bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved Estimation in Cumulative Link Models
Authors: Kosmidis Ioannis
Published: July 2013

For the estimation of cumulative link models for ordinal data, the bias reducing adjusted score equations of Firth in 1993 are obtained, whose solution ensures an estimator with smaller asymptotic bias than the maximum likelihood estimator. Their form suggests a parameter-dependent adjustment of the multinomial counts, which in turn suggests the solution of the adjusted score equations through iterated maximum likelihood fits on adjusted counts, greatly facilitating implementation. Like the maximum likelihood estimator, the reduced bias estimator is found to respect the invariance properties that make cumulative link models a good choice for the analysis of categorical data. Its additional finiteness and optimal frequentist properties, along with the adequate behaviour of related asymptotic inferential procedures, make the reduced bias estimator attractive as a default choice for practical applications. Furthermore, the estimator proposed enjoys certain shrinkage properties that are defensible from an experimental point of view relating to the nature of ordinal data.
Covariate Balancing Propensity Score
Authors: Imai Kosuke , Ratkovic Marc
Published: July 2013

The propensity score plays a central role in a variety of causal inference settings. In particular, matching and weighting methods based on the estimated propensity score have become increasingly common in the analysis of observational data. Despite their popularity and theoretical appeal, the main practical difficulty of these methods is that the propensity score must be estimated. Researchers have found that slight misspecification of the propensity score model can result in substantial bias of estimated treatment effects. We introduce covariate balancing propensity score (CBPS) methodology, which models treatment assignment while optimizing the covariate balance. The CBPS exploits the dual characteristics of the propensity score as a covariate balancing score and the conditional probability of treatment assignment. The estimation of the CBPS is done within the generalized method-of-moments or empirical likelihood framework. We find that the CBPS dramatically improves the poor empirical performance of propensity score matching and weighting methods reported in the literature. We also show that the CBPS can be extended to other important settings, including the estimation of the generalized propensity score for non-binary treatments and the generalization of experimental estimates to a target population. Open source software is available for implementing the methods proposed.
Cariogenic potential of medications used in treatment of children with HIV infection
Authors: Subramaniam Priya , Kumar Krishna
Published: July 2013

In children infected with human immunodeficiency virus (HIV), initiation of antiretroviral therapy (ART) commences at a very young age. These drugs are administered over a prolonged period and could be a possible risk factor for dental caries in these children.

Objectives

To assess endogenous pH, titratable acidity and type and concentration of sugars present in drugs used in treatment of HIV‐infected children.

Study design

Eleven drugs that are regularly prescribed to treat HIV infection in children (antiretrovirals, antibacterial, antifungal) were selected. The endogenous pH and titratable acidity of each drug was assessed. Type and concentration of sugars present in these medications was estimated using thin layer chromatography.

Results

Medications were mostly in syrup form and their pH ranged from 2.27 to 7.98. Titratable acidity varied between 0.01 to 0.37 mmol. Sucrose was present in all medications, and more than 60 g% of sucrose was present in anti‐acterial and antifungal preparations.

Conclusion

The physical properties and sugar content of medications used in ART pose a risk to dental health of children.
Air fuel ratio detector corrector for combustion engines using adaptive neuro-fuzzy networks
Authors: Arora Nidhi , Mehta Swati
Published: July 2013

A perfect mix of the air and fuel in internal combustion engines is desirable for proper combustion of fuel with air. The vehicles running on road emit harmful gases due to improper combustion. This problem is severe in heavy vehicles like locomotive engines. To overcome this problem, generally an operator opens or closes the valve of fuel injection pump of locomotive engines to control amount of air going inside the combustion chamber, which requires constant monitoring. A model is proposed in this paper to alleviate combustion process. The method involves recording the time-varying flow of fuel components in combustion chamber. A Fuzzy Neural Network is trained for around 40 fuels to ascertain the required amount of air to form a standard mix to produce non-harmful gases and about 12 fuels are used for testing the network’s performance. The network then adaptively determines the additional/subtractive amount of air required for proper combustion. Mean square error calculation ensures the effectiveness of the network’s performance.
Bactericidal Antibiotics Induce Mitochondrial Dysfunction and Oxidative Damage in Mammalian Cells
Authors: Kalghatgi Sameer , Spina Catherine S. , Costello James C. , Liesa Marc , Morones-Ramirez J. Ruben , Slomovic Shimyn , Molina Anthony , Shirihai Orian S. , Collins James J.
Published: July 2013

Mitochondrial dysfunction and oxidative damage induced by bactericidal antibiotics in mammalian cells may be alleviated by an antioxidant or prevented by preferential use of bacteriostatic antibiotics.
The Good and the Bad of Antibiotics
Authors: Chandel Navdeep S. , Budinger G. R. Scott
Published: July 2013

