bluuebunny/crossref_metadata_2025 huggingface dataset:
ESTIMATING A DOSE‐RESPONSE RELATIONSHIP BETWEEN LENGTH OF STAY AND FUTURE RECIDIVISM IN SERIOUS JUVENILE OFFENDERS*
Authors: LOUGHRAN THOMAS A. , MULVEY EDWARD P. , SCHUBERT CAROL A. , FAGAN JEFFREY , PIQUERO ALEX R. , LOSOYA SANDRA H.
Published: August 2009

The effect of sanctions on subsequent criminal activity is of central theoretical importance in criminology. A key question for juvenile justice policy is the degree to which serious juvenile offenders respond to sanctions and/or treatment administered by the juvenile court. The policy question germane to this debate is finding the level of confinement within the juvenile justice system that maximizes the public safety and therapeutic benefits of institutional confinement. Unfortunately, research on this issue has been limited with regard to serious juvenile offenders. We use longitudinal data from a large sample of serious juvenile offenders from two large cities to 1) estimate a causal treatment effect of institutional placement, as opposed to probation, on future rate of rearrest and 2) investigate the existence of a marginal effect (i.e., benefit) for longer length of stay once the institutional placement decision had been made. We accomplish the latter by determining a dose‐response relationship between the length of stay and future rates of rearrest and self‐reported offending. The results suggest that an overall null effect of placement exists on future rates of rearrest or self‐reported offending for serious juvenile offenders. We also find that, for the group placed out of the community, it is apparent that little or no marginal benefit exists for longer lengths of stay. Theoretical, empirical, and policy issues are outlined.
DO RETURNING PAROLEES AFFECT NEIGHBORHOOD CRIME? A CASE STUDY OF SACRAMENTO*
Authors: HIPP JOHN R. , YATES DANIEL K.
Published: August 2009

This study used a unique data set that combines information on parolees in the city of Sacramento, CA, over the 2003–2006 time period with information on monthly crime rates in Sacramento census tracts over this same period, providing us a fine‐grained temporal and geographical view of the relationship between the change in parolees in a census tract and the change in the crime rate. We find that an increase in the number of tract parolees in a month results in an increase in the crime rate. We find that more violent parolees have a particularly strong effect on murder and burglary rates. We find that the social capital of the neighborhood can moderate the effect of parolees on crime rates: Neighborhoods with greater residential stability dampen the effect of parolees on robbery rates, whereas neighborhoods with greater numbers of voluntary organizations dampen the effect of parolees on burglary and aggravated assault rates. Furthermore, this protective effect of voluntary organizations seems strongest for those organizations that provide services for youth. We show that the effect of single‐parent households in a neighborhood is moderated by the return of parolees, which suggests that these reunited families may increase the social control ability of the neighborhood.
Glycaemic index and glycaemic load intake patterns in older Australian women
Authors: O'SULLIVAN Therese A. , BREMNER Alexandra P. , CEDARO Pieta C. , O'NEILL Sheila , LYONS‐WALL Philippa
Published: August 2009

Aims:  Dietary glycaemic index and glycaemic load have been associated with risk of chronic diseases, yet limited research exists on patterns of consumption in Australia. Our aims were to investigate glycaemic carbohydrate in a population of older women, identify major contributing food sources and determine low, moderate and high ranges.

Methods:  Subjects were 459 Brisbane women aged 42–81 years participating in the Longitudinal Assessment of Ageing in Women. Diet history interviews were used to assess usual diet and results were analysed into energy and macronutrients using the FoodWorks dietary analysis program combined with a customised glycaemic index database.

Results:  Mean ± SD dietary glycaemic index was 55.6 ± 4.4% and mean dietary glycaemic load was 115 ± 25. A low glycaemic index in this population was ≤52.0, corresponding to the lowest quintile of dietary glycaemic index, and a low glycaemic load was ≤95. Glycaemic index showed a quadratic relationship with age (P= 0.01), with a slight decrease observed in women aged in their 60s relative to younger or older women. Glycaemic load decreased linearly with age (P < 0.001). Bread was the main contributor to carbohydrate and dietary glycaemic load (17.1% and 20.8%, respectively), followed by fruit (15.5% and 14.2%), and dairy for carbohydrate (9.0%), or breakfast cereals for glycaemic load (8.9%).

Conclusions:  In this population, dietary glycaemic load decreased with increasing age; however, this was likely to be a result of higher energy intakes in younger women. Focus on careful selection of lower‐glycaemic‐index items within bread and breakfast cereal food groups would be an effective strategy for decreasing dietary glycaemic load in this population of older women.
Dietary portfolio approach to reducing the risk of cardiovascular disease: The Polymeal revisited
Authors: CROWE Timothy C. , SHABANI Mehdi , BROCKBANK Cara M.
Published: August 2009

Aims: The Polymeal was first proposed as a ‘tastier and safer’ alternative to a polypharmacy approach to cardiovascular disease risk reduction. The present study aimed to examine the affordability of the Polymeal, and to propose modifications based on economic considerations, and the latest scientific evidence, to achieve consistency with current public health recommendations.

