bluuebunny/crossref_metadata_2025 huggingface dataset:
A BioBrick compatible strategy for genetic modification of plants
Authors: Boyle Patrick M , Burrill Devin R , Inniss Mara C , Agapakis Christina M , Deardon Aaron , DeWerd Jonathan G , Gedeon Michael A , Quinn Jacqueline Y , Paull Morgan L , Raman Anugraha M , Theilmann Mark R , Wang Lu , Winn Julia C , Medvedik Oliver , Schellenberg Kurt , Haynes Karmella A , Viel Alain , Brenner Tamara J , Church George M , Shah Jagesh V , Silver Pamela A
Published: June 2012

Background

Plant biotechnology can be leveraged to produce food, fuel, medicine, and materials. Standardized methods advocated by the synthetic biology community can accelerate the plant design cycle, ultimately making plant engineering more widely accessible to bioengineers who can contribute diverse creative input to the design process.

Results

This paper presents work done largely by undergraduate students participating in the 2010 International Genetically Engineered Machines (iGEM) competition. Described here is a framework for engineering the model plant Arabidopsis thaliana with standardized, BioBrick compatible vectors and parts available through the Registry of Standard Biological Parts (http://www.partsregistry.org). This system was used to engineer a proof-of-concept plant that exogenously expresses the taste-inverting protein miraculin.

Conclusions

Our work is intended to encourage future iGEM teams and other synthetic biologists to use plants as a genetic chassis. Our workflow simplifies the use of standardized parts in plant systems, allowing the construction and expression of heterologous genes in plants within the timeframe allotted for typical iGEM projects.
URPD: a specific product primer design tool
Authors: Chuang Li-Yeh , Cheng Yu-Huei , Yang Cheng-Hong
Published: June 2012

Background

Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users.

Findings

URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers.

Conclusions

URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.
Regional citrate anticoagulation in cardiac surgery patients at high risk of bleeding: a continuous veno-venous hemofiltration protocol with a low concentration citrate solution
Authors: Morabito Santo , Pistolesi Valentina , Tritapepe Luigi , Zeppilli Laura , Polistena Francesca , Strampelli Emanuela , Pierucci Alessandro
Published: June 2012

Introduction

Regional citrate anticoagulation (RCA) is a valid option in patients at high risk of bleeding who are undergoing continuous renal replacement therapy (CRRT). The aim of this study was to evaluate, in critically ill patients with severe acute kidney injury following cardiac surgery, the efficacy and safety of RCA-continuous veno-venous hemofiltration (CVVH) using a low concentration citrate solution.

Methods

In high bleeding-risk cardiac surgery patients, we adopted, as an alternative to heparin or no anticoagulation, RCA-CVVH using a 12 mmol/l citrate solution. For RCA-CVVH settings, we developed a mathematical model to roughly estimate citrate load and calcium loss. In order to minimize calcium chloride supplementation, a calcium-containing solution was used as post-dilution replacement fluid.

Statistical analysis was performed using the Student t-test or analysis of variance (ANOVA) with post-hoc tests, Wilcoxon or Kruskal-Wallis tests for non-parametric analysis, and Kaplan-Meier survival analysis with Log Rank test.

Results

Thirty-three patients (age 70.8 ± 9.5, Sequential Organ Failure Assessment (SOFA) score 13.9 ± 2.5) were switched to RCA-CVVH from no anticoagulation CRRT. Among them, 16 patients had been previously switched from heparin to no anticoagulation because of bleeding or heparin-related complications. RCA-CVVH filter life (49.8 ± 35.4 hours, median 41, 152 circuits) was significantly longer (P < 0.0001) when compared with heparin (30.6 ± 24.3 hours, median 22, 73 circuits) or no anticoagulation (25.7 ± 21.2 hours, median 20, 77 circuits). Target circuit and systemic Ca++ were easily maintained (0.37 ± 0.09 and 1.18 ± 0.13 mmol/l), while the persistence of a mild metabolic acidosis required bicarbonate supplementation (5.8 ± 5.9 mmol/hours) in 27 patients. The probability of circuit running at 24, 48, 72 hours was higher during RCA-CVVH (P < 0.0001), with a lower discrepancy between delivered and prescribed CRRT dose (P < 0.0001). RCA was associated with a lower transfusion rate (P < 0.02). Platelet count (P = 0.012) and antithrombin III activity (P = 0.004) increased throughout RCA-CVVH, reducing the need for supplementation.

Conclusions

RCA safely prolonged filter life while decreasing CRRT downtime, transfusion rates and supplementation needs for antithrombin III and platelets. In cardiac surgery patients with severe multiple organ dysfunction syndrome, the adoption of a 12 mmol/l citrate solution may provide a suboptimal buffers supply, easily overwhelmed by bicarbonate supplementation.
Increasing Lung Cancer Death Rates Among Young Women in Southern and Midwestern States
Authors: Jemal Ahmedin , Ma Jiemin , Rosenberg Philip S. , Siegel Rebecca , Anderson William F.
Published: June 2012

Purpose

Previous studies reported that declines in age-specific lung cancer death rates among women in the United States abruptly slowed in women younger than age 50 years (ie, women born after the 1950s). However, in view of substantial geographic differences in antitobacco measures and sociodemographic factors that affect smoking prevalence, it is unknown whether this change in the trend was similar across all states.