Bactericidal antibiotics induce generation of mitochondrial reactive oxygen species in mammalian cells (Kalghatgi
et al
., this issue).
Clinical Application of Volatile Organic Compound Analysis for Detecting Infectious Diseases
Authors: Sethi Shneh , Nanda Ranjan , Chakraborty Trinad
Published: July 2013

This review article introduces the significance of testing of volatile organic compounds (VOCs) in clinical samples and summarizes important features of some of the technologies. Compared to other human diseases such as cancer, studies on VOC analysis in cases of infectious diseases are limited. Here, we have described results of studies which have used some of the appropriate technologies to evaluate VOC biomarkers and biomarker profiles associated with infections. The publications reviewed include important infections of the respiratory tract, gastrointestinal tract, urinary tract, and nasal cavity. The results highlight the use of VOC biomarker profiles resulting from certain infectious diseases in discriminating between infected and healthy subjects. Infection-related VOC profiles measured in exhaled breath as well as from headspaces of feces or urine samples are a source of information with respect to disease detection. The volatiles emitted in clinical matrices may on the one hand represent metabolites of the infecting pathogen or on the other hand reflect pathogen-induced host responses or, indeed, a combination of both. Because exhaled-breath samples are easy to collect and online instruments are commercially available, VOC analysis in exhaled breath appears to be a promising tool for noninvasive detection and monitoring of infectious diseases.
Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology
Authors: Clark Andrew E. , Kaleta Erin J. , Arora Amit , Wolk Donna M.
Published: July 2013

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the “nuts and bolts” of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
β-Lactamase Production in Key Gram-Negative Pathogen Isolates from the Arabian Peninsula
Authors: Zowawi Hosam M. , Balkhy Hanan H. , Walsh Timothy R. , Paterson David L.
Published: July 2013

Infections due to Gram-negative bacilli (GNB) are a leading cause of morbidity and mortality worldwide. The extent of antibiotic resistance in GNB in countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, United Arab Emirates, Kuwait, Qatar, Oman, and Bahrain, has not been previously reviewed. These countries share a high prevalence of extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing GNB, most of which are associated with nosocomial infections. Well-known and widespread β-lactamases genes (such as those for CTX-M-15, OXA-48, and NDM-1) have found their way into isolates from the GCC states. However, less common and unique enzymes have also been identified. These include PER-7, GES-11, and PME-1. Several potential risk factors unique to the GCC states may have contributed to the emergence and spread of β-lactamases, including the unnecessary use of antibiotics and the large population of migrant workers, particularly from the Indian subcontinent. It is clear that active surveillance of antimicrobial resistance in the GCC states is urgently needed to address regional interventions that can contain the antimicrobial resistance issue.
Traditional and New Influenza Vaccines
Authors: Wong Sook-San , Webby Richard J.
Published: July 2013

The challenges in successful vaccination against influenza using conventional approaches lie in their variable efficacy in different age populations, the antigenic variability of the circulating virus, and the production and manufacturing limitations to ensure safe, timely, and adequate supply of vaccine. The conventional influenza vaccine platform is based on stimulating immunity against the major neutralizing antibody target, hemagglutinin (HA), by virus attenuation or inactivation. Improvements to this conventional system have focused primarily on improving production and immunogenicity. Cell culture, reverse genetics, and baculovirus expression technology allow for safe and scalable production, while adjuvants, dose variation, and alternate routes of delivery aim to improve vaccine immunogenicity. Fundamentally different approaches that are currently under development hope to signal new generations of influenza vaccines. Such approaches target nonvariable regions of antigenic proteins, with the idea of stimulating cross-protective antibodies and thus creating a “universal” influenza vaccine. While such approaches have obvious benefits, there are many hurdles yet to clear. Here, we discuss the process and challenges of the current influenza vaccine platform as well as new approaches that are being investigated based on the same antigenic target and newer technologies based on different antigenic targets.
Using Sequence Data To Infer the Antigenicity of Influenza Virus
Authors: Sun Hailiang , Yang Jialiang , Zhang Tong , Long Li-Ping , Jia Kun , Yang Guohua , Webby Richard J. , Wan Xiu-Feng
Published: July 2013

The efficacy of current influenza vaccines requires a close antigenic match between circulating and vaccine strains. As such, timely identification of emerging influenza virus antigenic variants is central to the success of influenza vaccination programs. Empirical methods to determine influenza virus antigenic properties are time-consuming and mid-throughput and require live viruses. Here, we present a novel, experimentally validated, computational method for determining influenza virus antigenicity on the basis of hemagglutinin (HA) sequence. This method integrates a bootstrapped ridge regression with antigenic mapping to quantify antigenic distances by using influenza HA1 sequences. Our method was applied to H3N2 seasonal influenza viruses and identified the 13 previously recognized H3N2 antigenic clusters and the antigenic drift event of 2009 that led to a change of the H3N2 vaccine strain.

