bluuebunny/crossref_metadata_2025_split huggingface dataset:
Covariate Balancing Propensity Score
Authors: Imai Kosuke , Ratkovic Marc 
Published: July 2013

SummaryThe 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

ABSTRACTIn 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.ObjectivesTo assess endogenous pH, titratable acidity and type and concentration of sugars present in drugs used in treatment of HIV‐infected children.Study designEleven 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.ResultsMedications 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.ConclusionThe physical properties and sugar content of medications used in ART pose a risk to dental health of children.
Clinical Application of Volatile Organic Compound Analysis for Detecting Infectious Diseases
Authors: Sethi Shneh , Nanda Ranjan , Chakraborty Trinad 
Published: July 2013

SUMMARYThis 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

SUMMARY
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

SUMMARYInfections 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

SUMMARYThe 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

ABSTRACTThe 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

ABSTRACT
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

ABSTRACTTreatment 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.
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.
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

AbstractBackground: 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.
A Multicenter, Randomized Trial of a Nurse-Led, Home-Based Intervention for Optimal Secondary Cardiac Prevention Suggests Some Benefits for Men but Not for Women
Authors: Carrington Melinda J. , Chan Yih-Kai , Calderone Alicia , Scuffham Paul A. , Esterman Adrian , Goldstein Stan , Stewart Simon 
Published: July 2013

Background—
We examined the impact of a prolonged secondary prevention program on recurrent hospitalization in cardiac patients with private health insurance.

Methods and Results—

The Young at Heart multicenter, randomized, controlled trial compared usual postdischarge care (UC) with nurse-led, home-based intervention (HBI). The primary end point was rate of all-cause hospital stay (31.5±7.5 months follow-up). In total, 602 patients (aged 70±10 years, 72% men) were randomized to UC (n=296) or HBI (n=306, 96% received ≥1 home visit). Overall, 42 patients (7.0%) died, and 492 patients (82%) accumulated 2397 all-cause hospitalizations associated with 10 258 hospital days costing >$17 million. There were minimal group differences (HBI versus UC) in the primary end point of all-cause hospital stay (5405 versus 4853 days; median [interquartile range], 0.08 [0.03–0.17] versus 0.07 [0.03–0.13]/patient per month). There were similar trends with respect to all hospitalizations (1197 versus 1200;
P
=0.802) and associated costs ($8.66 versus $8.58 million;
P
=0.375). At 2 years, however, more HBI versus UC (39% versus 27%; odds ratio, 1.67; 95% confidence interval, 1.15–2.41;
P
=0.007) patients were assessed as stable and optimally managed. For women, HBI outcomes were predominantly worse than UC outcomes. In men, HBI was associated with reduced risk of cardiovascular hospitalization (adjusted hazard ratio, 0.68; 95% confidence interval, 0.46–0.99;
P
=0.044) with less cardiovascular hospitalizations (192 versus 269;
P
=0.054) and costs ($2.49 versus $3.53 million;
P
=0.046).

Conclusions—
HBI did not reduce recurrent all-cause hospitalization compared with UC in privately insured cardiac patients overall. However, it did convey some benefits in cardiac outcomes for men.

Clinical Trial Registration—

Australian New Zealand Clinical Trials Registry Unique Identifier: 12608000014358. URL:
http://www.anzctr.org.au/trial_view.aspx?id=82509
.
Vascular Injury Involves the Overoxidation of Peroxiredoxin Type II and Is Recovered by the Peroxiredoxin Activity Mimetic That Induces Reendothelialization
Authors: Kang Dong Hoon , Lee Doo Jae , Kim Jiran , Lee Joo Young , Kim Hyun-Woo , Kwon Kihwan , Taylor W. Robert , Jo Hanjoong , Kang Sang Won 
Published: July 2013

Background—
Typical 2-Cys peroxiredoxin (Prx) is inactivated by overoxidation of the peroxidatic cysteine residue under oxidative stress. However, the significance in the context of vascular disease is unknown.