Methods

We examined female age-specific lung cancer death rates (1973 through 2007) by year of death and birth in each state by using age-period-cohort models. Cohort relative risks adjusted for age and period effects were used to compare the lung cancer death rate for a given birth cohort to a referent birth cohort (ie, the 1933 cohort herein).

Results

Age-specific lung cancer death rates declined continuously in white women in California, but the rates declined less quickly or even increased in the remaining states among women younger than age 50 years and women born after the 1950s, especially in several southern and midwestern states. For example, in some southern states (eg, Alabama), lung cancer death rates among women born in the 1960s were approximately double those of women born in the 1930s.

Conclusion

The unfavorable lung cancer trend in white women born after circa 1950 in southern and midwestern states underscores the need for additional interventions to promote smoking cessation in these high-risk populations, which could lead to more favorable future mortality trends for lung cancer and other smoking-related diseases.
Stable Inhibition of Specific Estrogen Receptor α (ERα) Phosphorylation Confers Increased Growth, Migration/Invasion, and Disruption of Estradiol Signaling in MCF-7 Breast Cancer Cells
Authors: Huderson B. P. , Duplessis T. T. , Williams C. C. , Seger H. C. , Marsden C. G. , Pouey K. J. , Hill S. M. , Rowan B. G.
Published: June 2012

Elevated phosphorylation of estrogen receptor α (ERα) at serines 118 (S118) and 167 (S167) is associated with favorable outcome for tamoxifen adjuvant therapy and may serve as surrogate markers for a functional ERα signaling pathway in breast cancer. It is possible that loss of phosphorylation at S118 and/or S167 could disrupt ERα signaling, resulting in aggressive ERα-independent breast cancer cells. To this end, MCF-7 breast cancer cells were stably transfected with an ERα-specific short hairpin RNA that reduced endogenous ERα. The resulting cell line was stably transfected with wild-type ERα (ER-AB cells), or ERα containing serine to alanine mutation at S118 or S167 (S118A cells and S167A cells, respectively). These stable cell lines expressed approximately equivalent ERα compared with parental MCF-7 cells and were evaluated for growth, morphology, migration/invasion, and ERα-regulated gene expression. S118A cells and S167A cells exhibited increased growth and migration/invasion in vitro. Forward- and side-scatter flow cytometry revealed that S167A cells were smaller in size, and both S118A and S167A cells exhibited less cellular complexity. S118A and S167A cells expressed pancytokeratin and membrane localization of β-catenin and did not express vimentin, indicating retention of epithelial lineage markers. Expression of ERα-target genes and other genes regulated by ERα signaling or involved in breast cancer were markedly altered in both S118A and S167A cells. In summary, attenuated phosphorylation of ERα at S118 and S167 significantly affected cellular physiology and behavior in MCF-7 breast cancer cells, resulting in increased growth, migration/invasion, compromised expression of ERα target genes, and markedly altered gene expression patterns.
Gsα Deficiency in the Paraventricular Nucleus of the Hypothalamus Partially Contributes to Obesity Associated with Gsα Mutations
Authors: Chen Min , Berger Alta , Kablan Ahmed , Zhang Jiandi , Gavrilova Oksana , Weinstein Lee S.
Published: June 2012

The G protein α-subunit Gsα mediates receptor-stimulated cAMP generation. Heterozygous inactivating Gsα mutations on the maternal allele result in obesity primarily due to reduced energy expenditure in Albright hereditary osteodystrophy patients and in mice. We previously showed that mice with central nervous system (CNS)-specific Gsα deletion on the maternal allele (mBrGs KO) also develop severe obesity with reduced energy expenditure and that Gsα is primarily expressed from the maternal allele in the paraventricular nucleus (PVN) of the hypothalamus, an important site of energy balance regulation. We now generated mice with PVN-specific Gsα deficiency by mating Single-minded 1-cre and Gsα-floxed mice. Homozygous Gsα deletion produced early lethality. Heterozygotes with maternal Gsα deletion (mPVNGsKO) also developed obesity and had small reductions in energy expenditure. However, this effect was much milder than that found in mBrGsKO mice and was more prominent in males. We previously showed mBrGsKO mice to have significant reductions in melanocortin receptor agonist-stimulated energy expenditure and now show that mBrGsKO mice have impaired cold-induced brown adipose tissue stimulation. In contrast, these effects were absent in mPVNGsKO mice. mPVNGsKO mice also had minimal effects on glucose metabolism as compared with mBrGsKO mice. Consistent with the presence of Gsα imprinting, paternal heterozygotes showed no changes in energy or glucose metabolism. These results indicate that although Gsα deficiency in PVN partially contributes to the metabolic phenotype resulting from maternal Gsα mutations, Gsα imprinting in other CNS regions is also important in mediating the CNS effects of Gsα mutations on energy and glucose metabolism.
Nickel/Lewis Acid-Catalyzed Carbocyanation of Unsaturated Compounds
Authors: Nakao Yoshiaki
Published: June 2012