IMPORTANCEThis report supplies a novel method for quantifying antigenic distance and identifying antigenic variants using sequences alone. This method will be useful in influenza vaccine strain selection by significantly reducing the human labor efforts for serological characterization and will increase the likelihood of correct influenza vaccine candidate selection.
Envelope Protein Dynamics in Paramyxovirus Entry
Authors: Plattet Philippe , Plemper Richard K.
Published: July 2013

Paramyxoviruses include major pathogens with significant global health and economic impact. This large family of enveloped RNA viruses infects cells by employing two surface glycoproteins that tightly cooperate to fuse their lipid envelopes with the target cell plasma membrane, an attachment and a fusion (F) protein. Membrane fusion is believed to depend on receptor-induced conformational changes within the attachment protein that lead to the activation and subsequent refolding of F. While structural and mechanistic studies have considerably advanced our insight into paramyxovirus cell adhesion and the structural basis of F refolding, how precisely the attachment protein links receptor engagement to F triggering remained poorly understood. Recent reports based on work with several paramyxovirus family members have transformed our understanding of the triggering mechanism of the membrane fusion machinery. Here, we review these recent findings, which (i) offer a broader mechanistic understanding of the paramyxovirus cell entry system, (ii) illuminate key similarities and differences between entry strategies of different paramyxovirus family members, and (iii) suggest new strategies for the development of novel therapeutics.
Streptomycin-Induced Inflammation Enhances Escherichia coli Gut Colonization Through Nitrate Respiration
Authors: Spees Alanna M. , Wangdi Tamding , Lopez Christopher A. , Kingsbury Dawn D. , Xavier Mariana N. , Winter Sebastian E. , Tsolis Renée M. , Bäumler Andreas J.
Published: July 2013

Treatment with streptomycin enhances the growth of human commensalEscherichia coliisolates in the mouse intestine, suggesting that the resident microbial community (microbiota) can inhibit the growth of invading microbes, a phenomenon known as “colonization resistance.” However, the precise mechanisms by which streptomycin treatment lowers colonization resistance remain obscure. Here we show that streptomycin treatment rendered mice more susceptible to the development of chemically induced colitis, raising the possibility that the antibiotic might lower colonization resistance by changing mucosal immune responses rather than by preventing microbe-microbe interactions. Investigation of the underlying mechanism revealed a mild inflammatory infiltrate in the cecal mucosa of streptomycin-treated mice, which was accompanied by elevated expression ofNos2, the gene that encodes inducible nitric oxide synthase. In turn, this inflammatory response enhanced the luminal growth ofE. coliby nitrate respiration in aNos2-dependent fashion. These data identify low-level intestinal inflammation as one of the factors responsible for the loss of resistance toE. colicolonization after streptomycin treatment.

IMPORTANCEOur intestine is host to a complex microbial community that confers benefits by educating the immune system and providing niche protection. Perturbation of intestinal communities by streptomycin treatment lowers “colonization resistance” through unknown mechanisms. Here we show that streptomycin increases the inflammatory tone of the intestinal mucosa, thereby making the bowel more susceptible to dextran sulfate sodium treatment and boosting theNos2-dependent growth of commensalEscherichia coliby nitrate respiration. These data point to the generation of alternative electron acceptors as a by-product of the inflammatory host response as an important factor responsible for lowering resistance to colonization by facultative anaerobic bacteria such asE. coli.
PORTFOLIO PERFORMANCE BENCHMARKING WITH DATA ENVELOPMENT ANALYSIS
Authors: WONG PHILIP Y. L. , LEUNG STEPHEN C. H. , GILLEARD JOHN D.
Published: July 2013

This paper proposes data envelopment analysis (DEA) as a suitable data analysis tool to overcome facility management (FM) benchmarking difficulties: FM performance benchmarking analysis is often unsophisticated, relying heavily on simple statistical representation, linking hard cost data with soft customer satisfaction data is often problematic. A case study is presented to show that DEA can provide FM personnel with an objective view on performance improvements. An objective of the case study is to investigate the relative efficiency of nine facilities with the same goals and to determine the most efficient facility. The case is limited to nine buildings in FM on four inputs and nine output criteria. The paper concludes by demonstrating that DEA-generated improvement targets can be applied when formulating FM outsourcing policies, strategies and improvements. Facility manager can apply DEA-generated improvement targets in formulating FM outsourcing policies, specifications development, FM strategy and planning. FM benchmarking with DEA can enhance continuous improvement in service efficiency and cost saving. This will help reduce utility cost as well as pollution. This paper fills the gap in the research of FM benchmarking by applying DEA which studies both soft and hard data simultaneously. It also contributes to a future research of a trade-off sensitivity test between FM cost, services performance and reliability.
ON THE DRESSING METHOD FOR THE GENERALIZED COUPLED DISPERSIONLESS INTEGRABLE SYSTEM
Authors: MUSHAHID NOSHEEN , UL HASSAN MAHMOOD
Published: July 2013