Methods: Prices for each food component specified in the Polymeal were obtained from a major and independent supermarket chain in a representative middle socioeconomic demographic region of metropolitan Melbourne, Australia. Items included fish (114 g, four times/week), fruits and vegetables (400 g/day), dark chocolate (100 g/day), garlic (2.7 g/day), almonds (68 g/day) and red wine (150 mL/day). Prices were calculated using an average of the major brands, or the most commonly eaten fruits, vegetables or fish. Modifications of the Polymeal were proposed based on published research and public health recommendations since the Polymeal was first proposed.

Results: Average price of the Polymeal was AU$11.89 per day falling to AU$8.46 if the cheapest food items were chosen. Modifications to the Polymeal included: consuming fish oil capsules instead of fish, reduction in the quantity of dark chocolate and removal of red wine. These modifications halved the cost of the Polymeal, while choosing the cheapest food items further lowered the cost to AU$3.49 per day. Modification of the Polymeal gave substantial reductions in both energy and saturated fat (51% and 84%, respectively).

Conclusion: The modified Polymeal is a more affordable variation of the Polymeal, which takes into account current scientific evidence and public health recommendations.
General practitioner and paediatrician self‐reported capacity for the diagnosis and management of childhood and adolescent overweight and obesity
Authors: MCFARLANE Julie , SCOTT Hayley , ROBERTSON Val , GLEESON Catherine , VANDERKROFT Dawn , WILSON Kate
Published: August 2009

Aim:  The purpose of the present study was to assess and document the self‐reported capacity, knowledge, skill and confidence of Central Coast general practitioners and paediatricians in the identification and management of overweight and obesity in children and adolescents, to investigate the barriers they experience in this area of practice and to consider how the local public sector nutrition service may assist.

Methods:  Forty general practitioners and three paediatricians were interviewed using a semistructured purpose‐designed questionnaire.

Results:  Most participating doctors perceived that public sector dietitians are not available to assist them in managing overweight and obese paediatric patients. Few (23%) doctors reported using published guidelines and most reported significant barriers limiting their capacity to identify and manage this patient group effectively. All doctors identified at least one way in which the public health system can better support doctors in this role.

Conclusions:  The findings suggest that many doctors may benefit from increased training and a health system that better remunerates them for the time investment needed to provide management consistent with best practice. Reorientation of local public sector nutrition services may also provide them with better support when managing overweight and obese paediatric clients. Future research should examine the actual practices of doctors and how public sector dietitians can best communicate and interact with them to facilitate effective management of these patients.
GF: A Multilingual Grammar Formalism
Authors: Ranta Aarne
Published: August 2009

GF (Grammatical Framework) is a grammar formalism designed for dealing with many languages simultaneously. A multilingual GF grammar has a language‐independent abstract syntax that deals with pure tree structures, and a set of language‐dependent concrete syntaxes that specify how the trees are expressed in different languages. Multilingual grammars formalize the idea that the same grammatical categories (such as noun phrases and verb phrases) and syntax rules (such as predication) can appear in different languages. They are also a powerful tool for natural language engineering, used for applications ranging from a translator of mathematical exercises to a dialogue system usable for talking with devices in a car. As a programming language, GF has constructs inherited from functional programming languages, an optimizing grammar compiler and code generation into several other formats. The most ambitious multilingual grammar is the GF Resource Grammar Library, which implements the main grammar rules of 12 languages. This library enables non‐linguist programmers to build linguistically correct applications. It is at the same time a linguistic experiment showing how far one can go in sharing structure between languages.
Cognitive Research in GIScience: Recent Achievements and Future Prospects
Authors: Montello Daniel R
Published: August 2009

In this article, recent achievements of cognitive research in geographic information science (GIScience) are reviewed and prospects for future directions discussed. Cognitive research in GIScience concerns human knowledge and knowing involving geographic information and geographic information systems (GIS). It includes both internal mental and external symbolic structures and processes, and is practically motivated by the desire to improve the usability, efficiency, equity, and profitability of geographic information and GIS. Taking 1992 as the start of modern GIScience, recent cognitive research falls into six areas: human factors of GIS, geovisualization, navigation systems, cognitive geo‐ontologies, geographic and environmental spatial thinking and memory, and cognitive aspects of geographic education. Future prospects for cognitive GIScience research include recommendations for methods, including eye‐movement recordings and fMRI; theoretical approaches, including situated cognition, evolutionary cognition, and cognitive neuroscience; and specific problems, including how users incorporate uncertainty metadata in reasoning and decision making, the role of GIS in teaching K‐12 students to think spatially, and the potential detrimental effects of over‐reliance on digital navigation systems.
Autoethnography
Authors: Butz David , Besio Kathryn
Published: August 2009

The term autoethnography was described by Reed‐Danahay as ‘a form of self‐narrative that places the self within a social context’. We outline autoethnography’s main characteristics, situate it in relation to the so‐called ‘crisis of representation’, and describe five loosely configured categories of autoethnographic practice. We argue that all types of authoethnography dissolve to some extent the boundary between authors and objects of representation, as authors become part of what they are studying, and research subjects are re‐imagined as reflexive narrators of self. Dismantling the author/represented boundary in this way has implications for how researchers understand their objects of research and ethnographic knowledge itself. The study discusses the relevance for geographers of the various categories of autoethnographic practice and of a broader autoethnographic sensibility.
Airborne Hyperspectral Imagery for Mapping Crop Yield Variability
Authors: Yang Chenghai
Published: August 2009