Addition reactions of the organic and cyano groups of nitriles through cleavage of the C–CN bonds, namely carbocyanation, have been developed using nickel/Lewis acid (LA) cooperative catalysis. Originally, the reaction was performed with a nickel catalyst alone and was limited to the use of aryl and allyl cyanides as the nitrile substrates. By employing LA cocatalysts, the rate of the arylcyanation was accelerated significantly and the scope of nitriles used in the reaction across alkynes was expanded to include alkenyl, alkynyl, and alkyl cyanides. The high chemo-, regio-, and stereoselectivities of the alkyne–carbocyanation reactions were highlighted by the syntheses of biologically active compounds including the synthetic precursor of P-3622 and plaunotol, which possess defined tri- or tetrasubstituted ethene structures. Intramolecular arylcyanation of alkenes was also achieved by cooperative catalysis. Mechanistic studies on this particular transformation allowed us to identify several reaction intermediates, which revealed the modes of the cooperative catalysis derived from nickel- and aluminum-based LA. Intramolecular arylcyanation was achieved in an enantioselective manner using optically active bidentate phosphorus ligands, affording a protocol to introduce both a quaternary stereocenter and a cyano functionality without by-product generation.
Ambiguity Aversion: Implications for the Uncovered Interest Rate Parity Puzzle
Authors: Ilut Cosmin
Published: June 2012

High interest rate currencies tend to appreciate in the future relative to low interest rate currencies instead of depreciating as uncovered interest parity (UIP) predicts. I construct a model of exchange rate determination in which ambiguity-averse agents face a dynamic filtering problem featuring signals of uncertain precision. Solving a max-min problem, agents act upon a worst-case signal precision and systematically underestimate the hidden state that controls payoffs. Thus, on average, agents next periods perceive positive innovations, which generates an upward re-evaluation of the strategy's profitability and implies ex post departures from UIP. The model also produces predictable expectational errors, negative skewness, and time-series momentum for currency speculation payoffs. (JEL D81, F31, G15)
Social Security Reforms: Benefit Claiming, Labor Force Participation, and Long-run Sustainability
Authors: İmrohoroğlu Selahattin , Kitao Sagiri
Published: June 2012

This paper develops a general equilibrium life-cycle model with endogenous labor supply in both intensive and extensive margins, consumption, saving, and benefit claiming to measure the long-run effects of a proposed Social Security reform. Agents in the model face medical expenditure, wage, health, and survival shocks. Raising the normal retirement age by two years increases labor supply by 2.8 percent and the capital stock by 12.6 percent, showing that both margins of adjustment are critical. General equilibrium effects are important to account for the effects of reform on savings, although the effects on labor supply are less important. (JEL D91, E21, H55, I13, J22)
18F-FDG PET/CT and PET for evaluation of pathological response to neoadjuvant chemotherapy in breast cancer: a meta-analysis
Authors: Cheng Xu , Li Yongjun , Liu Biao , Xu Zhaoqiang , Bao Lihua , Wang Jie
Published: June 2012

Background

Neoadjuvant chemotherapy is increasingly the treatment for patients with inoperable breast cancer. Considering the side-effects of chemotherapy, there is a need for early evaluating response to neoadjuvant chemotherapy.

Purpose

To determinate the diagnostic performance of 18F-fluorodeoxyglucose position emission tomography/computed tomography (FDG PET/CT) and FDG PET for evaluating response to neoadjuvant chemotherapy in patients with breast cancer.

Material and Methods

“PubMed” (MEDLINE included) database, EMBASE, and Cochrane Database of Systematic Reviews were searched for relevant articles. We assessed the methodological quality of included study with Quality Assessment of Diagnosis Accuracy Studies (QUADAS) score tool, and used “Meta-DiSc” statistic software to obtain pooled estimates of sensitivity, specificity, diagnostic odds ratio (DOR), and summary receiver-operating characteristic (SROC) curve.

Results

Seventeen studies (a total of 781 subjects) met the inclusion criteria. The pooled sensitivity was 0.840 (95% confidence interval [CI] 0.796–0.878). The pooled specificity was 0.713 (95% CI 0.667–0.756). For FDG PET/CT (10 studies included), the pooled sensitivity was 0.847 (95% CI 0.793–0.892), the pooled specificity was 0.661 (95% CI 0.598–0.720). The pooled likelihood ratio (LR+), negative likelihood ratio (LR–), and diagnostic odds ratio (DOR) were 2.835 (95% CI 1.640–4.900), 0.221 (95% CI 0.160–0.305), and 17.628 (95% CI 7.431–41.818). The area under the SROC curve (AUC) was 0.8934. For FDG PET (7 studies included), the pooled sensitivity and specificity were 0.826 (95% CI 0.741–0.892) and 0.789 (95% CI 0.719–0.849). The pooled LR + , LR–, and DOR were 3.601 (95% CI 2.601–4.986), 0.242 (95% CI 0.157–0.374), and 13.641 (95% CI 7.433–25.030). The AUC was 0.8764.