The dressing method of Zakharov and Shabat [Funct. Anal. Appl.8, 226 (1974) and ibid.13, 166 (1980)] has been employed to the generalized coupled dispersionless integrable system in two dimensions. The dressed solutions to the Lax pair and to the nonlinear matrix equation have been obtained in terms of Hermitian projectors. The dressing method has been related with the quasi-determinant solutions obtained by using the standard matrix Darboux transformation. The iteration of dressing procedure has been shown to give N-soliton solutions of the system. At the end, the explicit soliton solution has been obtained for the system based on Lie group SU(2).
SHORT TO MEDIUM RESULTS USING THE REMOTION TOTAL WRIST REPLACEMENT FOR RHEUMATOID ARTHRITIS
Authors: Bidwai A. S. C. , Cashin F. , Richards A. , Brown D. J.
Published: July 2013

We present the clinical outcome of patients who underwent RE-MOTION Total Wrist Replacement (TWR) for the treatment of Rheumatoid arthritis involving the wrist.

Ten patients were available for follow-up, ranging from one to five years after index surgery. Two patients required surgical intervention for wound breakdown, including one patient who required a radial forearm flap for skin coverage. No patients required revision surgery or conversion to fusion. Patients who did not have complications gained statistically significant pain relief and improvement in mean overall flexion.

In this small case series with short to medium results patients reported an improvement in terms of flexion and pain. Despite this, the question of efficacy of TWR compared to fusion in the long term remains unanswered due to the high rate of complications.
OUTCOMES OF FOUR-CORNER ARTHRODESIS USING THE HUBCAPTM CIRCULAR PLATE
Authors: Khan Sameer K. , Ali Syed M. , McKee Andrew , Jones Jonathan W. M.
Published: July 2013

We present results of four-corner carpal arthrodesis with the Acumed® HubcapTM circular plate performed at our unit. Eight patients underwent eight procedures over five years, for scapholunate advanced collapse (five wrists) and scaphoid non-union advanced collapse (three wrists). Outcomes included range of motion, quickDASH scores, and visual analogue scores for satisfaction. At final follow-up, mean flexion-extension arc was 56°, mean radial-ulnar deviation 29° and mean quickDASH score was 23/100. Mean score for satisfaction was 7.7/10 (77%). Seven out of eight (87.5%) patients said they would have it done again, and would also recommend it to others. Radiological union was achieved in all cases. One screw broke in one arthrodesis without causing symptoms. The functional outcomes with our use of the HubcapTM are comparable to those reported in literature to date with other circular plates (e.g. Spider plate). There were no non-unions, which is the main reported complication with these plates.
NECROTISING SOFT TISSUE INFECTION OF BILATERAL UPPER LIMB CAUSED BY THE INJECTION OF ORAL BACTERIA: A CASE REPORT
Authors: Yoshii Yuichi , Ishii Tomoo , Sakai Shinsuke
Published: July 2013

Necrotising soft tissue infection is a rare and rapid process with devastating consequence. We report one case of necrotising soft tissue infection in a bilateral upper limb with uncommon oral bacteria. Radiological imaging revealed the presence of gas in upper limb soft tissues, and an MRI showed the localised signal changes in the biceps muscle of the right upper arm, and the subcutaneous tissue of the left elbow. The patient was treated with surgical resection of the infected muscle and wide debridement of the subcutaneous tissue. Antibiotics were initiated. The patient recovered immediately without functional deficit. The unique features of this patient were possible to observe in the progression of the necrotising soft tissue infection in the bilateral upper limb with intentional injection of oral bacteria, and the effect of biceps brachii resection in a prime age worker.
A CASE OF ROTATIONAL RESTRICTION OF THE FOREARM DUE TO ABNORMAL CONFIGURATION OF PRONATOR QUADRATUS MUSCLE
Authors: Mochizuki Yusuke , Sawaizumi Takuya , Tsunoda Ryu , Horiguchi Gen , Matsui Syuhei , Takai Shinro
Published: July 2013

We present a case of rotational restriction of the forearm due to abnormal configuration of the pronator quadratus muscle. A 20-year-old man developed right wrist joint pain on pitching of a baseball game and thereafter displayed rotational disorder of the forearm. Magnetic resonance imaging (MRI) revealed a space-occupying lesion from the volar side of the radius to the dorsal side of the ulna. The lesion was iso-hyperintense on T1-weighted (T1W) images and showed a mixed pattern of high intensities on T2-weighted (T2W) images. His symptoms were immediately reduced after removal of the mass. Histological examination showed that the mass contained much skeletal muscle and revealed myxoid degeneration of striated muscles. We assumed that his pronator quadratus muscle had been a divided form of deep layer and superficial layer tissue, possibly congenitally. We supposed that the deep layer had degenerated due to chronic stimulation and had extended around to the dorsal side of the ulna, which caused rotational restriction from the resulting impaired distal radioulnar joint. To our knowledge, there has been no similar case reported in the literature.
BILATERAL MACRODYSTROPHIA LIPOMATOSA WITH SYNDACTYLY: A CASE REPORT AND LITERATURE REVIEW
Authors: Albright Steven B. , Wolfswinkel Erik M. , Caceres Kevin J. , Weathers William M. , Hollier Larry H.
Published: July 2013

