an eLearning System: A Structural Equation Modelling Analysis
Authors: Abbad Muneer , Morris David , Al-Ayyoub Abdel-Elah , Abbad Jumma'a
Published: December 2009

This research investigates and identifies some of the major factors affecting studentsâ?? adoption of an e-learning system at Arab Open University in Jordan. E-learning adoption is approached from the information systems acceptance point of view. An extended version of the Technology Acceptance Model (TAM) was developed to investigate the underlying factors that influence studentsâ?? decisions to use an e-learning system. The proposed model uses the actual use of an e-learning system. It is different from most of the prior TAM studies, which only used a single dependent variable (intention to use). The model was estimated using Structural Equation Modelling (SEM). The final models derived from this study indicated that beliefs of usefulness and ease of use partially mediate the relationship between external factors and intention to use and actual use of e-learning systems.
A Reappraisal of Online Mathematics Teaching Using LaTeX
Authors: Costello Eamon , Fox Seamus , Walsh Elaine
Published: December 2009

The mathematics language LaTeX is often seen outside of academic circles as a legacy technology that is awkward to use. MathML - a verbose language designed for data-exchange, and to be written and understood by machines - is sometimes by contrast seen as something that will aid online mathematics and lack of browser support for it bemoaned. However LaTeX can already do many of the things that MathML might promise. LaTeX is here proposed as a language from which small fragments, with concise syntax, can be used by people to easily create and share mathematical expressions online. The capability to embed fragments of LaTeX code in online discussions is described here and its impact on a group of educators and learners evaluated. Here LaTeX is posited as a useful tool for facilitating asynchronous, online, collaborative learning of mathematics.
Understanding the Need of Mobile ICT Learning as an Elderly Learning Tool
Authors: Lam Sanches , Chung W.
Published: December 2009

With a rapid deployment of mobile devices, mobile learning gives rise to new possibilities for extending learning opportunities. Nevertheless, current research on mobile learning has mostly been aimed at enhancing learning of school or college students. In this light, the paper seeks to throw light on the potential of mobile learning for elderly. We describe in this paper a research study for examining needs that determine the adoption and usage of mobile devices by elderly population. The elderly are an often neglected group in product development and marketing, but they are the only growing age group in most developed societies. By using semi-structured interviews with a number of different stakeholders interested in elderly people, we identify a set of issues that need to be taken into account when designing strategy for the elderly learners. The results of our study indicate that elderly people are interested in using mobile devices and services, but these services need to deliver real value for them.
Pelze, Gold und Weihwasser: Handel und mission in Afrika und Amerika
Authors: Stenschke Christoph
Published: December 2009

Marx lehrt als Professor f�r au�ereurop�ische Geschichte an der Universit�t Duisburg-Essen. Sein Spezialgebiet ist die Geschichte des s�dlichen Afrika.
Recent Applications of Palladium‐Catalyzed Coupling Reactions in the Pharmaceutical, Agrochemical, and Fine Chemical Industries
Authors: Torborg Christian , Beller Matthias
Published: December 2009

Palladium‐catalyzed coupling reactions have become a central tool for the synthesis of biologically active compounds both in academia and industry. Most of these transformations make use of easily available substrates and allow for a shorter and more selective preparation of substituted arenes and heteroarenes compared to non‐catalytic pathways. Notably, molecular‐defined palladium catalysts offer high chemoselectivity and broad functional group tolerance. Considering these advantages, it is not surprising that several palladium‐catalyzed coupling reactions have been implemented in the last decade into the industrial manufacture of pharmaceuticals and fine chemicals. In this review different examples from 2001–2008 are highlighted, which have been performed at least on a kilogram scale in the chemical and pharmaceutical industries.
Highly Enantioselective Biginelli Reaction Promoted by Chiral Bifunctional Primary Amine‐Thiourea Catalysts: Asymmetric Synthesis of Dihydropyrimidines
Authors: Wang Yangyun , Yang Haitao , Yu Jipan , Miao Zhiwei , Chen Ruyu
Published: December 2009