Conclusion

Our results indicate that FDG PET/CT and PET have reasonable sensitivity in evaluating response to neoadjuvant chemotherapy in breast cancer; however, the specificity is relative low. The combination of other imaging methods with FDG PET/CT or PET is recommended.
Surgical management of pleural empyema in the very elderly
Authors: Schweigert M , Solymosi N , Dubecz A , Beron M , Thumfart L , Oefner-Velano D , Stein HJ
Published: June 2012

INTRODUCTION

Parapneumonic pleural empyema is a critical illness. Age is an acknowledged risk factor for both pneumonia and pleural empyema. Furthermore, elderly patients often have severe co-morbidity. In the case of pleural empyema, their clinical condition is likely to deteriorate fast, resulting in life threatening septic disease. To prevent this disastrous situation we adapted early surgical debridement as the primary treatment option even in very elderly patients. This study shows the outcome of surgically managed patients with pleural empyema who are 80 years or older.

METHODS

The outcomes of 222 consecutive patients who received surgical therapy for parapneumonic pleural empyema at a German tertiary referral hospital between 2006 and 2010 were reviewed in a retrospective case study. Patients older than 80 years were identified.

RESULTS

There were 159 male and 63 female patients. The mean age was 60.5 years and the overall in-hospital mortality rate was 7%. Of the 222 patients, 37 were 80 years or older (range: 80–95 years). The frequencies of predominantly cardiac co-morbidity and high ASA (American Society of Anesthesiologists) grades were significantly higher for very elderly patients (p<0.001). A minimally invasive approach was feasible in 34 cases (92%). Of the 37 patients aged over 80, 36 recovered while one died from severe sepsis (in-hospital mortality 3%). There was no significant difference in mortality between the very elderly and the younger sufferers (p=0.476).

CONCLUSIONS

Early surgical treatment of parapneumonic pleural empyema shows excellent results even in very elderly patients. Despite considerable co-morbidity and often delayed diagnosis, minimally invasive surgery was feasible in 34 patients (92%). The in-hospital mortality of very elderly patients was low. It can therefore be concluded that advanced age is no contraindication for early surgical therapy.
Adverse Drug Reactions in Elderly Hospitalized Patients: A 12-Year Population-Based Retrospective Cohort Study
Authors: Sikdar Khokan C , Dowden Jeffrey , Alaghehbandan Reza , MacDonald Don , Wang Peizhong Peter , Gadag Veeresh
Published: June 2012

BACKGROUND:

Although research has identified some risk factors for first-time adverse drug reactions (ADRs), little is known about the risks associated with the number of ADRs. Modeling ADR counts is relatively complex because of the rarity of the events, requiring careful consideration of appropriate models that best present the observed data.

OBJECTIVE:

To determine the incidence of ADRs among elderly hospitalized patients, assess patient-related risk factors for the number of ADRs, and review drug classes commonly responsible for ADRs.

METHODS:

This retrospective cohort study used a population-based large administrative database on hospital separations from all acute care hospitals in the Canadian province of Newfoundland and Labrador. Patients aged 65 years or older with at least 1 hospital admission from April 1, 1995, to March 31, 2007, were included. Comorbidities, Charlson Comorbidity Index (CCI), and sociodemographic factors were assessed as predictors of ADR counts. A zero-inflated negative binomial regression model was used for analysis.

RESULTS:

The study cohort contained 64,446 patients. The incidence of ADRs was 15.2 per 1000 person-years (95% CI 14.8 to 15.7). Of those having an ADR, 15.4% had recurrent ADRs. The most common drug category implicated in ADRs was cardiovascular agents (17.7%). A dose-response relationship was found between CCI and ADR counts (rate ratio [RR] 1.67, 95% CI 1.41 to 1.98 for CCI 2-3; RR 2.38, 95% CI 1.98 to 2.87 for CCI 4-5; and RR 3.83, 95% CI 3.21-4.57 for CCI ≥6). Comorbid conditions including congestive heart failure (RR 1.58, 95% CI 1.33 to 1.89), diabetes (RR 2.42, 95% CI 1.64 to 3.56), and cancer (RR 3.12, 95% CI 2.58 to 3.76) were strong predictors. Rural areas (RR 1.22, 95% CI 1.01 to 1.46) were associated with increased risk for ADRs, whereas age and sex had no effect.

CONCLUSIONS:

Comorbidity from chronic diseases and severity of illness, rather than individual characteristics (advancing age and sex), increased the likelihood of ADRs. Changes in the delivery of care focusing on the monitoring of prescribed drugs in elderly patients with comorbidities could mitigate ADRs.
Planning a Pharmacy-Led Medical Mission Trip, Part 3: Development and Implementation of an Elective Medical Missions Advanced Pharmacy Practice Experience (APPE) Rotation
Authors: Brown Dana A , Ferrill Mary J
Published: June 2012

This article, focusing on developing an elective advanced pharmacy practice experience (APPE) rotation for international and domestic medical missions, including provision of products, is the third in a 4-part series on pharmacist-led medical mission trips. Part 4, “An Exploratory Study of Student Experiences,” is an evaluation of data collected from both APPE and non-APPE student participants on Gregory School of Pharmacy mission trips during the summer of 2011. Specifically, it examines the issue of professionalism and the personal impact that mission trips may have on pharmacy students.