Macrodystrophia lipomatosa is a rare, non-hereditary form of congenital local gigantism characterised by enlargement and hypertrophy of all mesenchymal tissue components with a disproportionate increase in adipose tissue. This form of macrodactyly has been reported in association with other anomalies including polydactyly, brachydactyly, syndactyly, and symphalangism. We describe a previously unreported case of bilateral upper extremity macrodystrophia lipomatosa with syndactyly in a 23-month-old boy. In this report, we emphasise the importance of establishing a diagnosis with imaging and review the described surgical approaches to treating this difficult condition.
BIPEDICLED HOMODIGITAL NEUROVASCULAR ISLAND FLAP FOR RESURFACING DORSAL DIGITAL DEFECTS AMPUTATION
Authors: Foo Tun Lin , Chew E. M. , Arul M.
Published: July 2013

Critical defects distal to the proximal interphalangeal joint are usually treated by heterodigital or reverse-flow homodigital flaps. Drawbacks of the former are potential donor digit stiffness and scarring, while the latter might be complicated by flap congestion. A bipedicled neurovascular island transposition flap design that preserves both proximal and distal extent of digital nerve and artery was employed to treat critical dorsal skin defect in two patients with encouraging results. Technical details and cadaveric study concepts are presented.
FINGER TOURNIQUETS: TWO SAFE AND COST EFFECTIVE TECHNIQUES AND A DISCUSSION OF THE LITERATURE
Authors: Martin-Smith J. D. , van der Rijt R. , Kelly J.
Published: July 2013

Finger tourniquets are used in a variety of operative procedures in both the trauma and elective setting. A wide range of methods are used in clinical practise as there is no standardised method. Many of the methods in use have significant drawbacks such as the inability to exsanguinate the digit or the more concerning problem of inadvertently leaving the tourniquet on the digit on completion of the procedure. We discuss two techniques that are quick, cheap and easy that do not have these drawbacks. There is a brief discussion of the literature assessing the various attributes of published methods. We feel that the adoption of these methods could result in easier and safer finger exsanguination and haemostasis.
OSTEOCUTANEOUS VY FLAP TO PRESERVE LENGTH IN CORONAL OBLIQUE FINGERTIP AMPUTATION
Authors: Foo Tun Lin , Arul M.
Published: July 2013

Radial or ulnar oblique amputations treated by nailbed levelling and local digital flap reconstruction can result in significantly shortened fingertip, narrowed pulp and nail shape distortion. A VY type flap containing bone, sterile matrix, and skin was conceptualised to restore nail and pulp contour for coronal oblique amputations. Technical details and a clinical case are discussed.
MULTISYMPLECTIC BRST
Authors: PELLING SIMON , ROGERS ALICE
Published: July 2013

After briefly describing Hamiltonian BRST methods and the multisymplectic approach to field theory, a symmetric geometric Lagrangian is studied by extending the BRST method to the multisymplectic setting. This work uses ideas first introduced by Hrabak [On the multisymplectic origin of the nonabelian deformation algebra of pseudoholomorphic embeddings in strictly almost Kähler ambient manifolds, and the corresponding BRST algebra, preprint (1999), arXiv: math-ph/9904026].
A SIMULTANEOUS MULTI-PROBE DETECTION LABEL-FREE OPTICAL-RESOLUTION PHOTOACOUSTIC MICROSCOPY TECHNIQUE BASED ON MICROCAVITY TRANSDUCER
Authors: WU YONGBO , TANG ZHILIE , CHI YAN , WU LIRU
Published: July 2013

We demonstrate the feasibility of simultaneous multi-probe detection for an optical-resolution photoacoustic microscopy (OR-PAM) system. OR-PAM has elicited the attention of biomedical imaging researchers because of its optical absorption contrast and high spatial resolution with great imaging depth. OR-PAM allows label-free and noninvasive imaging by maximizing the optical absorption of endogenous biomolecules. However, given the inadequate absorption of some biomolecules, detection sensitivity at the same incident intensity requires improvement. In this study, a modulated continuous wave with power density less than 3 mW/cm2 (1/4 of the ANSI safety limit) excited the weak photoacoustic (PA) signals of biological cells. A microcavity transducer is developed based on the bulk modulus of gas five orders of magnitude lower than that of solid; air pressure variation is inversely proportional to cavity volume at the same temperature increase. Considering that a PA wave expands in various directions, detecting PA signals from different positions and adding them together can increase detection sensitivity and signal-to-noise ratio. Therefore, we employ four detectors to acquire tiny PA signals simultaneously. Experimental results show that the developed OR-PAM system allows the label-free imaging of cells with weak optical absorption.
CHARACTERISTIC FEATURES OF MUELLER MATRIX PATTERNS FOR POLARIZATION SCATTERING MODEL OF BIOLOGICAL TISSUES
Authors: DU E , HE HONGHUI , ZENG NAN , LIU CELONG , GUO YIHONG , LIAO RAN , SUN MINGHAO , HE YONGHONG , MA HUI
Published: July 2013

