bluuebunny/crossref_metadata_2025 huggingface dataset:
Flavor Variability and Flavor Stability of U.S.‐Produced Whole Milk Powder
Authors: Lloyd M.A. , Drake M.A. , Gerard P.D.
Published: August 2009

ABSTRACT: Flavor variability and stability of U.S.‐produced whole milk powder (WMP) are important parameters for maximizing quality and global competitiveness of this commodity. This study characterized flavor and flavor stability of domestic WMP. Freshly produced (<1 mo) WMP was collected from 4 U.S. production facilities 5 times over a 1 y period. Each sample was analyzed initially and every 2 mo for sensory profile, volatiles, color, water activity, and moisture through 12 mo storage. Selected volatiles were quantified using solid phase microextraction (SPME) with gas chromatography/mass‐spectrometry: dimethyl sulfide, 2‐methylbutanal, 3‐methylbutanal, hexanal, 2‐heptanone, heptanal, 1‐octen‐3‐ol, octanal, 3‐octen‐2‐one, and nonanal. Multiple linear regression with backwards elimination was applied to generate equations to predict grassy and painty flavors based on selected volatiles. All WMP were between 2% and 3% moisture and 0.11 and 0.25 water activity initially. WMP varied in initial flavor profiles with varying levels of cooked, milk fat, and sweet aromatic flavors. During storage, grassy and painty flavors developed while sweet aromatic flavor intensities decreased (P < 0.05). Painty and grassy flavors were confirmed by increased levels (P < 0.05) of lipid oxidation products such as hexanal, heptanal, and octanal. Hexanal, 2‐heptanone, 1‐octen‐3‐ol, and nonanal concentrations were best predictors of grassy flavor (R2= 0.38, P < 0.0001) while hexanal, 2‐methylbutanal, 3‐methylbutanal, octanal, and 3‐octen‐2‐one concentrations were best predictors of painty flavor (R2= 0.61, P < 0.0001). These results provide baseline information to determine specific factors that can be controlled to optimize U.S. WMP flavor and flavor stability.
Conceptualizing and Treating Problem Gambling as a Family Issue
Authors: McComb Jennifer L. , Lee Bonnie K. , Sprenkle Douglas H.
Published: August 2009

Few family therapists have training in the identification, assessment, and treatment of problem gambling and its impact on couple and family relationships. The authors conceptualize problem gambling (PG) as a family issue and encourage clinicians and researchers to pay attention to the systemic antecedents and consequences of PG on family relationships. A review of the literature and clinicians’ experiences regarding the impact of PG on couple and family relationships are presented and discussed. In light of the limited systemic‐based treatments for PG, marriage and family therapists are urged to begin paying attention to this emerging issue that has significant couple and family ramifications.
Career Aspirations and Perceived Level of Preparedness Among Marriage and Family Therapy Doctoral Students
Authors: Miller John K. , Lambert‐Shute Jennifer
Published: August 2009

The authors conducted a survey of marriage and family therapy (MFT) doctoral students in programs accredited by the Commission on Accreditation for Marriage and Family Therapy Education (COAMFTE). MFT doctoral students (N = 82) from across the United States responded to a web‐based survey that focused on career aspirations, training opportunities, and the level of preparedness they experienced during their doctoral education. Results of this survey indicated that students felt they were well prepared for many aspects of their chosen career path. Some respondents desired more training to prepare them for careers in academia. More men than women indicated a career in academia as their primary career aspiration. While most of the respondents perceived that their internship experiences were beneficial, some expressed the desire for more opportunities to supervise master’s‐level students, to write grants, and to teach graduate‐level MFT courses. The authors conclude with a discussion of how these findings may influence the development of core competencies specific to doctoral education in MFT.
Adaptive Management of Stream Channel Maintenance at Bridge Crossings in the Northern Tier Region, Pennsylvania1
Authors: Newlin Jessica T. , Johnson Peggy A.
Published: August 2009