The diastereospecific formation of dihydropyrimidines (DHPMs) has been achieved in moderate to high yields with up to 99% ee by a Biginelli reaction. The reaction was performed by using a combined catalyst consisting of a chiral bifunctional primary amine‐thiourea 9f and a Brønsted acid with tert‐butylammonium trifluoroacetate (t‐BuNH2⋅TFA) as additive in dichloromethane at room temperature. The possible mechanism for the reaction has been proposed to explain the origin of the activation and the asymmetric induction.
Copper‐in‐Charcoal‐Catalyzed, Tandem One‐Pot Diazo Transfer‐Click Reactions
Authors: Lee Ching‐Tien , Huang Shenlin , Lipshutz Bruce H.
Published: December 2009

Copper‐in‐charcoal (Cu/C) is an effective heterogeneous catalyst for tandem diazo transfer/click reactions. In the presence of Cu/C, various azides can be generated in situ from the corresponding amines, and subsequently undergo [3+2] cycloaddition with terminal alkynes to afford triazoles in good yields. The catalyst is also easily recycled.
3,5‐Bis(n‐perfluorooctyl)benzyltriethylammonium Bromide (F‐TEBA): An Efficient, Easily Recoverable Fluorous Catalyst for Solid‐Liquid PTC Reactions
Authors: Pozzi Gianluca , Mihali Voichiţa , Foschi Francesca , Penso Michele , Quici Silvio , Fish Richard H.
Published: December 2009

A readily available 3,5‐bis(perfluorooctyl)benzyl bromide and triethylamine were reacted under mild conditions to give 3,5‐bis(n‐perfluorooctyl)benzyltriethylammonium bromide (F‐TEBA), an analogue of the versatile phase‐transfer catalyst, benzyltriethylammonium chloride (TEBA), containing two fluorous ponytails. This perfluoroalkylated quaternary ammonium salt was successfully employed as a catalyst in a variety of reactions run under solid‐liquid phase‐transfer catalysis (SL‐PTC) conditions. Thus, being both hydrophobic and lipophobic, F‐TEBA could be quickly recovered in quantitative yields, and reused without loss of activity over several reaction cycles.
Tuberculosis and leprosy in perspective
Authors: Stone Anne C. , Wilbur Alicia K. , Buikstra Jane E. , Roberts Charlotte A.
Published: December 2009

Two of humankind's most socially and psychologically devastating diseases, tuberculosis and leprosy, have been the subject of intensive paleopathological research due to their antiquity, a presumed association with human settlement and subsistence patterns, and their propensity to leave characteristic lesions on skeletal and mummified remains. Despite a long history of medical research and the development of effective chemotherapy, these diseases remain global health threats even in the 21st century, and as such, their causative agentsMycobacterium tuberculosisandM. leprae, respectively, have recently been the subject of molecular genetics research. The new genome‐level data for several mycobacterial species have informed extensive phylogenetic analyses that call into question previously accepted theories concerning the origins and antiquity of these diseases. Of special note is the fact that all new models are in broad agreement that human TB predated that in other animals, including cattle and other domesticates, and that this disease originated at least 35,000 years ago and probably closer to 2.6 million years ago. In this work, we review current phylogenetic and biogeographic models derived from molecular biology and explore their implications for the global development of TB and leprosy, past and present. In so doing, we also briefly review the skeletal evidence for TB and leprosy, explore the current status of these pathogens, critically consider current methods for identifying ancient mycobacterial DNA, and evaluate coevolutionary models. Yrbk Phys Anthropol 52:66–94, 2009. © 2009 Wiley‐Liss, Inc.
Imaging and Quantitative Assessment of Long Bone Vascularization in the Adult Rat Using Microcomputed Tomography
Authors: Jia Fei , Françoise Peyrin , Malaval Luc , Laurence Vico , Marie‐Hélène Lafage‐Proust
Published: December 2009