We developed a model to describe polarized photon scattering in biological tissues. In this model, tissues are simplified to a mixture of scatterers and surrounding medium. There are two types of scatterers in the model: solid spheres and infinitely long solid cylinders. Variables related to the scatterers include: the densities and sizes of the spheres and cylinders, the orientation and angular distribution of cylinders. Variables related to the surrounding medium include: the refractive index, absorption coefficient and birefringence. In this paper, as a development we introduce an optical activity effect to the model. By comparing experiments and Monte Carlo simulations, we analyze the backscattering Mueller matrix patterns of several tissue-like media, and summarize the different effects coming from anisotropic scattering and optical properties. In addition, we propose a possible method to extract the optical activity values for tissues. Both the experimental and simulated results show that, by analyzing the Mueller matrix patterns, the microstructure and optical properties of the medium can be obtained. The characteristic features of Mueller matrix patterns are potentially powerful tools for studying the contrast mechanisms of polarization imaging for medical diagnosis.
The potential role of igneous intrusions on hydrocarbon migration, West of Shetland
Authors: Rateau Rémi , Schofield Nick , Smith Michael
Published: July 2013

Numerous challenges for petroleum exploration exist within basins containing sequences of intrusive and extrusive rocks, ranging from seismic imaging to drilling. One poorly understood element in dealing with volcanic-affected basins is assessing the impact magmatism has on the elements of the petroleum system. Within this study we attempt to evaluate the potential impact that the extensive sequence of igneous intrusions of the Faroe–Shetland Basin may have on hydrocarbon migration. Using available well data combined with regional 3D seismic surveys, we show that geometrical relationships between sills location and overlying hydrocarbons shows, together with several cases of gas-charged open fractures in the sills, point toward the recognition of igneous intrusions as a factor in hydrocarbon migration through sill intrusions acting as both barriers or conduits to hydrocarbon migration. We also provide a series of general conceptual models dealing with hydrocarbon migration and igneous compartmentalization within sedimentary basins, which can be applied not just to the Faroe–Shetland Basin, but to other sedimentary basins world-wide if it is found (via well data or other methods) that the intrusions are interacting with a petroleum system.
Determinants of Breast Cancer Treatment Delay Differ for African American and White Women
Authors: McGee Sasha A. , Durham Danielle D. , Tse Chiu-Kit , Millikan Robert C.
Published: July 2013

Background: Timeliness of care may contribute to racial disparities in breast cancer mortality. African American women experience greater treatment delay than White women in most, but not all studies. Understanding these disparities is challenging as many studies lack patient-reported data and use administrative data sources that collect limited types of information. We used interview and medical record data from the Carolina Breast Cancer Study (CBCS) to identify determinants of delay and assess whether disparities exist between White and African American women (n = 601).

Methods: The CBCS is a population-based study of North Carolina women. We investigated the association of demographic and socioeconomic characteristics, healthcare access, clinical factors, and measures of emotional and functional well-being with treatment delay. The association of race and selected characteristics with delays of more than 30 days was assessed using logistic regression.

Results: Household size, losing a job due to one's diagnosis, and immediate reconstruction were associated with delay in the overall population and among White women. Immediate reconstruction and treatment type were associated with delay among African American women. Racial disparities in treatment delay were not evident in the overall population. In the adjusted models, African American women experienced greater delay than White women for younger age groups: OR, 3.34; 95% confidence interval (CI), 1.07–10.38 for ages 20 to 39 years, and OR, 3.40; 95% CI, 1.76–6.54 for ages 40 to 49 years.

Conclusions: Determinants of treatment delay vary by race. Racial disparities in treatment delay exist among women younger than 50 years.