Abstract:  An adaptive management framework is applied to the problem of identifying mitigation measures for sediment deposition near bridge crossings in small streams in the Northern Tier region of northern Pennsylvania. The presence of the rigid bridge infrastructure introduces a challenge for applying adaptive management practices, because the integrity of the bridge structure itself has to be maintained regardless of the mitigation practices used in the stream channel near the bridge. In an effort to overcome the unacceptable risk that field‐scale adaptive management experiments present to rigid bridge infrastructure, an adaptive management approach for laboratory‐scale experimentation of mitigation methods at bridge crossings in the Northern Tier region is presented as a way to decrease the level of uncertainty about channel response to mitigation measures and increase the rate of learning about the effectiveness of these measures. Four cycles of adaptive management experiments are discussed to demonstrate that this approach results in fast and efficient learning about channel response to mitigation methods for the given conditions. The value of monitoring and of assessment of monitored data in the overall efficiency of the adaptive management approach is highlighted. Assessment of what was learned in the adaptive management experiment cycles presented here leads to new directions to continually improve management policies and practices in stream channels at bridge crossings in the Northern Tier region. The adaptive management process, rather than continuing with a normally risk‐averse management approach, results in opportunities for learning new information about a system’s response.
Performance of the Revitalised Flood Hydrograph method
Authors: Faulkner D. S. , Barber S.
Published: August 2009

The Revitalised Flood Hydrograph (ReFH) method is used for estimation of design flood hydrographs in the United Kingdom. This paper comments on aspects of the method, discussing its strengths and weaknesses and comparing its results with those of other methods. Design flood peaks estimated using the ReFH method and the statistical method presented in the Flood Estimation Handbook are compared at a sample of locations across Great Britain. The ReFH method gives higher flows at two‐thirds of the sites; on average 16% higher for a flood return period of 100 years. Differences between the results of the two methods are greatest on catchments with significant reservoirs and lakes and catchments with high average rainfall. Recommendations for users of the ReFH method and suggestions for further research are offered, the most urgent of which is to improve the performance of the method on heavily urbanised catchments.
Isolation and characterization of microsatellite markers in the newly discovered invasive fruit fly pest in Africa, Bactrocera invadens (Diptera: Tephritidae)
Authors: KHAMIS F. , KARAM N. , GUGLIELMINO C. R. , EKESI S. , MASIGA D. , DE MEYER M. , KENYA E. U. , MALACRIDA A. R.
Published: August 2009

We describe the isolation and characterization of 11 polymorphic microsatellite loci from the recently discovered fruit fly pest, Bactrocera invadens. The polymorphism of these loci was tested in individual flies from two natural populations (Sri Lanka and Democratic Republic of Congo). Allele number per locus ranged from three to 15 and eight loci displayed a polymorphic information content greater than 0.5. These microsatellite loci provide useful markers for studies of population dynamics and invasion history of this pest species.
Applying Modified MIMO DIVSC to Synchronism and Tension Control of Dual Motor Systems
Authors: Chuang Chin-Wen , Chiang Chin-Lung , Kao Chih-Cheng , Fung Rong-Fong
Published: August 2009

In industrial manufacturing systems, one or more client motors are often arranged to follow the velocity of the master motor. The speed difference between these motors will affect the tension of the product. Hence, the synchronized control and the tension control are the important research topics in the manufacturing process. This paper proposes a novel modified multi-input-multi-output (MIMO) discrete integral variable structure control (DIVSC) for the synchronism and tension control of dual motor systems. By the Grey model theory, the unknown model of tension control can be established on-line to be a pseudo-Grey model. Based on these pseudo-Grey models, the model-based MIMO DIVSC can proceed with the design procedures. Finally, a prototype of the dual motor system is developed for testing the performance of the proposed control scheme. Experimental results will show the robust potential and the practicability of the proposed controller.
Blind Identification of Two-Channel IIR Systems With Application to Central Cardiovascular Monitoring
Authors: Hahn Jin-Oh , Reisner Andrew T. , Asada H. Harry
Published: August 2009