Information concerning the spatial variation in crop yield has become necessary for site‐specific crop management. Traditional satellite imagery has long been used to monitor crop growing conditions and to estimate crop yields over large geographic areas. However, this type of imagery has limited use for assessing within‐field yield variability because of its coarse spatial resolution. Therefore, high‐resolution airborne multispectral and hyperspectral imagery has been used for this purpose. This study presents an overview on the use of remote sensing imagery for mapping crop yield variability and illustrates how airborne hyperspectral imagery can be used for crop yield estimation based on the work conducted at the US Department of Agriculture’s Kika de la Garza Subtropical Agricultural Research Center at Weslaco, Texas. Some of the challenges and considerations on the use of hyperspectral imagery for yield mapping are discussed.
Dendritic Cell Therapy of High‐Grade Gliomas
Authors: Van Gool Stefaan , Maes Wim , Ardon Hilko , Verschuere Tina , Van Cauter Sofie , De Vleeschouwer Steven
Published: September 2009

The prognosis of patients with malignant glioma is poor in spite of multimodal treatment approaches consisting of neurosurgery, radiochemotherapy and maintenance chemotherapy. Among innovative treatment strategies like targeted therapy, antiangiogenesis and gene therapy approaches, immunotherapy emerges as a meaningful and feasible treatment approach for inducing long‐term survival in at least a subpopulation of these patients. Setting up immunotherapy for an inherent immunosuppressive tumor located in an immune‐privileged environment requires integration of a lot of scientific input and knowledge of both tumor immunology and neuro‐oncology. The field of immunotherapy is moving into the direction of active specific immunotherapy using autologous dendritic cells (DCs) as vehicle for immunization. In the translational research program of the authors, the whole cascade from bench to bed to bench of active specific immunotherapy for malignant glioma is covered, including proof of principle experiments to demonstrate immunogenicity of patient‐derived mature DCs loaded with autologous tumor lysate, preclinical in vivo experiments in a murine orthotopic glioma model, early phase I/II clinical trials for relapsing patients, a phase II trial for patients with newly diagnosed glioblastoma (GBM) for whom immunotherapy is integrated in the current multimodal treatment, and laboratory analyses of patient samples. The strategies and results of this program are discussed in the light of the internationally available scientific literature in this fast‐moving field of basic science and translational clinical research.
Does Live Supervision Make a Difference? A Multilevel Analysis
Authors: Bartle‐Haring Suzanne , Silverthorn Brandon C. , Meyer Kevin , Toviessi Paula
Published: August 2009

While the benefit of live supervision on clinical training is largely unquestioned, research that examines how live supervision affects the therapeutic process is lacking. Although marriage and family therapy has embraced this method of supervision, there is little empirical evidence suggesting it “works.” This study uses hierarchical linear modeling to examine how therapy cases utilizing live supervision affect perceptions of progress on the problem. Findings indicated that live supervision does appear to make a difference for therapists’ ratings of progress on the problem over the course of therapy; however, clients did not rate their progress as improving to the same degree. Implications for the use of live supervision as well as limitations of the study are discussed.
Evidence‐Based Medicine and Knowledge Dissemination, Translation, and Utilization: Challenges of Getting Evidence‐Based Treatments to Patient Care and Service Delivery
Authors: Soydan Haluk
Published: August 2009

The aim of this article is to explore challenges associated with effective utilization of best available scientific evidence on what works and what is potentially harmful in health, mental health, and social care. A gap exists between the production of high quality evidence on what has proven to be successful and the utilization of this evidence in human services. Patients and service users do not always receive interventions supported by the best available scientific evidence. Methods of evidence‐based medicine and evidence‐based practice have emerged as promising approaches to remedy this deficit. Furthermore, implementation and translational research, supported by multi‐disciplinary efforts, is emerging as another approach to bring best available evidence to service delivery settings. Although these approaches are promoted by diverse stakeholders in many countries, we are still waiting for rigorous evaluations of these approaches to understand their effectiveness in comparison to traditional ways of delivering interventions and other types of services in human services organizations.
The immunopathogenesis of periodontal disease
Authors: Ohlrich EJ , Cullinan MP , Seymour GJ
Published: September 2009