The objective of this study was to develop and validate a technique for both 3D imaging and quantification of the vascular network of bone tissue in the rat. Five month‐old male Wistar rats were divided into tail‐suspension (21 days) and control groups. Sixty percent barium sulfate solution was infused into the vena cava. The tibiae were evaluated in 2D and 3D before and after decalcification, using conventional microcomputerized tomography (μCT) at 10 and 5 μm resolution and synchrotron radiation (SR) μCT. The perfusion technique and tomography exhibited excellent bone vasculature imaging. Significant positive correlations were observed between 2D histomorphometric and 3D μCT vascular parameters (P < 0.05). 3DμCT discriminated significant changes of vessel structures in unloading condition: vessel number decreased by 25%, (P < 0.005), vessel separation increased by 27%, P < 0.01. SRμCT could image sinusoid clusters in bone. μCT is an accurate and reproducible technique for 3D quantitative evaluation of long bone vascularisation in the rat. Anat Rec, 2010. © 2009 Wiley‐Liss, Inc.
Hair Whorls in the Dog (Canis familiaris), Part II: Asymmetries
Authors: Tomkins Lisa M. , McGreevy Paul D.
Published: December 2009

In horses and cattle, hair whorls have been shown to act as a structural marker of reactivity and behavioral lateralization. Few studies on canine whorls have been reported and none have assessed whorl position or direction of flow. This study describes the distribution and characteristics of whorl in each of 10 regions in which whorls are typically located in dogs. Hair whorls were assessed in dogs (n = 120) and were recorded as clockwise or counterclockwise in the cephalic, cervical (dorsal, lateral, ventral), thoracic and brachial axillary, chest, shoulders, elbows, abdominal, and ischiatic regions. Bilateral whorls, including brachial axillary, elbow, abdominal and ischiatic whorls, rotated in opposing directions, allowing the dog's overall hair coat to be symmetrical. Cephalic, brachial axillary, and ischiatic whorls were consistent in their direction; cephalic and ischiatic whorls were clockwise on the right side of the body, and counterclockwise on the left, whereas right brachial axillary whorls were counterclockwise and left were clockwise. The central chest whorl was predominantly counterclockwise (91.21%). Direction of whorls was associated with several factors, including coat length, coat thickness, sex and source of the dog. Anat Rec, 2010. © 2009 Wiley‐Liss, Inc.
A novel approach to the extraction of roots from Arabic words using bigrams
Authors: Hmeidi Ismail I. , Al‐Shalabi Riyad F. , Al‐Taani Ahmad T. , Najadat Hassan , Al‐Hazaimeh Shaker A.
Published: December 2009

Root extraction is one of the most important topics in information retrieval (IR), natural language processing (NLP), text summarization, and many other important fields. In the last two decades, several algorithms have been proposed to extract Arabic roots. Most of these algorithms dealt with triliteral roots only, and some with fixed length words only. In this study, a novel approach to the extraction of roots from Arabic words using bigrams is proposed. Two similarity measures are used, the dissimilarity measure called the “Manhattan distance,” and Dice's measure of similarity. The proposed algorithm is tested on the Holy Qu'ran and on a corpus of 242 abstracts from the Proceedings of the Saudi Arabian National Computer Conferences. The two files used contain a wide range of data: the Holy Qu'ran contains most of the ancient Arabic words while the other file contains some modern Arabic words and some words borrowed from foreign languages in addition to the original Arabic words. The results of this study showed that combining N‐grams with the Dice measure gives better results than using the Manhattan distance measure.
Development and testing of a novel microcantilever technique for measuring the cohesive strength of intact biofilms
Authors: Aggarwal Srijan , Poppele Eric H. , Hozalski Raymond M.
Published: December 2009