This paper presents a new approach to blind identification of a class of two-channel infinite impulse response (IIR) systems with applicability to clinical cardiovascular monitoring. Specifically, this paper deals with a class of two-channel IIR systems describing wave propagation dynamics. For this class of systems, this paper first derives a blind identifiability condition and develops a blind identification algorithm, which is able to determine both the numerator and denominator polynomials of the channel dynamics uniquely. This paper also develops a new input signal deconvolution algorithm that can reconstruct the input signal from the identified two-channel dynamics and the associated two-channel measurements. These methods are applied to identify the pressure wave propagation dynamics in the cardiovascular system and reconstruct the aortic blood pressure and flow signals from blood pressure measurements taken at two distinct extremity locations. Persistent excitation, model identifiability, and asymptotic variance are analyzed to quantify the method’s validity, accuracy, and reliability without employing direct measurement of the aortic blood pressure and flow signals. The experimental results based on 83 data segments obtained from a swine subject illustrate how the cardiovascular dynamics can be identified accurately and reliably, and the aortic blood pressure and flow signals can be stably reconstructed from two distinct peripheral blood pressure signals under diverse physiologic conditions.
Complementary Filter to Estimate Inertial Velocity
Authors: Williams Daniel E.
Published: August 2009

Long appreciated advantageous stability and performance properties of “skyhook damping” are dependent on availability of an inertially referenced velocity signal. In this work a practical complementary filter using acceleration and position measurements is proposed to construct a high quality inertial velocity signal. The filter was used in a hydraulic suspension system, which isolates the cab of a semitractor from pitching motion of the frame. Low frequency pseudo-integration properties previously limited actual system performance on the vehicle. When the proposed complimentary filter was implemented, a nearly 10 dB improvement in resonant frequency attenuation was achieved while maintaining consistent stability margins.
From the AAPT Executive Officer
Authors: Hein Warren
Published: August 2009

Figure 8b in the print version of the journal is an unintended repeat of Fig. 8a. The correct version of the figure appears below and is also correct in the online version of the paper. We apologize for the error, which was introduced during the production process.
Time Trials — An AP Physics Challenge Lab
Authors: Jones David
Published: August 2009

I have come to the conclusion that for high school physics classroom and laboratory experiences, simpler is better! In this paper I describe a very simple and effective lab experience that my AP students have thoroughly enjoyed year after year. I call this lab exercise “Time Trials.” The experiment is simple in design and it is a lot of fun for students. Time Trials is the type of lab experience that I call a “design challenge lab” or just “challenge lab.” A “challenge lab” is basically an experiment where physics students attempt to obtain a specific outcome under some sort of constraint conditions set by the instructor. The students must work within the constraints set by the instructor and they must work only with the equipment given by the instructor.
The ‘Nut-Drop‘ Experiment—Bringing Millikan's Challenge to Introductory Students
Authors: McCann Lowell I. , Blodgett Earl D.
Published: August 2009

One of the difficulties in teaching 20th-century physics ideas in introductory physics is that many seminal experiments that are discussed in textbooks are difficult or expensive for students to access experimentally. In this paper, we discuss an analogous exercise to Millikan's oil-drop experiment that lets students experience some of the physics involved in the experiment and some of the difficulties Millikan faced.
Only a Theory: Evolution and the Battle for America's Soul: Kenneth R. Miller
Authors: Roeder John L.
Published: August 2009

Only a Theory: Evolution and the Battle for America's Soul, by Kenneth R. Miller and published by Viking, New York, NY (2008), xi + 244 pp., $25.95 ISBN 978-0-670-01883-3.
Dosimetric effects near implanted vascular access ports: an examination of external photon beam dose calculations
Authors: Gossman Michael S. , Seuntjens Jan P. , Serban Monica F. , Christian Kelly J. , Lawson Raymond C. , Robertson Mary A. , Lopez Jeffrey P. , Justice Terry E.
Published: August 2009