Impact: Specific populations need to be targeted when identifying and addressing determinants of treatment delay. Cancer Epidemiol Biomarkers Prev; 22(7); 1227–38. ©2013 AACR.
Hepatic Arterial Infusion with Irinotecan in Patients with Liver Metastases of Colorectal Cancer: Results of an Extended Phase I Study
Authors: Eichler K. , Dufas T. , Hammerstingl R. , Gruber-Rouh T. , Vogl T.J. , Zangos S.
Published: July 2013

Background: To define the maximum tolerated dose (MTD) tolerability and efficacy of intra-arterial chemotherapy with irinotecan in patients with liver metastases of colorectal carcinoma (CRC). Methods: Superselective intra-arterial irinotecan was applied on days 1, 14, 28 and 42. The initial dose was 140 mg/m2 with escalation in the subsequent patient group to 160 mg/m2. The final protocol toxicity evaluation was 260 mg/m2. Patients required histologically proven disease and adequate bone marrow, liver and renal function, no extrahepatic metastasis and a life expectancy >12 weeks. Results: Thirty-three patients were enrolled (median age 65, range 49-78 years). On dose level VI (240 mg/m2), 1 case of dose-limiting toxicity (DLT) (granulocytopenia) was observed, leading to an enlarged cohort of 6 patients. As no additional DLT was detected on this level, an escalation to level VII was performed. On the dose level of 260 mg/m2, irinotecan DLTs were observed, resulting in the termination of escalation and the declaration of dose level VI as MTD. Imaging follow-up with Response Evaluation Criteria in Solid Tumors (RECIST) criteria revealed a complete response in 1 patient, stable disease in 31 patients, and progressed disease in 1 patient. The median time to progression was 4.7 months, the median overall survival 15.6 months. Conclusion: The method of intra-arterial chemotherapy with irinotecan is well tolerated and shows promising local response rates in liver metastases of CRC.
Specific Nucleotide Changes in the Subgenomic Promoter Region Influence Infectivity of the Sindbis Virus
Authors: Zhu Wu-yang , Zhao Ting , Liang Guo-dong
Published: July 2013

Transcription of the subgenomic mRNA of Sindbis virus (SINV) is initiated at a subgenomic promoter (SP). Alignment of SINV sequences identified a 68-nucleotide conserved domain spanning -19 to +49 relative to the subgenomic mRNA start site. Nucleotide T or C is present at -18 or +49 in all known SINVs while a Sindbis-like virus XJ-160 has an A or T at a corresponding position. Our results indicate that deletion or substitution of the T at +49 decreased the activity of SP, while substituting T for A at -18 did not decrease the activity of SP or genetic stability of recombinant SINV.
Proficiency Test for Human Papillomavirus Genotyping in China
Authors: Zhang Rui , Huang Jie , Wang Pu , Sun Yu , Zhang Kuo , Xie Jiehong , Gao Shangxian , Wang Lunan , Li Jinming
Published: July 2013

Background: In China, various assays for human papillomavirus (HPV) genotyping are currently used for cervical cancer screening. However, a proficiency test system is not available for standardizing and evaluating assay performance. The aim of this study was to evaluate the performance of clinical laboratories for their ability to discriminate 9 HPV types with the proficiency panel. Methods: The panel of 24 samples included cloned genomic DNAs for HPV types 6, 11, 16, 18, 31, 33, 39, 51 and 52 at different concentrations, which were distributed to 76 clinical laboratories. Results reported by participants were compared with the reference results. Results: The samples containing 106 IU HPV-16/ml and 106 IU HPV-18/ml were (98.7 and 96.0%, respectively) identified correctly most often. For other high-risk HPV types, about 90% of data sets correctly identified samples containing 106 GE/ml of HPV-6, HPV-31, HPV-33 and HPV-52, while HPV-51, HPV-11 and HPV-39 in 106 GE/ml were correctly identified by only 42.7, 55.6 and 21.3% of laboratories, respectively. Conclusion: Our proficiency test system provided a traceable panel and showed that the differences in performance between laboratories were high, indicating that it is necessary for the laboratories to improve their operation and standardization of HPV genotyping.
Molecular Epidemiology and Genetic History of Hepatitis C Virus Subtype 3a Infection in Thailand
Authors: Akkarathamrongsin Srunthron , Hacharoen Pitchaya , Tangkijvanich Pisit , Theamboonlers Apiradee , Tanaka Yasuhito , Mizokami Masashi , Poovorawan Yong
Published: July 2013

Objective: Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. Methods: Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. Results: Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. Conclusion: The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.
Oral Mucosal Grafts: Old Technique in New Light
Authors: Mai Christian , Bertelmann Eckart
Published: July 2013

Purpose: To present an update on indications and efficacy of oral mucosal grafts in the clinical management of ocular surface diseases focusing on the new developments of the last 5 years. Methods: Pubmed research on the databases of the years 2007 up to 2012 for the key words mucous membrane graft and eye, fornix reconstruction, eyelid reconstruction, and conjunctival replacement. Results: Well-documented clinical indications for oral mucosal grafting to the ocular surface include correction of restricted socket syndrome, ocular adnexal reconstruction after tumor resection, cicatricial ocular surface diseases and therapy-refractory pterygia. New indications are conjunctival insufficiency after filtrating glaucoma surgery and the combination of mucosa and amniotic membrane grafting for fornix reconstruction. Moreover, different strategies for ex vivo mucous epithelial cell expansion are under discussion. Conclusions: Oral mucosal grafting is a viable option for the replacement of the conjunctiva. Advantages include easily accessibility of grafts in sufficient size even for repeated procedures and a high stability of the grafts. On the other hand, nasal mucosal grafts are superior for some indications due to the lack of goblet cells in the oral mucosa.
Influence of Human Saliva on the Development of Artificial Erosions
Authors: Hellwig E. , Lussi A. , Goetz F.
Published: July 2013