With an increasing number of new pharmacy schools/colleges and expansion of existing ones, pharmacy schools/colleges are often in need of elective rotation experiences as part of the final year advanced pharmacy practice experience (APPE) program. Offering a medical missions elective APPE in either a domestic or international setting is a unique opportunity to expose pharmacy students to direct patient care. APPE students can be involved in triaging patients, compounding and dispensing medications, and providing patient education. As part of this APPE, pharmacy students are expected to complete projects such as formulary development, case presentations, book club discussions, journal reflections, manuscript preparations, and trip logistics planning. An elective APPE focused on medical missions facilitates the learning process and promotes the emergence of team leaders and leadership skills in general.
Do Racial and Ethnic Differences in Contraceptive Attitudes and Knowledge Explain Disparities In Method Use?
Authors: Rocca Corinne H. , Harper Cynthia C.
Published: June 2012

CONTEXT

Sustained efforts have not attenuated racial and ethnic disparities in unintended pregnancy and effective contraceptive use in the United States. The roles of attitudes toward contraception, pregnancy and fertility remain relatively unexplored.

METHODS

Knowledge of contraceptive methods and attitudes about contraception, pregnancy, childbearing and fertility were assessed among 602 unmarried women aged 18–29 at risk for unintended pregnancy who participated in the 2009 National Survey of Reproductive and Contraceptive Knowledge. The contribution of attitudes to racial and ethnic disparities in effective method use was assessed via mediation analysis, using a series of regression models.

RESULTS

Blacks and Latinas were more likely than whites to believe that the government encourages contraceptive use to limit minority populations (odds ratio, 2.5 for each). Compared with white women, Latinas held more favorable attitudes toward pregnancy (2.5) and childbearing (coefficient, 0.3) and were more fatalistic about the timing of pregnancy (odds ratio, 2.3); blacks were more fatalistic about life in general (2.0). Only one attitude, skepticism that the government ensures contraceptive safety, was associated with contraceptive use (0.7), but this belief did not differ by race or ethnicity. Although blacks and Latinas used less effective methods than whites (0.3 and 0.4, respectively), attitudes did not explain disparities. Lower contraceptive knowledge partially explained Latinas’ use of less effective methods.

CONCLUSIONS

Providing basic information about effective methods might help to decrease ethnic disparities in use. Research should examine other variables that might account for these disparities, including health system characteristics and provider behavior.
Determination of Optical Coefficients and Fractal Dimensional Parameters of Cancerous and Normal Prostate Tissues
Authors: Pu Yang , Wang Wubao , Al-Rubaiee Mohammad , Gayen Swapan Kumar , Xu Min
Published: June 2012

Optical extinction and diffuse reflection spectra of cancerous and normal prostate tissues in the 750 to 860 nm spectral range were measured. Optical extinction measurements using thin ex vivo prostate tissue samples were used to determine the scattering coefficient (μ′s), while diffuse reflection measurements using thick prostate tissue samples were used to extract the absorption coefficient (μa) and the reduced scattering coefficient (μ′s). The anisotropy factor ( g) was obtained using the extracted values of μs and μ′s. The values of fractal dimension ( Df) of cancerous and normal prostate tissues were obtained by fitting to the wavelength dependence of μ′s. The number of scattering particles contributing to μs as a function of particle size and the cutoff diameter dmax as a function of g were investigated using the fractal soft tissue model and Mie theory. Results show that dmax of the normal tissue is larger than that of the cancerous tissue. The cutoff diameter dmax is observed to agree with the nuclear size for the normal tissues and the nucleolar size for the cancerous tissues. Transmission spectral polarization imaging measurements were performed that could distinguish the cancerous prostate tissue samples from the normal tissue samples based on the differences between their absorption and scattering parameters.
Differentiation of Neotropical Fish Species with Statistical Analysis of Fourier Transform Infrared Photoacoustic Spectroscopy Data
Authors: Almeida Francylaine S. , Lima Sandro M. , Andrade Luis H.C. , Súarez Yzel R.
Published: June 2012

Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) was applied to nineteen fish species in Brazil's Upper Paraná River basin to identify differences in the structural composition of their scales. To differentiate the species, a canonical discriminant analysis was used to indicate the most important absorption peaks in the mid-infrared region. Significant differences were found in the chemical composition of scales among the studied fish species, with Wilk's lambda = 5.2 × 10−6, F(13,18,394) = 37.57, and P < 0.001, indicating that O–CH2 wag at 1396 cm−1 can be used as a biomarker of this species group. The species could be categorized into four groups according to phylogenetic similarity, suggesting that the O–CH2 1396 cm−1 absorbance is related to the biological traits of each species. This procedure can also be used to complement evolutionary studies.
Determination of Hydrodynamic Properties of Bare Gold and Silver Nanoparticles as a Fluorescent Probe Using its Surface-Plasmon-Induced Photoluminescence by Fluorescence Correlation Spectroscopy
Authors: Prashanthi Suthari , Lanke Srinivasa Rao , Kumar Pippara Hemant , Siva Doddi , Bangal Prakriti Ranjan
Published: June 2012