Treatment planning in periodontics, as with any disease, must be based on an understanding of the aetiology and pathogenesis of the disease. In this context, it has slowly become recognized over the past three decades that while plaque is the cause of the disease, it is the innate susceptibility of the host that determines the ultimate outcome of the disease process. Innate susceptibility, in turn, is determined by the nature of the immune response to the specific periodontopathic complexes comprising the plaque biofilm. The aim of this review was to examine current understanding of the immunopathogenesis of chronic periodontitis with respect to its possible clinical implications in terms of treatment planning and risk assessment. Numerous studies have demonstrated that the periodontitis lesion itself involves predominantly B cells and plasma cells, while the gingivitis lesion is primarily a T cell mediated response. This led to the concept over 30 years ago that the development of periodontitis involves a switch from a T cell lesion to one involving large numbers of B cells and plasma cells. It is also well recognized that control of this shift is mediated by a balance between the so‐called Th1 and Th2 subsets of T cells, with chronic periodontitis being mediated by Th2 cells. More recently, T regulatory (Treg) and Th17 cells have been demonstrated in periodontal tissues, raising the possibility that these cells are also important in the immunoregulation of periodontal disease. The clinical implications of these observations can be seen in the fact that identification of Th1/Th2 and Treg/Th17 cytokine gene expression in the peripheral blood and salivary transcriptomes is now being trialled as a possible marker of disease susceptibility. If this proves to be the case, a chairside salivary diagnostic could be developed within the next five to 10 years.
Periodontal regeneration
Authors: Ivanovski S
Published: September 2009

The ultimate goal of periodontal therapy is the regeneration of the tissues destroyed as a result of periodontal disease. Currently, two clinical techniques, based on the principles of “guided tissue regeneration” (GTR) or utilization of the biologically active agent “enamel matrix derivative” (EMD), can be used for the regeneration of intrabony and Class II mandibular furcation periodontal defects. In cases where additional support and space‐making requirements are necessary, both of these procedures can be combined with a bone replacement graft. There is no evidence that the combined use of GTR and EMD results in superior clinical results compared to the use of each material in isolation. Great variability in clinical outcomes has been reported in relation to the use of both EMD and GTR, and these procedures can be generally considered to be unpredictable. Careful case selection and treatment planning, including consideration of patient, tooth, site and surgical factors, is required in order to optimize the outcomes of treatment. There are limited data available for the clinical effectiveness of other biologically active molecules, such as growth factors and platelet concentrates, and although promising results have been reported, further clinical trials are required in order to confirm their effectiveness. Current active areas of research are centred on tissue engineering and gene therapy strategies which may result in more predictable regenerative outcomes in the future.
Engineering Silicone Rubbers for In Vitro Studies: Creating AAA Models and ILT Analogues With Physiological Properties
Authors: Corbett T. J. , Doyle B. J. , Callanan A. , Walsh M. T. , McGloughlin T. M.
Published: September 2009

In vitro studies of abdominal aortic aneurysm (AAA) have been widely reported. Frequently mock artery models with intraluminal thrombus (ILT) analogs are used to mimic the in vivo AAA. While the models used may be physiological, their properties are frequently either not reported or investigated. This study is concerned with the testing and characterization of previously used vessel analog materials and the development of new materials for the manufacture of AAA models. These materials were used in conjunction with a previously validated injection molding technique to manufacture AAA models of ideal geometry. To determine the model properties (stiffness (β) and compliance), the diameter change of each AAA model was investigated under incrementally increasing internal pressures and compared with published in vivo studies to determine if the models behaved physiologically. A FEA study was implemented to determine if the pressure-diameter change behavior of the models could be predicted numerically. ILT analogs were also manufactured and characterized. Ideal models were manufactured with ILT analog internal to the aneurysm region, and the effect of the ILT analog on the model compliance and stiffness was investigated. The wall materials had similar properties (Einit 2.22 MPa and 1.57 MPa) to aortic tissue at physiological pressures (1.8 MPa (from literature)). ILT analogs had a similar Young’s modulus (0.24 MPa and 0.33 MPa) to the medial layer of ILT (0.28 MPa (from literature)). All models had aneurysm sac compliance (2.62–8.01×10−4/mm Hg) in the physiological range (1.8–9.4×10−4/mm Hg (from literature)). The necks of the AAA models had similar stiffness (20.44–29.83) to healthy aortas (17.5±5.5 (from literature)). Good agreement was seen between the diameter changes due to pressurization in the experimental and FEA wall models with a maximum difference of 7.3% at 120 mm Hg. It was also determined that the inclusion of ILT analog in the sac of the models could have an effect on the compliance of the model neck. Ideal AAA models with physiological properties were manufactured. The behavior of these models due to pressurization was predicted using finite element analysis, validating this technique for the future design of realistic physiological AAA models. Addition of ILT analogs in the aneurysm sac was shown to affect neck behavior. This could have implications for endovascular AAA repair due to the importance of the neck for stent-graft fixation.
Evolution of surface morphology of dry-etched ZnO with Cl2/Ar plasma
Authors: Hsueh Kuang-Po , Hou Ren-Jie , Tun Chun-Ju
Published: August 2009

This work elucidates the surface morphologies of dry-etched ZnO films formed by reactive ion etching using a Cl2/Ar mixture. The root-mean-square (rms) roughness and etching rate were obtained by varying the gas flow ratio, the radio-frequency (rf) plasma power, and the chamber pressure. Atomic force microscopy results and surface topographies are discussed. The rms roughness is highest, 24.20 nm, at a Cl2/Ar flow rate of 150/10 SCCM (SCCM denotes cubic centimeter per minute at STP), a working pressure of 190 mTorr, and a rf power of 300 W. Such films are suitable for use as roughened transparent contact layers in light-emitting diodes. Bearing ratio analysis reveals that under the aforementioned condition, the nanorods covered 25.4% of the total surface area and their maximum height was approximately 150.83 nm. Moreover, high and low etching rates of 300 and 16 Å/min were obtained at rf powers of 300 and 50 W, respectively, supporting the ZnO-based devices and the gate-recess process.
Effect of liquid dispensing on flow field for immersion lithography
Authors: Chen Wenyu , Chen Ying , Zou Jun , Fu Xin , Yang Huayong , Ruan Xiaodong , Gong Guofang
Published: August 2009