It was hypothesized that saliva from patients with erosion exhibits lower protective efficacy compared to saliva from patients without erosion, based on in vitro enamel softening studies. A total of 645 enamel specimens were distributed among seven experimental groups. Saliva was gathered from each of 10 volunteers without clinical signs of dental erosion and from 10 patients exhibiting severe erosive defects. Aliquots of 50 ml of saliva from each patient were mixed with sour drops or citric acid, respectively. Pooled saliva, sour drops and citric acid mixed with water served as controls. The enamel specimens were soaked in the respective mixture for 5 min and were subsequently incubated in pure saliva for 2 min. This cycle was repeated three times, then the specimens were kept in 100 ml of saliva for 8 h. Surface microhardness was evaluated at the beginning of the experiment and after each cycle. During the experiments, microhardness decreased significantly in all groups except for the pure saliva group. For sour drops and citric acid mixed with saliva from patients without erosion, the final microhardness was higher compared to the mixture of the two erosive compounds with saliva from patients with erosion. The storage of saliva for 8 h resulted in a certain amount of rehardening, with the highest level of rehardening being observed in the group that was least demineralized (sour drops plus saliva from patients without erosion). It is concluded that salivary components play a crucial role in the development of dental erosion.
Revisiting the Dioecy-Polyploidy Association: Alternate Pathways and Research Opportunities
Authors: Ashman T.-L. , Kwok A. , Husband B.C.
Published: July 2013

The evolutionary transition from hermaphroditism (combined sexes) to dioecy (separate sexes) is associated with whole genome duplication (polyploidy) in several flowering plant genera. Moreover, there is evidence for transitions in the opposite direction, i.e. a loss of dioecy with an increase in ploidy. Here, we review evidence for these associations, synthesize previous ideas on the mechanism underlying the patterns and explore alternative pathways. Specifically, we examine potential ecological and genetic mechanisms, differentiated by whether ploidy or gender (functional sex expression of the plant) changes are the primary cause and whether the effect is direct or indirect. An analysis of 22 genera variable for both ploidy and gender indicates that gender monomorphism (hermaphroditism, monoecy) is more common among diploid than polyploid species, whereas gender dimorphism (dioecy, gynodioecy, subdioecy) is more frequent among polyploid species. The transition from diploid hermaphroditic to polyploid gender-dimorphic taxa may arise directly through changes in gender as a result of genome duplication through genomic rearrangements or homeologous recombination, or changes in gender may result in increased unreduced gamete production leading to polyploid formation. Alternatively, the transition may occur through the indirect effects of genome duplication on mating system and inbreeding depression, which favor selection for unisexuality, or habitat shifts associated with unisexuality may simultaneously cause increased unreduced gamete production. Novel mechanisms for transitions in the opposite direction (from dioecy to hermaphroditism with increase in ploidy) include disruption of genetic sex determination and the benefits of reproductive assurance. We highlight key questions requiring further attention and promising approaches for answering them and better clarifying the genesis of sexual system polyploidy associations. See also the sister article focusing on animals by Wertheim et al. in this themed issue.
The Role of Galectin-3 as a Marker of Cancer and Inflammation in a Stage IV Ovarian Cancer Patient with Underlying Pro-Inflammatory Comorbidities
Authors: Eliaz Isaac
Published: July 2013

In this case study, I report on a patient with stage IV ovarian cancer and underlying pro-inflammatory comorbidities. Initially, the patient's inflammatory condition was treated with an intensive integrative anti-inflammatory protocol using a combination of oral and intravenous nutrients and botanicals along with pharmaceutical intervention. This was followed by a standard course of chemotherapy supported by an individualized integrative protocol - with excellent response. Galectin-3 levels as well as other inflammatory and tumor markers were monitored throughout the course of treatment. Correlation with other markers, the clinical course of the disease, and symptomatology are presented. Galectin-3, a novel marker with potential clinical importance in cancer progression as well as inflammation and fibrosis, has been extensively researched in multiple in vitro, in vivo, and epidemiological studies. In this paper, a case in which galectin-3 has been used to assess and monitor patient progress is presented for the first time. This case is of further interest because of its complexity, with the coexistence of acute inflammatory conditions combined with progressing metastatic cancer. Galectin-3 monitoring reflected this complexity; nevertheless, it provided useful information and correlation with other inflammatory markers. The results suggest that monitoring serum galectin-3 as a marker for both inflammatory processes and cancer progression to a higher probability of metastasis may have clinical relevance. Additional clinical research is warranted.