Noble-metal nanoparticles labeled with fluorescent molecules are used in a variety of applications requiring the measurement of size and diffusion properties of single nanoprobes. We have successfully used intrinsic surface-plasmon-induced photoluminescence (SPPL) signatures of monodispersed bare gold and silver nanoparticles in water to detect and measure their precise diffusion coefficient, concentration and hydrodynamic radius by fluorescence correlation spectroscopy (FCS). Measurement of the effective hydrodynamic radius confirms particle size to be 80 ± 8 and 64 ± 14 nm for gold and silver, respectively, which is in excellent agreement with scanning electron microscopic measurements made on the same particles. Detection of bare gold and silver nanoparticles at the single-molecule level with moderately high value of “per particle brightness” (PPB) confirms those particles to be used as fluorescent probes in biological research and in different medical and biotechnology applications where fluorescence detection plays a vital role. Additionally, these results demonstrate an alternative method for measuring hydrodynamic properties, particularly the size-distribution of bare noble-metal nanoparticles in solution using data-fitting algorithm for FCS based on the maximum entropy method (MEMFCS).
Characteristic Spectral Features of the Polarized Fluorescence of Human Breast Cancer in the Wavelet Domain
Authors: Gharekhan Anita H. , Biswal Nrusingh C. , Gupta Sharad , Panigrahi Prasanta K. , Pradhan Asima
Published: June 2012

Wavelet transform of polarized fluorescence spectra of human breast tissues is found to localize spectral features that can reliably differentiate normal and malignant tissue types. The intensity differences of parallel and perpendicularly polarized fluorescence spectra are subjected to investigation, since they are relatively free of diffusive background. A number of parameters, capturing spectral variations and subtle changes in the diseased tissues in the visible wavelength regime, are clearly identifiable in the wavelet domain. These manifest both in the average low-pass and high frequency high-pass wavelet coefficients.
Insights into the Binding of 2-Aminobenzothiazole with Human Serum Albumin (HSA): Spectroscopic Investigation and Molecular Modeling Studies
Authors: Sun Yajing , Su Baoling , Xu Qifei , Liu Rutao
Published: June 2012

As one of the important thiazole derivatives, 2-aminobenzothiazole (2-ABT) has been widely used as a structural unit in the synthesis of antioxidants, anti-inflammatories, herbicides, antibiotics, and thermoplastic polymers. In this study, the interaction of 2-ABT with human serum albumin (HSA) was investigated in vitro under simulated physiological conditions, using multi-spectroscopic techniques and a molecular modeling study. The binding constant and binding sites were determined through fluorescence quenching spectra. The site-competitive replacement experiments revealed that the precise binding site of 2-ABT on HSA was site II (subdomain IIIA). Moreover, molecular docking results illustrated the electrostatic interaction between Glu 450 and 2-ABT, in accordance with the conclusions from the calculated thermodynamic parameters and the effect of ionic strength. The effect of 2-ABT on the conformational changes of HSA were evaluated by ultraviolet–visible (UV-Vis) absorption, three-dimensional (3D) fluorescence, synchronous fluorescence, and circular dichroism (CD) spectroscopy. This work facilitates comprehensive understanding of the binding of 2-ABT with HSA, contributing to evaluate the molecular transportation mechanism and biotoxicity of 2-aminobenzothiazole derivatives in vivo.
New Seeding Methodology for Gas Concentration Measurements
Authors: Chan Qing N. , Medwell Paul R. , Dally Bassam B. , Alwahabi Zeyad T. , Nathan Graham J.
Published: June 2012

This paper presents the first demonstration of the pulsed laser ablation technique to seed a laminar non-reacting gaseous jet at atmospheric pressure. The focused, second harmonic from a pulsed Nd:YAG laser is used to ablate a neutral indium rod at atmospheric pressure and temperature. The ablation products generated with the new seeding method are used to seed the jet, as a marker of the scalar field. The neutral indium atoms so generated are found to be stable and survive a convection time of the order of tens of seconds before entering the interrogation region. The measurements of planar laser-induced fluorescence (PLIF) with indium and laser nephelometry measurements with the ablation products are both reported. The resulting average and root mean square (RMS) of the measurements are found to agree reasonably well although some differences are found. The results show that the pulsed laser ablation method has potential to provide scalar measurement for mixing studies.
Spatially Resolved Characterization of Cellulose Nanocrystal–Polypropylene Composite by Confocal Raman Microscopy
Authors: Agarwal Umesh P. , Sabo Ronald , Reiner Richard S. , Clemons Craig M. , Rudie Alan W.
Published: June 2012

Raman spectroscopy was used to analyze cellulose nanocrystal (CNC)–polypropylene (PP) composites and to investigate the spatial distribution of CNCs in extruded composite filaments. Three composites were made from two forms of nanocellulose (CNCs from wood pulp and the nano-scale fraction of microcrystalline cellulose) and two of the three composites investigated used maleated PP as a coupling agent. Raman maps, based on cellulose and PP bands at 1098 and 1460 cm−1, respectively, obtained at 1 μm spatial resolution showed that the CNCs were aggregated to various degrees in the PP matrix. Of the three composites analyzed, two showed clear existence of phase-separated regions: Raman images with strong PP and absent/weak cellulose or vice versa. For the third composite, the situation was slightly improved but a clear transition interface between the PP-abundant and CNC-abundant regions was observed, indicating that the CNC remained poorly dispersed. The spectroscopic approach to investigating spatial distribution of the composite components was helpful in evaluating CNC dispersion in the composite at the microscopic level, which helped explain the relatively modest reinforcement of PP by the CNCs.
In-Line Monitoring of the Thickness of Printed Layers by Near-Infrared (NIR) Spectroscopy at a Printing Press
Authors: Mirschel Gabriele , Heymann Katja , Savchuk Olesya , Genest Beatrix , Scherzer Tom
Published: June 2012