Immersion lithography has been proposed as a method for improving optical lithography resolution to 50nm and below. The premise behind the concept is to increase the refraction index in the space between the lens and the wafer by insertion of a high refractive index liquid in place of the low refractive index air that currently fills the gap. During the scanning and exposure process, immersion liquid is injected into the space between the wafer and the lens with certain inlet pressure and angle. Because the liquid will act as a lens component during the lithographic process, it must maintain high uniform optical quality. One source of optical degradation may be due to liquid contamination by chemical products or impurities during exposure period. Immersion liquid renovation is probably the best solution. Refreshing cycle time and flow field velocity distribution were investigated by experimental and simulation methods. An empirical formula of velocity distribution was proposed in this article. The other source of optical degradation may be due to lens distortion caused by the pressure distribution nonuniformity in the flow field of the immersion liquid. Consequently, any deviations of pressure distribution on the flow field boundary in direct contact with lens may damage the uniform optical path. Three-dimensional computational fluid dynamics models were built to assess the pressure distribution characteristics relevant to flow rates and injecting angles of the immersion liquid. Compared with experimental results, the numerical simulation results were presented and discussed, featuring flow field stream patterns, lens normal and shear pressure, and injection flow, considering fluid injecting velocity, dispense ports quantity, and direction angles.
Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target
Authors: Walker Laura M. , Phogat Sanjay K. , Chan-Hui Po-Ying , Wagner Denise , Phung Pham , Goss Julie L. , Wrin Terri , Simek Melissa D. , Fling Steven , Mitcham Jennifer L. , Lehrman Jennifer K. , Priddy Frances H. , Olsen Ole A. , Frey Steven M. , Hammond Phillip W. ,   Protocol G Principal Investigators, Kaminsky Stephen , Zamb Timothy , Moyle Matthew , Koff Wayne C. , Poignard Pascal , Burton Dennis R.
Published: September 2009

Anti-HIV Antibodies

One of the top priorities for an HIV vaccine is the ability to elicit a broadly neutralizing antibody response, which should provide the best protection against infection. In the 25 years since the discovery of HIV, very few broadly neutralizing antibodies have been identified, and those that do exist were discovered nearly two decades ago. Using a high-throughput culture system,

Walker
et al.

(p.
285
; published online 3 September) now identify two additional broadly neutralizing antibodies isolated from a clade A HIV-infected African donor. These antibodies exhibit great potency and, in contrast to other known broadly neutralizing antibodies, are able to neutralize a wide range of viruses from many different clades. The antibodies recognize a motif in the trimerized viral envelope protein that is found in conserved regions of the variable loops of the gp120 subunit. Identification of this motif provides an intriguing new target for vaccine development.
Dirac Strings and Magnetic Monopoles in the Spin Ice Dy
2
Ti
2
O
7
Authors: Morris D. J. P. , Tennant D. A. , Grigera S. A. , Klemke B. , Castelnovo C. , Moessner R. , Czternasty C. , Meissner M. , Rule K. C. , Hoffmann J.-U. , Kiefer K. , Gerischer S. , Slobinsky D. , Perry R. S.
Published: September 2009

Magnetic Monopoles

Magnets come with a north and a south pole. Despite being predicted to exist, searches in astronomy and in high-energy particle physics experiments for magnetic monopoles (either north or south on their own) have defied observation. Theoretical work in condensed-matter systems has predicted that spin-ice structures may harbor such elusive particles (see the Perspective by

Gingras

).

Fennell
et al.

(p.
415
, published online 3 September) and

Morris
et al.

(p.
411
, published online 3 September) used polarized neutron scattering to probe the spin structure forming in two spin-ice compounds—Ho
2
Ti
2
O
7
and Dy
2
Ti
2
O
7
—and present results in support of the presence of magnetic monopoles in both materials.
High-Level Rifampin Resistance Correlates with Multiple Mutations in therpoBGene of Pulmonary Tuberculosis Isolates from the Afghanistan Border of Iran
Authors: Bahrmand Ahmad Reza , Titov Leonid P. , Tasbiti Alireza Hadizadeh , Yari Shamsi , Graviss Edward A.
Published: August 2009