Cohesive strength is an important parameter for understanding and modeling the mechanics of biomass detachment from bacterial biofilms. It is challenging to measure the mechanical properties of biofilms, however, because biofilms may desiccate when removed from liquid medium and they are inherently fragile. Poppele and Hozalski (Poppele and Hozalski, 2003, J Microb Methods 55:607–615) presented a microcantilever method for measuring the tensile strength of detached biofilm fragments while submersed in liquid medium. Here we present a modification of the microcantilever method to quantify the strength of intact bacterial biofilms. Initial testing was performed on Pseudomonas aeruginosa biofilms and on Staphylococcus epidermidis biofilms grown in rotating disk reactors. The cohesive strength values were highly variable (i.e., coefficients of variation ranging from 71% to 143%) and ranged from 59 to 18,900 Pa for the P. aeruginosa biofilms and from 61 to 5,840 Pa for the S. epidermidis biofilms. The biofilms also appeared to be isotropic as strength did not vary with angle of testing relative to the direction of applied shear. Strength testing using both the intact and fragment methods was performed on five samples of P. aeruginosa biofilms, and the strength populations were not from the same distribution in three cases. Equivalent diameters for the fragments detached from biofilms during strength testing ranged from 5 to 500 µm, which is within the range of size of biofilm fragments observed in the effluents of lab‐scale and full‐scale bioreactors. The microcantilever is a simple yet powerful tool for measuring the cohesive strength of intact biofilms at a relevant scale. Biotechnol. Bioeng. 2010;105: 924–934. © 2009 Wiley Periodicals, Inc.
A multichamber fluidic device for 3D cultures under interstitial flow with live imaging: Development, characterization, and applications
Authors: Bonvin Carmen , Overney Jan , Shieh Adrian C. , Dixon J. Brandon , Swartz Melody A.
Published: December 2009

Interstitial flow is an important biophysical cue that can affect capillary morphogenesis, tumor cell migration, and fibroblast remodeling of the extracellular matrix, among others. Current models that incorporate interstitial flow and that are suitable for live imaging lack the ability to perform multiple simultaneous experiments, for example, to compare effects of growth factors, extracellular matrix composition, etc. We present a nine‐chamber radial flow device that allows simultaneous 3D fluidic experiments for relatively long‐term culture with live imaging capabilities. Flow velocity profiles were characterized by fluorescence recovery after photobleaching (FRAP) for flow uniformity and estimating the hydraulic conductivity. We demonstrate lymphatic and blood capillary morphogenesis in fibrin gels over 10 days, comparing flow with static conditions as well as the effects of an engineered variant of VEGF that binds fibrin via Factor XIII. We also demonstrate the culture of contractile fibroblasts and co‐cultures with tumor cells for modeling the tumor microenvironment. Therefore, this device is useful for studies of capillary morphogenesis, cell migration, contractile cells like fibroblasts, and multicellular cultures, all under interstitial flow. Biotechnol. Bioeng. 2010;105: 982–991. © 2009 Wiley Periodicals, Inc.
Complex responses to culture conditions in Pseudomonas syringae pv. tomato DC3000 continuous cultures: The role of iron in cell growth and virulence factor induction
Authors: Kim Beum Jun , Schneider David J. , Cartinhour Samuel W. , Shuler Michael L.
Published: December 2009

The growth of a model plant pathogen, Pseudomonas syringae pv. tomato DC3000, was investigated using a chemostat culture system to examine environmentally regulated responses. Using minimal medium with iron as the limiting nutrient, four different types of responses were obtained in a customized continuous culture system: (1) stable steady state, (2) damped oscillation, (3) normal washout due to high dilution rates exceeding the maximum growth rate, and (4) washout at low dilution rates due to negative growth rates. The type of response was determined by a combination of initial cell mass and dilution rate. Stable steady states were obtained with dilution rates ranging from 0.059 to 0.086 h−1 with an initial cell mass of less than 0.6 OD600. Damped oscillations and negative growth rates are unusual observations for bacterial systems. We have observed these responses at values of initial cell mass of 0.9 OD600 or higher, or at low dilution rates (<0.05 h−1) irrespectively of initial cell mass. This response suggests complex dynamics including the possibility of multiple steady states.