In this work, it is demonstrated that the coating weight of printed layers can be determined in-line in a running printing press by near-infrared (NIR) reflection spectroscopy assisted by chemometric methods. Three different unpigmented lacquer systems, i.e., a conventional oil-based printing lacquer, an ultraviolet (UV)-curable formulation, and a water-based dispersion varnish, were printed on paper with coating weights between about 0.5 and 7 g m−2. NIR spectra for calibration were recorded with a special metal reflector simulating the mounting conditions of the probe head at the printing press. Calibration models were developed on the basis of the partial least squares (PLS) algorithm and evaluated by independent test samples. The prediction performance of the developed models was examined at a sheet-fed offset printing press at line speeds between 90 and 180 m min−1. Results show an excellent correlation of data predicted in-line from the NIR spectra with reference values obtained off-line by gravimetry. The prediction errors were found to be ≤ 0.2 g m−2, which confirms the suitability of the developed spectroscopic method for process control in technical printing processes.
Interaction of (–)-Epigallocatechin Gallate with Lysozyme-Conjugated Silver Nanoparticles
Authors: Chandra Goutam Kumar , Tripathy Debi Ranjan , Dasgupta Swagata , Roy Anushree
Published: June 2012

The interaction of lysozyme (Lyz)-conjugated silver (Ag) nanoparticles with (–)-epigallocatechin gallate (EGCG), one of the major components of green tea, has been investigated. Interaction of a protein with ligand/drug molecules perturbs the conformation of secondary and tertiary structures of the protein. We have demonstrated the conformational changes in the tertiary structures of the Lyz molecules on EGCG binding using surface-enhanced Raman scattering (SERS) and circular dichroism (CD) spectroscopic measurements. From the analysis of the amide I band of Lyz in SERS and CD spectra, the site of interaction of EGCG with protein molecules in Lyz-conjugated Ag particles has been identified. Spectroscopic evidence for the conformational response of Trp62 and Trp63, in the β-domain of the protein, to the binding of EGCG has been discussed.
Ultraviolet (UV) Raman Spectroscopy Study of the Soret Effect in High-Pressure CO2–Water Solutions
Authors: Windisch Charles F. , Maupin Gary D. , McGrail B. Peter
Published: June 2012

Spatially resolved deep-ultraviolet (UV) Raman spectroscopy was applied to solutions of CO2 and H2O or D2O subject to a temperature gradient in a thermally regulated high-pressure concentric-tube Raman cell in an attempt to measure a Soret effect in the vicinity of the critical point of CO2. Although Raman spectra of solutions of CO2 dissolved in D2O, at 10 MPa and temperatures near the critical point of CO2, had adequate signal-to-noise and spatial resolution to observe a Soret effect with a Soret coefficient with magnitude | ST| > 0.03, no evidence for an effect of this size was obtained for applied temperature gradients up to 19 °C. In contrast, the concentration of CO2 dissolved in H2O was shown to vary significantly across the temperature gradient when excess CO2 was present, but the results could be explained simply by the variation in CO2 solubility over the temperature range and not by kinetic factors. For mixtures of D2O dissolved in scCO2 at 10 MPa and temperatures close to the critical point of CO2, the Raman peaks for D2O were too weak to measure with confidence even at the limit of D2O solubility.
Fluorescence Spectral Analysis for the Discrimination of Complex, Similar Mixtures with the Aid of Chemometrics
Authors: Ni Yongnian , Lai Yanhua , Kokot Serge
Published: June 2012

An analytical method for the classification of complex real-world samples was researched and developed with the use of excitation-emission fluorescence matrix (EEFM) spectroscopy, using the medicinal herbs, Rhizoma corydalis decumbentis (RCD) and Rhizoma corydalis (RC) as example samples. The data set was obtained from various authentic RCD-A and RC-A, adulterated AD, and commercial RCD-C and RC-C samples. The spectra (range: λex=215∼395 nm and λem=290∼560 nm), arranged in two- and three-way data matrix formats, were processed using principal component analysis (PCA) and parallel factor analysis (PARAFAC) to produce two-dimensional component-by-component plots for qualitative data classification. The RCD-A and RC-A object groups were clearly discriminated, but the AD and the RCD-C as well as RC-C samples were less well separated. PARAFAC analysis produced somewhat better discrimination, and loadings plots revealed the presence of the marker compound Protopine—a strongly fluorescing substance—as well as at least two other unidentified fluorescent components. Classification performance of the common K-nearest neighbors (KNN) and linear discrimination analysis (LDA) methods was relatively poor when compared with that of the back propagation- and radial basis function-artificial neural networks (BP-ANN and RBF-ANN) models on the basis of two- and three-way formatted data. The best results were obtained with the three-way fingerprints and the RBF-ANN model. Subsequently, the quality of the commercial samples (RCD-C and RC-C) was classified on the best optimized RBF-ANN model. Thus, EEFM spectroscopy, which provides three-way measured data, is potentially a powerful analytical technique for the analysis of complex real-world substances provided the classification is performed by the RBF-ANN or similar ANN methods.
Measurement of the Raman Line Widths of Neat Benzenethiol and a Self-Assembled Monolayer (SAM) of Benzenethiol on a Silver-Coated Surface-Enhanced Raman Scattering (SERS) Substrate
Authors: Aggarwal Roshan L. , Farrar Lewis W. , Greeneltch Nathan G. , Van Duyne Richard P. , Polla Dennis L.
Published: June 2012