The aim of this study was to investigate the significance of multiple mutations in therpoBgene as well as predominant nucleotide changes and their correlation with high levels of resistance to rifampin (rifampicin) inMycobacterium tuberculosisisolates that were randomly collected from the sputa of 46 patients with primary and secondary cases of active pulmonary tuberculosis from the southern region (Afghanistan border) of Iran where tuberculosis is endemic. Drug susceptibility testing was performed using the CDC standard conventional proportional method. DNA extraction,rpoBgene amplification, and DNA sequencing analysis were performed. Thirty-five (76.09%) isolates were found to have multiple mutations (two to four) in therpoB(β-subunit) gene. Furthermore, we demonstrate that the combination of mutations with more prevalent nucleotide changes were observed in codons 523, 526, and 531, indicating higher frequencies of mutations among patients with secondary infection. In this study, 76.08% (n= 35) of all isolates found to have mutation combinations involving nucleotide changes in codons 523 (GGG→GCG), 531 (TCG→TTG or TTC), and 526 (CAC→CGC, TTC, AAC, or CAA) demonstrated an association with higher levels of resistance to rifampin (MIC, ≥100 μg/ml).
The Remarkable Frequency of Human Immunodeficiency Virus Type 1 Genetic Recombination
Authors: Onafuwa-Nuga Adewunmi , Telesnitsky Alice
Published: August 2009

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) results from a combination of point mutations and genetic recombination, and rates of both processes are unusually high. This review focuses on the mechanisms and outcomes of HIV-1 genetic recombination and on the parameters that make recombination so remarkably frequent. Experimental work has demonstrated that the process that leads to recombination—a copy choice mechanism involving the migration of reverse transcriptase between viral RNA templates—occurs several times on average during every round of HIV-1 DNA synthesis. Key biological factors that lead to high recombination rates for all retroviruses are the recombination-prone nature of their reverse transcription machinery and their pseudodiploid RNA genomes. However, HIV-1 genes recombine even more frequently than do those of many other retroviruses. This reflects the way in which HIV-1 selects genomic RNAs for coencapsidation as well as cell-to-cell transmission properties that lead to unusually frequent associations between distinct viral genotypes. HIV-1 faces strong and changeable selective conditions during replication within patients. The mode of HIV-1 persistence as integrated proviruses and strong selection for defective proviruses in vivo provide conditions for archiving alleles, which can be resuscitated years after initial provirus establishment. Recombination can facilitate drug resistance and may allow superinfecting HIV-1 strains to evade preexisting immune responses, thus adding to challenges in vaccine development. These properties converge to provide HIV-1 with the means, motive, and opportunity to recombine its genetic material at an unprecedented high rate and to allow genetic recombination to serve as one of the highest barriers to HIV-1 eradication.
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
Authors: van Hijum Sacha A. F. T. , Medema Marnix H. , Kuipers Oscar P.
Published: August 2009

A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been very innovative in creating intricate mechanisms by which different regulatory signals operate and interact at promoters to drive gene expression. The regulation of target gene expression by transcription factors (TFs) is governed by control logic brought about by the interaction of regulators with TF binding sites (TFBSs) incis-regulatory regions. A factor that in large part determines the strength of the response of a target to a given TF is motif stringency, the extent to which the TFBS fits the optimal TFBS sequence for a given TF. Advances in high-throughput technologies and computational genomics allow reconstruction of transcriptional regulatory networks in silico. To optimize the prediction of transcriptional regulatory networks, i.e., to separate direct regulation from indirect regulation, a thorough understanding of the control logic underlying the regulation of gene expression is required. This review summarizes the state of the art of the elements that determine the functionality of TFBSs by focusing on the molecular biological mechanisms and evolutionary origins ofcis-regulatory regions.
QTc: how long is too long?
Authors: Johnson J N , Ackerman M J
Published: September 2009

Congenital long QT syndrome (LQTS) affects an estimated 1 in 2500 people and typically presents with syncope, seizures or sudden death. Whereas someone exhibiting marked prolongation of the QT interval with QTc exceeding 500 ms who was just externally defibrillated from torsades de pointes while swimming poses negligible diagnostic challenge as to the unequivocal probability of LQTS, the certainty is considerably less for the otherwise asymptomatic person who happens to host a QTc value coined “borderline” (QTc ⩾440 ms). Although a normal QT interval imparts a much lower risk of life-threatening events, it does not preclude a patient from nevertheless harbouring a potentially lethal LQTS-causing genetic mutation. Indeed, genetic testing exerts significant diagnostic, prognostic and therapeutic implications. However, the 12-lead ECG remains the universal initial diagnostic test in the evaluation of LQTS and is subject to miscalculation, misinterpretation and mishandling. This review discusses the components of accurate QTc measurement and diagnosis, re-examines what is known about factors affecting QT interval measurement, and clarifies current recommendations regarding diagnosis of so-called “borderline” QT interval prolongation. The current guideline recommendations for the athlete with LQTS are also summarised.
Primitive non-neural granular cell tumour with lymph node metastasis
Authors: Habeeb A Al , Weinreb I , Ghazarian D
Published: September 2009

Primitive non-neural granular cell tumour (PNGCT) is a rare tumour of uncertain lineage. This report describes a case of PGNCT with lymph node metastasis. This is thought to be only the second reported case with lymph node involvement.
MATRIX AIRY FUNCTIONS FOR COMPACT LIE GROUPS
Authors: FERNANDEZ RAHUL N. , VARADARAJAN V. S.
Published: August 2009