Vascular access ports are used widely in the administering of drugs for radiation oncology patients. Their dosimetric effect on radiation therapy delivery in photon beams has not been rigorously established. In this work, the effects on external beam fields when any of a variety of vascular access ports were included in the path of a high energy beam are studied. This study specifically identifies sidescatter and backscatter consequences as well as attenuation effects. The study was divided into two parts. First, a total of 18 ports underwent extended HU range CT scanning followed by 3D computer treatment planning, where homogeneous and heterogeneous plans were created for photon beams of energy 6 MV and 18 MV using a Pencil Beam Convolution (PBC) algorithm. Dose points were analyzed at locations around each device. A total of 1,440 points were reviewed in this section of the study. A replicate of the largest vascular access port was created in the treatment planning workspace for further investigation with alternative treatment planning algorithms. Then, plans were generated identical to the above and compared to the results of dose computation between the Pencil Beam Convolution algorithm, the Analytical Anisotropic Algorithm (AAA), and the EGSnrc Monte Carlo algorithm with user code DOSRZnrc (MC). A total of 300 points were reviewed in this part of the study. It was concluded that ports with more bulky construction and those with partial metal composition create the largest changes. Similar effects were observed for similar port configurations. Considerable differences between the PBC and AAA in comparison to MC are noted and discussed. By thorough examination of planning system results, the presented vascular access ports may now be ranked according to the greatest amount of change exhibited within a treatment planning system. Effects of backscatter, lateral scatter, and attenuation are up to 5.0%, 3.4% and 16.8% for 6 MV and 7.0%, 7.7% and 7.2% for 18 MV, respectively.

PACS numbers: 87.56.bd, 61.82.Bg, 41.50.+h, 87.19.Hh, 87.55.Gh, 87.55.K−, 87.55.N−, 87.55.−x, 81.40.Wx, 87.55.−x, 87.53.Bn, and 87.59.bd
Evaluation of the effects of sagging shifts on isocenter accuracy and image quality of cone‐beam CT from kV on‐board imagers*
Authors: Ali Imad , Ahmad Salahuddin
Published: August 2009

To investigate the effects of sagging shifts of three on‐board kV imaging systems (OBI) on the isocenter positioning accuracy and image quality of cone‐beam CT (CBCT). A cubical phantom having a metal marker in the center that can be aligned with the radiation isocenter was used to measure sagging shifts and their variation with gantry angle on three Varian linacs with kV on‐board imaging systems. A marker‐tracking algorithm was applied to detect the shadow of the metal marker and localize its center in the two‐dimensional cone‐beam radiographic projections. This tracking algorithm is based on finding the position of maximum cross‐correlation between a region‐of‐interest from a template image (including the metal marker) and the projections containing the shadow of the metal marker. Sagging shifts were corrected by mapping the center of the metal marker to a reference position for all projections acquired over a full gantry rotation (0–360°). The sag‐corrected radiographic projections were then used to reconstruct CBCT using Feldkamp back‐projection. A standard quality assurance phantom was used to evaluate the image quality of CBCT before and after sagging correction. Sagging affects both the positioning accuracy of the OBI isocenter and the CBCT image quality. For example, on one linac, the position of the marker on the cone‐beam radiographic projections depends on the angular view and has maximal shifts of about 2 mm along the imager x‐direction (patient's cross‐plane). Sagging produces systematic shifts of the OBI isocenter as large as 1 mm posterior and 1 mm left in patient coordinates relative to the radiation isocenter. Further, it causes spatial distortion and blurring in CBCT image reconstructed from radiographic projections that are not corrected for OBI sagging. CBCT numbers vary by about 1% in full‐fan scans and up to 3.5% in half‐fan scans because of sagging. In order to achieve better localization accuracy in image‐guided radiation therapy, sagging shifts of the kV OBI need to be corrected. In addition, correction of sagging improves image and provides better visualization of internal structures. Frequent quality assurance is required to monitor and maintain standards of variations in the mechanical accuracy of isocenter and image quality of CBCT because of sagging shifts.

PACS number: 87.57.Q, 87.57.cp
Structural Plasticity in Actin and Tubulin Polymer Dynamics
Authors: Kueh Hao Yuan , Mitchison Timothy J.
Published: August 2009

Discussing Polymerization Dynamics

Actin and tubulin represent the major components of microfilaments and microtubules, which are responsible for the cytoskeletal framework of cells. Together with their recently discovered bacterial counterparts, the mechanisms of assembly and disassembly of polymers of these proteins are fundamental to our understanding of cytoplasmic organization and motility.
Kueh and Mitchison
(p.
960
) review mechanisms of cytoskeleton polymerization dynamics and discuss the relative importance of structural plasticity in regulating polymerization.
Dopamine Controls Persistence of Long-Term Memory Storage
Authors: Rossato Janine I. , Bevilaqua Lia R. M. , Izquierdo Iván , Medina Jorge H. , Cammarota Martín
Published: August 2009

Making Memories Last

How can memory traces persist over days or weeks, despite the short-lived nature and rapid turnover of their molecular substrates? It has recently been reported that, in order to persist, an otherwise rapidly forgotten long-term memory requires BDNF (brain-derived neurotrophic factor) expression in the hippocampus 12 hours post training.