Methods and Results—

Immunohistochemical analyses revealed that 2-Cys Prxs, particularly Prx type II, are heavily overoxidized in balloon-injured rodent carotid vessels and in human atherosclerotic lesions. Consistent with this observation, the selective depletion of Prx II exacerbated neointimal hyperplasia in injured carotid vessels. We also found that the epipolythiodioxopiperazine class of fungal metabolites exhibited an enzyme-like activity mimicking 2-Cys Prx peroxidase and manifestly eliminated the intracellular H
2
O
2
in the vascular cells. Functionally, the epipolythiodioxopiperazines reciprocally regulated the platelet-derived growth factor receptor-β– and vascular endothelial growth factor receptor–mediated signaling in these vascular cells by replacing Prx II. As a consequence, the epipolythiodioxopiperazines inhibited the proliferative and migratory activities of smooth muscle cells but promoted those of endothelial cells in vitro. Moreover, administration of the epipolythiodioxopiperazines to the injured carotid vessels resulted in a successful recovery by inhibiting neointimal hyperplasia without causing cytotoxicity and simultaneously inducing reendothelialization.

Conclusions—
This study reveals for the first time the involvement of the 2-Cys Prx overoxidation and thus the therapeutic use of their activity mimetic in vascular injuries like stenting.
The correct name of Aloe plicatilis in Kumara (Xanthorrhoeaceae subfam. Asphodeloideae)
Authors: Klopper Ronell 
Published: July 2013

The genus Kumara Medikus (1786: 69) was recently reinstated in the Xanthorrhoeaceae: Asphodeloideae (alternatively Asphodelaceae: Alooideae) comprising only one species, namely the fan aloe, Kumara disticha Medikus (1786: 70) [with Aloe plicatilis (Linnaeus 1753: 321) Miller (1768: 7) given as a synonym] (Grace et al. 2013). However, if the fan aloe, currently nown as Aloe plicatilis, is treated as a species of Kumara, the epithet plicatilis has priority and a new combination in Kumara is required. The new combination is made here.
Second Cancer Incidence, Risk Factor, and Specific Mortality in Head and Neck Squamous Cell Carcinoma
Authors: Lee Dong Hwan , Roh Jong‐Lyel , Baek Seunghee , Jung Jae Hoon , Choi Seung‐Ho , Nam Soon Yuhl , Kim Sang Yoon 
Published: July 2013

ObjectiveSecond primary malignancies (SPMs) are common in patients with head and neck squamous cell carcinoma (HNSCC) and have a negative impact on their survival. This study aimed to evaluate risk factors for SPM occurrence and cause‐specific mortality in Asian HNSCC patients.Study DesignA retrospective cohort study.SettingUniversity teaching hospital.SubjectsNine hundred and thirty‐seven patients without previous cancer history who were treated between 2000 and 2009 and followed for at least 2 years.MethodsConfirmation of SPMs was performed by histopathology. The cumulative probability of a SPM among survivors of index HNSCC was calculated using a competing risk model. Univariate and multivariate analyses were utilized to determine factors predictive of SPM occurrence and cause‐specific mortality.ResultsOf 937 patients, cumulative incidence of SPMs was 7.2% at 0 to 6 months (synchronous), 17.9% at 5 years, and 23.1% at 10 years after index tumor diagnosis. In multivariate analyses, old age (>60 years) (P =. 002), hypopharyngeal index tumor site (P =. 001), and heavy drinker (P =. 001) were independently associated with the development of SPMs, and hypopharyngeal index tumor site were independent variables for SPM‐specific survival (P <. 001). Cumulative incidence function of SPM‐specific mortality according to index tumor sites was significantly higher in the hypopharynx than other sites (P =. 011).ConclusionElderly patients, hypopharyngeal index cancer patients, or heavy drinkers may require careful surveillance for the development of SPMs. Our results may help identify and properly manage Asian patients at high risk of SPMs.