The classical Airy function has been generalized by Kontsevich to a function of a matrix argument, which is an integral over the space of skew-hermitian matrices of a unitary-invariant exponential kernel. In this paper, the Kontsevich integral is further generalized to integrals over the Lie algebra of an arbitrary connected compact Lie group, using exponential kernels invariant under the group. The (real) polynomial defining this kernel is said to have the Airy property if the integral defines a function of moderate growth. A very general sufficient criterion for a polynomial to have the Airy property is given. It is shown that an invariant polynomial on the Lie algebra has the Airy property if its restriction to a Cartan subalgebra has the Airy property. This result is used to evaluate these invariant integrals completely and explicitly on the hermitian matrices, obtaining formulae that contain those of Kontsevich as special cases.
ADDING A UNITON VIA THE DPW METHOD
Authors: CORREIA N. , PACHECO R.
Published: August 2009

In this paper we describe how the operation of adding a uniton arises via the DPW method of obtaining harmonic maps into compact Riemannian symmetric spaces from certain holomorphic 1-forms. We exploit this point of view to investigate which unitons preserve finite type property of harmonic maps. In particular, we prove that the Gauss bundle of a harmonic map of finite type into a Grassmannian is also of finite type.
ON THE CONNECTEDNESS OF THE LOCUS OF REAL ELLIPTIC-HYPERELLIPTIC RIEMANN SURFACES
Authors: BUJALANCE JOSÉ A. , COSTA ANTONIO F. , PORTO ANA M.
Published: August 2009

A Riemann surface X of genus g > 2 is elliptic-hyperelliptic if it admits a conformal involution h such that the orbit space X/〈h〉 has genus one. This elliptic-hyperelliptic involution h is unique for g > 5 [1]. In a previous article [3], we established the non-connectedness of the subspace [Formula: see text] of real elliptic-hyperelliptic algebraic curves in the moduli space [Formula: see text] of Riemann surfaces of genus g, when g is even and > 5. In this paper we improve this result and give a complete answer to the connectedness problem of the space [Formula: see text] of real elliptic-hyperelliptic surfaces of genus > 5: we show that [Formula: see text] is connected if g is odd and has exactly two connected components if g is even; in both cases the closure [Formula: see text] of [Formula: see text] in the compactified moduli space [Formula: see text] is connected.
2-STRING FREE TANGLES AND INCOMPRESSIBLE SURFACES
Authors: LI YANNAN
Published: August 2009

Suppose k is a connected sum of two knots, one of which admits a 2-string essential free tangle decomposition, then the exterior of k contains an incompressible surface of genus n for each positive integer n.
GENERALIZED KNOT GROUPS DISTINGUISH THE SQUARE AND GRANNY KNOTS (WITH AN APPENDIX BY DAVID SAVITT)
Authors: TUFFLEY CHRISTOPHER
Published: August 2009

Given a knot K we may construct a group Gn(K) from the fundamental group of K by adjoining an nth root of the meridian that commutes with the corresponding longitude. These "generalized knot groups" were introduced independently by Wada and Kelly, and contain the fundamental group as a subgroup. The square knot SK and the granny knot GK are a well-known example of a pair of distinct knots with isomorphic fundamental groups. We show that Gn(SK) and Gn(GK) are non-isomorphic for all n ≥ 2. This confirms a conjecture of Lin and Nelson, and shows that the isomorphism type of Gn(K), n ≥ 2, carries more information about K than the isomorphism type of the fundamental group. The appendix contains some results on representations of the trefoil group in PSL(2, p) that are needed for the proof.
CYCLOTOMIC BIRMAN–WENZL–MURAKAMI ALGEBRAS, I: FREENESS AND REALIZATION AS TANGLE ALGEBRAS
Authors: GOODMAN FREDERICK M. , MOSLEY HOLLY HAUSCHILD
Published: August 2009

The cyclotomic Birman–Wenzl–Murakami algebras are quotients of the affine BMW algebras in which the affine generator satisfies a polynomial relation. We show that the cyclotomic BMW algebras are free modules over any admissible, integral ground ring, and that they are isomorphic to cyclotomic versions of the Kauffman tangle algebras.
Geodynamic evolution of the 2.25-2.0 Ga Palaeoproterozoic magmatic rocks in the Man-Leo Shield of the West African Craton. A model of subsidence of an oceanic plateau
Authors: Lompo M.
Published: September 2009