Iron, which was reported earlier as a growth limiting nutrient in a widely used minimal medium, enhances both growth and virulence factor induction in iron‐supplemented cultures compared to unsupplemented controls. Intracellular iron concentration is correlated to the early induction (6 h) of virulence factors in both batch and chemostat cultures. A reduction in aconitase activity (a TCA cycle enzyme) and ATP levels in iron‐limited chemostat cultures was observed compared to iron‐supplemented chemostat cultures, indicating that iron affects central metabolic pathways. We conclude that DC3000 cultures are particularly dependent on the environment and iron is likely a key nutrient in determining physiology. Biotechnol. Bioeng. 2010;105: 955–964. © 2009 Wiley Periodicals, Inc.
Effect of the size of yeast flocs and zinc supplementation on continuous ethanol fermentation performance and metabolic flux distribution under very high concentration conditions
Authors: Xue C. , Zhao X.Q. , Bai F.W.
Published: December 2009

Taking continuous ethanol fermentation with the self‐flocculating yeast SPSC01 under very high concentration conditions as an example, the fermentation performance of the yeast flocs and their metabolic flux distribution were investigated by controlling their average sizes at 100, 200, and 300 µm using the focused beam reflectance online measurement system. In addition, the impact of zinc supplementation was evaluated for the yeast flocs at the size of 300 µm grown in presence or absence of 0.05 g L−1 zinc sulfate. Among the yeast flocs with different sizes, the group with the average size of 300 µm exhibited highest ethanol production (110.0 g L−1) and glucose uptake rate (286.69 C mmol L−1 h−1), which are in accordance with the increased flux from pyruvate to ethanol and decreased flux to glycerol. And in the meantime, zinc supplementation further increased ethanol production and cell viability comparing with the control. Zinc addition enhanced the carbon fluxes to the biosynthesis of ergosterol (28.6%) and trehalose (43.3%), whereas the fluxes towards glycerol, protein biosynthesis, and tricarboxylic acid cycle significantly decreased by 37.7%, 19.5%, and 27.8%, respectively. This work presents the first report on the regulation of metabolic flux by the size of yeast flocs and zinc supplementation, which provides the potential for developing engineering strategy to optimize the fermentation system. Biotechnol. Bioeng. 2010;105: 935–944. © 2009 Wiley Periodicals, Inc.
Anoxic oxidation of arsenite linked to chemolithotrophic denitrification in continuous bioreactors
Authors: Sun Wenjie , Sierra‐Alvarez Reyes , Hsu Ivann , Rowlette Pieter , Field Jim A.
Published: December 2009

In this study, the anoxic oxidation of arsenite (As(III)) linked to chemolithotrophic denitrification was shown to be feasible in continuous bioreactors. Biological oxidation of As(III) was stable over prolonged periods of operation ranging up to 3 years in continuous denitrifying bioreactors with granular biofilms. As(III) was removed with a high conversion efficiency (>92%) to arsenate (As(V)) in periods with high volumetric loadings (e.g., 3.5–5.1 mmol As L day−1). The maximum specific activity of sampled granular sludge from the bioreactors was 0.98 ± 0.04 mmol As(V) formed g−1 VSS day−1 when determined at an initial concentration of 0.5 mM As(III). The microbial population adapted to high influent concentrations of As(III) up to 5.2 mM. However, the As(III) oxidation process was severely inhibited when 7.6–8.1 mM As(III) was fed. Activity was restored upon lowering the As(III) concentration to 3.8 mM. Several experimental strategies were utilized to demonstrate a dependence of the nitrate removal on As(III) oxidation as well as a dependence of the As(III) removal on nitrate reduction. The molar stoichiometric ratio of As(V) formed to nitrate removed (corrected for endogenous denitrification) in the bioreactors approximated 2.5, indicating complete denitrification was occurring. As(III) oxidation was also shown to be linked to the complete denitrification of NO to N2 gas by demonstrating a significantly enhanced production of N2 beyond the background endogenous production in a batch bioassay spiked with 3.5 mM As(III). The N2 production also corresponded closely to the expected stoichiometry of 2.5 mol As(III) mol−1 N2–N for complete denitrification. Biotechnol. Bioeng. 2010;105: 909–917. © 2009 Wiley Periodicals, Inc.
On‐demand three‐dimensional freeform fabrication of multi‐layered hydrogel scaffold with fluidic channels
Authors: Lee Wonhye , Lee Vivian , Polio Samuel , Keegan Phillip , Lee Jong‐Hwan , Fischer Krisztina , Park Je‐Kyun , Yoo Seung‐Schik
Published: December 2009