Raman line widths of neat benzenethiol and a self-assembled monolayer (SAM) of benzenethiol on a surface-enhanced Raman scattering (SERS) substrate have been measured using a mini spectrometer with a resolution (full width at half-maximum) of 3.3 ± 0.2 cm−1. Values of 7.3 ± 0.7, 4.6 ± 0.6, 2.4 ± 0.6, 3.2 ± 0.5, 8.8 ± 0.9, and 11.0 ± 1.1 cm−1 have been determined for the Raman line widths of the 414, 700, 1001, 1026, 1093, and 1584 cm−1 modes of neat benzenethiol. Values of 13.3 ± 0.7, 9.1 ± 0.7, 5.1 ± 0.6, 5.9 ± 0.6, 13.3 ± 0.5, and 8.7 ± 0.5 cm−1 have been determined for the SERS line widths of a benzenethiol SAM on a silver-coated SERS substrate for the corresponding frequency-shifted modes at 420, 691, 1000, 1023, 1072, and 1574 cm−1. The line widths for the SERS modes at 420, 691, 1000, 1023, and 1072 cm−1 are about a factor of two larger than those of the corresponding Raman modes. However, the line width of the SERS mode at 1574 cm−1 is slightly smaller than the corresponding Raman mode at 1584 cm−1.
Circumvention anxieties: Contemporary economies of dis/belief
Authors: Lauder Adam
Published: June 2012

In an economy that increasingly trades in electronic information products, the copy assumes a new reversibility, as a figure at once valued for its rapid exchangeability and vilified for of its associations with counterfeit and fraud. The incorporation of confidence measures into the
design of electronic information products is symptomatic of a primary crisis of belief installed within empiricist epistemologies, of which anti-circumvention technologies and knock-off economies are merely the incorrigible children. The aesthetic strategies practiced by Albert Oehlen and
N.E. Thing Co., which mirror the information hiding techniques employed by steganography software and technologies of trust as well as the circumvention tactics employed to defeat them, register an emergent preoccupation in contemporary visual culture with structures of belief. They also disclose
a Humean attention to processes of devivification, which figures in these artists’ work as an effect of the multiplication of the same. The trope of the ‘false bottom’ deployed in the 1930s novels of British artist and author Wyndham Lewis serves as intertext in this genealogical
investigation of the politics of circumvention.
The Lyric Speaker Goes to Gaol: British Poetry and Radical Prisoners, 1820–1845
Authors: LeGette Casie
Published: June 2012

This essay considers a collection of poems written by nineteenth-century political prisoners and published in the radical press. I situate these poems in the context of debates that raged at the time over whether or not political prisoners should have access to reading and writing materials. Thanks both to the sheer number of these prisoners and to their determination to remain politically active, the prison became a primary site of nineteenth-century radical print culture. Although radical prisoners wrote in a variety of genres, the short lyric poem offered a particularly apt form for expression. The familiar tropes of the Romantic lyric are regularly deployed in these poems, but, given the material conditions of imprisonment, these tropes can start to look quite different. Here, I consider the implications of this particular cultural moment, when metaphors of imprisonment and solitude butted up against the lived experience of prison. I examine the ways in which radical prisoners made the Romantic lyric their own, but also the ways in which imprisonment conditioned Romanticism itself.
The Apparatus of the Dark: Emily Dickinson and the Epistemology of Metaphor
Authors: Kohler Michelle
Published: June 2012

This essay argues that Emily Dickinson’s poetry intervenes in the broad cultural assessment of epistemology provoked by the evolutionary debates of the 1860s. While scholars have begun to explore the thematic correspondences between Dickinson’s poetry and some aspects of this cultural conversation, this essay examines the ways in which her intervention occurs at the level of poetic form and is in fact profoundly dependent upon form. Specifically, it analyzes a set of her poems from the early 1860s through the early 1870s in which she uses the dual structure of metaphor to elicit a way of thinking about truth that is aligned with the empirical methods of research that were widely embraced in the mid nineteenth century; however, in the face of an increasingly contingent notion of truth, Dickinson’s way of thinking significantly revises cultural assumptions about what those methods might yield. The metaphors examined here amplify the distinctions between two material entities—lightning and fork, or sunset and lilac, for example—rather than merging them or leaping beyond them to stable, transcendent meaning. What Dickinson plays with is the possibility of a revised version of revelation or truth, one that is not only derived from the observation of material difference through the two parts of a metaphor, but that is more radically contingent on the perpetuity of such dual perception. Altogether, Dickinson’s metaphors are both critical and recuperative, as they contribute to the dismantling of fixed truth while embracing the limited revelations made possible by—only made possible by—sustained process.