The West African Craton is defined by the presence of Archaean and Palaeoproterozoic (Birimian) rocks. Since 1990, researchers have published several papers proposing various regional scale accretionary models for the evolution of the Birimian series and the Eburnean orogeny. The Birimian lithostratigraphic succession starts with a major sequence of tholeiitic pillow basalts with intercalations of sediments, overlain by detrital and carbonate sediments, associated with calc-alkaline volcanics and plutons. A global scheme for the geodynamical evolution can be reasonably constrained using the characteristics of early tholeiitic plutono-volcanic and granitoid rocks. Geochemical, geochronological and structural characteristics of Palaeoproterozoic magmatic rocks of the Man-Leo Shield distinguish three tholeiitic (PTH1, PTH2, PTH3) and two granitic (PAG, PBG) series and date three principal events that have characterized the 2250–2000 Ma period: (1) Event I (2250–2200 Ma) characterized by tholeiitic volcanism with a widespread first tholeiite generation (PTH1), interpreted as the eruption of a mantle plume in an oceanic basin floor; (2) Event II (2200–2150 Ma) marked by second (PTH2) and third (PTH3) tholeiite generations and a calc-alkaline magma setting; high granitization and amphibole-bearing (PAG) granitoid emplacement with greenstone belt deformation. This event has been favoured by a crustal subsidence in a broad synclinorium mega-structure followed by vertical tectonics; (3) Event III (2150–2000 Ma) characterized by main biotite±muscovite (without amphibole) bearing (PBG) granitoid emplacement in a context of transcurrent deformation. There are many similarities between West African Palaeoproterozoic rocks and Archaean formations and their crustal evolution also may be similar.
The Ecology and Evolution of Microbes that Manipulate Host Reproduction
Authors: Engelstädter Jan , Hurst Gregory D.D.
Published: August 2009

Inherited microorganisms that manipulate the reproduction of their host are a common feature in arthropod biology. Although research initially concentrated on why these manipulations were observed, more recent study has emphasized the profound effects they may have on the ecology and evolution of their host. We review the natural history and evolutionary ecology of inherited reproductive parasites, before examining their impact on host ecology and evolution. We posit that sex-ratio distorting microorganisms sometimes dominate their host's microevolution and reproductive ecology, driving extremely rapid natural selection, altering the molecular evolution landscape, and potentially causing evolution in conserved systems such as sex determination. The evolutionary importance of symbionts inducing cytoplasmic incompatibility lies more in the barriers to gene flow they can produce, which may then contribute to reproductive isolation and speciation. Throughout, we link theory with empirical data, point to areas of ignorance, and identify promising avenues of future research.
Gene Flow and Isolation among Populations of Marine Animals
Authors: Hellberg Michael E.
Published: August 2009

Successful dispersal between populations leaves a genetic wake that can reveal historical and contemporary patterns of connectivity. Genetic studies of differentiation in the sea suggest the role of larval dispersal is often tempered by adult ecology, that changes in differentiation with geographic distance are limited by disequilibrium between drift and migration, and that phylogeographic breaks reflect shared barriers to movement in the present more than common historical divisions. Recurring complications include the presence of cryptic species, selection on markers, and a failure to account for differences in heterozygosity among markers and species. A better understanding of effective population sizes is needed. Studies that infer parentage or kinship and coalescent analyses employing more markers are both likely to spur progress, with analyses based on linkage disequilibrium potentially bridging results from these studies and reconciling patterns that vary at ecological and evolutionary timescales.
Geologic and Biologic Controls on the Evolution of Reefs
Authors: Kiessling Wolfgang
Published: August 2009

The shallow, tropical reef environment differs from other marine environments in its more intense competition for space, more limited nutrient concentrations, proliferation of clonal animals, and greater habitat complexity. The evolutionary consequences of these ecologic peculiarities are still poorly understood, but they seem to cause greater turnover rates of reef taxa than nonreef taxa and an especially volatile record of reefs on geologic timescales. The boom and bust pattern of Phanerozoic reef construction is impossible to explain by linear responses to physicochemical changes. Threshold effects appear to be involved not only in reef crises but also in reef expansions. Long-term climate change seems to influence the biotic composition of reefs, but neither climate nor sea-level nor chemical changes in the oceans can elucidate the waxing and waning of reefs. Biological factors affecting spatial competition are thus probably more important than geologic controls on reef evolution.
Latex: A Model for Understanding Mechanisms, Ecology, and Evolution of Plant Defense Against Herbivory
Authors: Agrawal Anurag A. , Konno Kotaro
Published: August 2009

Latex is a sticky emulsion that exudes upon damage from specialized canals in about 10% of flowering plant species. Latex has no known primary metabolic function and has been strongly implicated in defense against herbivorous insects. Here we review historical hypotheses about the function of latex, evidence that it serves as a potent defense, and the chemistry and mode of action of the major constituent defense chemicals and proteins across a diversity of plant species. We further attempt to synthesize the characteristics of latex as a coordinated plant defense system. Herbivores that feed on latex-bearing plants typically evade contact with latex by severing the laticifers or feeding intercellularly, or may possess physiological adaptations. Convergent evolution appears to be rampant both in plants with latex and insects that exploit latex-bearing plants. Because latex shows phenotypic plasticity, heritability, and macoevolutionary lability, it is an ideal system to study plant-herbivore interactions using evolutionary approaches.
Diagnosis and Treatment of Neurocysticercosis
Authors: Coyle Christina M. , Tanowitz Herbert B.
Published: August 2009

Neurocysticercosis, the infection caused by the larval form of the tapewormTaenia solium, is the most common parasitic disease of the central nervous system and the most common cause of acquired epilepsy worldwide. This has primarily been a disease that remains endemic in low-socioeconomic countries, but because of increased migration neurocysticercosis is being diagnosed more frequently in high-income countries. During the past three decades improved diagnostics, imaging, and treatment have led to more accurate diagnosis and improved prognosis for patients. This article reviews the current literature on neurocysticercosis, including newer diagnostics and treatment developments.