One of the challenges in tissue engineering is to provide adequate supplies of oxygen and nutrients to cells within the engineered tissue construct. Soft‐lithographic techniques have allowed the generation of hydrogel scaffolds containing a network of fluidic channels, but at the cost of complicated and often time‐consuming manufacturing steps. We report a three‐dimensional (3D) direct printing technique to construct hydrogel scaffolds containing fluidic channels. Cells can also be printed on to and embedded in the scaffold with this technique. Collagen hydrogel precursor was printed and subsequently crosslinked via nebulized sodium bicarbonate solution. A heated gelatin solution, which served as a sacrificial element for the fluidic channels, was printed between the collagen layers. The process was repeated layer‐by‐layer to form a 3D hydrogel block. The printed hydrogel block was heated to 37°C, which allowed the gelatin to be selectively liquefied and drained, generating a hollow channel within the collagen scaffold. The dermal fibroblasts grown in a scaffold containing fluidic channels showed significantly elevated cell viability compared to the ones without any channels. The on‐demand capability to print fluidic channel structures and cells in a 3D hydrogel scaffold offers flexibility in generating perfusable 3D artificial tissue composites. Biotechnol. Bioeng. 2010;105: 1178–1186. © 2009 Wiley Periodicals, Inc.
Morphology engineering of Aspergillus niger for improved enzyme production
Authors: Driouch Habib , Sommer Becky , Wittmann Christoph
Published: December 2009

Supplementation with silicate microparticles was used as novel approach to control the morphological development of Aspergillus niger, important as the major world source of citric acid and higher‐value enzymes, in submerged culture. With careful variation of size and concentration of the micromaterial added, a number of distinct morphological forms including pellets of different size, free dispersed mycelium, and short hyphae fragments could be reproducibly created. Aluminum oxide particles similarly affected morphology, showing that this effect is largely independent of the chemical particle composition. Image analysis of morphological development of A. niger during the cultivation process showed that the microparticles influence the morphology by collision‐induced disruption of conidia aggregates and probably also the hindrance of new spore–spore interactions in the very early stage of the process. Exemplified for different recombinant A. niger strains enzyme production could be strongly enhanced by the addition of microparticles. Linked to the formation of freely dispersed mycelium, titers for glucoamylase (GA) expressed as intracellular enzyme (88 U/mL) and fructofuranosidase secreted into the supernatant (77 U/mL), were up to fourfold higher in shake flasks. Moreover, accumulation of the undesired by‐product oxalate was suppressed by up to 90%. The microparticle strategy could be successfully transferred to fructofuranosidase production in bioreactor, where a final titer of 160 U/mL could be reached. Using co‐expression of GA with green fluorescent protein, enzyme production was localized in the cellular aggregates of A. niger. For pelleted growth, protein production was maximal only within a thin layer at the pellet surface and markedly decreased in the pellet interior, whereas the interaction with the microparticles created a highly active biocatalyst with the dominant fraction of cells contributing to production. Biotechnol. Bioeng. 2010;105: 1058–1068. © 2009 Wiley Periodicals, Inc.
Reactive antibodies against bacillus Calmette‐Guerin heat‐shock protein‐65 potentially predict the outcome of immunotherapy for high‐grade transitional cell carcinoma of the bladder
Authors: Ardelt Peter U. , Kneitz Burkhard , Adam Patrick , Reiss Cora , Kocot Arkadius , Fensterle Joachim , Chen Limor , Pasqualini Renata , Arap Wadih , Gerharz Elmar W. , Riedmiller Hubertus
Published: December 2009

BACKGROUND:

Intravesical immunotherapy with Mycobacterium
bovis (M. bovis) bacillus Calmette‐Guerin (BCG) is the current standard of care against superficial, high‐grade transitional cell carcinoma (TCC) of the urinary bladder (carcinoma in situ and pathologic T1, grade 3 disease). However, individual patient outcome is barely predictable because of the lack of serum markers. Consequently, progression to muscle‐invasive bladder cancer and critical delay of treatments (such as neoadjuvant combination chemotherapy and/or radical cystectomy) often occur. The objectives of this study were to identify a marker for measuring the BCG‐induced immune response and to predict the outcomes and potential improvements of BCG immunotherapy.

METHODS:

Because host immunoresponse mediates BCG activity, the authors screened a combinatorial random peptide library on the circulating pool of immunoglobulins (Igs) purified from an index patient after successful BCG immunotherapy to identify the corresponding target antigen(s).

RESULTS:

An immunogenic peptide motif was selected, isolated, and validated from M. bovis BCG heat‐shock protein 65 (HSP‐65) as a dominant epitope of the humoral response to treatment. Increasing IgA and IgG anti‐HSP‐65 titers specifically predicted a positive patient outcome in a cohort of patients with bladder cancer relative to several cohorts of control patients.

CONCLUSIONS:

The current results indicated that antibody production against M. bovis BCG HSP‐65 can serve as a serologic marker for the predictive outcome of BCG immunotherapy. Subsequent studies will determine the value of this candidate marker to modify BCG‐based treatment for individual patients with bladder cancer. Cancer 2010. © 2009 American Cancer Society.
Paired specimens
Authors: Haas Naomi B
Published: December 2009

This editorial in response to “Histologic Evaluation of Metastases in Renal Cell Carcinoma With Sarcomatoid Transformation and Its Implications for Systemic Therapy” concludes that a molecular analysis of paired specimens is critical in determining whether sarcomatoid features will play a role in future therapy for this poor prognosis cancer.
SPEC MPI2007—an application benchmark suite for parallel systems using MPI
Authors: Müller Matthias S. , van Waveren Matthijs , Lieberman Ron , Whitney Brian , Saito Hideki , Kumaran Kalyan , Baron John , Brantley William C. , Parrott Chris , Elken Tom , Feng Huiyu , Ponder Carl
Published: December 2009

The SPEC High‐Performance Group has developed the benchmark suite SPEC MPI2007 and its run rules over the last few years. The purpose of the SPEC MPI2007 benchmark and its run rules is to further the cause of fair and objective benchmarking of high‐performance computing systems. The rules help to ensure that the published results are meaningful, comparable to other results, and reproducible. MPI2007 includes 13 technical computing applications from the fields of computational fluid dynamics, molecular dynamics, electromagnetism, geophysics, ray tracing, and hydrodynamics. We describe the benchmark suite, and compare it with other benchmark suites. Copyright © 2009 John Wiley & Sons, Ltd.
Surface Patterning of Silver using an Electron‐ or Photon‐Assisted Oxidation Reaction
Authors: Günther Sebastian , Böcklein Sebastian , Reichelt Robert , Wintterlin Joost , Barinov Alexej , Menteş Tefvik O. , Niño Miguel Á. , Locatelli Andrea
Published: December 2009

We have investigated a recently developed method of patterning Ag surfaces. The method uses an electron beam to irradiate Ag surfaces during NO2 dosing at 300 K and leads to sharp oxide patterns on otherwise metallic surfaces. Investigations were performed on an Ag(111) single crystal and on an Ag foil with LEEM (low‐energy electron microscopy), LEED (low‐energy electron diffraction), MEM (mirror electron microscopy), and XPEEM (X‐ray photo‐emission electron microscopy). The oxidation reaction, which is based on the electron‐induced desorption of NO molecules, proceeds in steps, from a layer of O atoms adsorbed on the metallic Ag via an intermediate phase to an amorphous Ag2O film. Our measurements evidence a high cross section for electron‐induced NO desorption with 30–40 eV electrons, indicating that only a few electrons per adsorbing NO2 molecule are required to initiate the process. The intermediate phase, which forms a partially ordered quadratic structure, contains oxygen species in an oxide‐like environment, coexisting with an adsorbate covered metallic Ag(111) surface. While the intermediate phase dissolves within hours under UHV conditions, fully developed oxide patches, consisting of several layers of thick, amorphous Ag2O, are kinetically stable. The oxidation method also works with 40 eV (and 700 eV) photons instead of electrons. In preliminary experiments local patterns could also be created with photons, suggesting that mask techniques can be applied for the process.