Rossato
et al.

(p.
1017
) now show that this mechanism is gated into action by activation of the ventral tegmental area acting upon dopamine D1 receptors in the hippocampus. Time-limited
N
-methyl-
d
-aspartate receptor–dependent activity in the ventral tegmental area–hippocampal circuitry underlies the delayed increase in BDNF levels in the hippocampus 12 hours after inhibitory avoidance, a hippocampus-dependent form of learning.
Homogeneous Distribution of
26
Al in the Solar System from the Mg Isotopic Composition of Chondrules
Authors: Villeneuve Johan , Chaussidon Marc , Libourel Guy
Published: August 2009

Solar Chronometer

The use of the short-lived radioactive isotope
26
Al as a precise chronometer of early solar system processes relies on the assumption that it was uniformly distributed in the initial solar accretion disk.

Villeneuve
et al.

(p.
985
; see the Perspective by

Davis

) validate this assumption on the basis of high-precision isotopic analyses of primitive meteoritic materials. Furthermore, chondrules—constituents of the most common type of meteorites and among the first materials to have formed in the solar system—formed episodically over a period of more than one million years.
Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism
Authors: Oliver Kerry M. , Degnan Patrick H. , Hunter Martha S. , Moran Nancy A.
Published: August 2009

Attacks Wasps

The bacterium
Hamiltonella defensa
infects aphids and carries virulence determinants from a bacteriophage virus.

Oliver
et al.

(p.
992
) have now found that the toxin-bearing phage does not harm the aphid host of the bacterium, but targets the larvae of parasitoid wasps that infest the aphids. If an aphid population is not infested by wasps, the allied bacteriophage is shed by the bacterium, presumably because there is a cost to carrying it. If the wasps then resume their predation, the aphids are no longer protected and succumb to the parasitoid.
Structures of the Ribosome in Intermediate States of Ratcheting
Authors: Zhang Wen , Dunkle Jack A. , Cate Jamie H. D.
Published: August 2009

Translational Rearrangements

Conformational changes in the ribosome are required to translocate messenger RNA and transfer RNA (tRNA) during protein biosynthesis. For example, after peptide bond formation, rotation of the large and small subunits results in a hybrid state of tRNA binding—tRNAs are bound respectively in the aminoacyl-tRNA (A) and peptidyl-tRNA (P) sites in the small subunit, but in the P and exit-tRNA (E) sites on the large subunit.

Zhang
et al.

(p.
1014
) now describe x-ray structures of the intact
Escherichia coli
ribosome, either in the apo form or with one or two anticodon stem-loop tRNA mimics bound, which show intermediate states of intersubunit rotation. The structures provide insight into how the interface between the large and small subunits rearranges in discrete steps to reach the hybrid state.
Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice
Authors: Fukuoka Shuichi , Saka Norikuni , Koga Hironori , Ono Kazuko , Shimizu Takehiko , Ebana Kaworu , Hayashi Nagao , Takahashi Akira , Hirochika Hirohiko , Okuno Kazutoshi , Yano Masahiro
Published: August 2009

Blast-Resistant Rice

The durability of disease resistance for an agricultural crop reflects the extent to which the defense stands up to evolutionary dodges on the part of the pathogen.
Pi21
, which is a quantitative trait locus (QTL) of rice, contributes to a particularly durable resistance to a fungal rice blast disease: Rice plants carrying the resistant allele have been in cultivation for more than a century, and yet the pathogen has been unable to find a way through the defense.

Fukuoka
et al.

(p.
998
; see the news story by

Normile

) have now cloned the responsible
Pi21
QTL allele and were able to separate
Pi21
resistance from tightly linked reductions in grain quality, paving the way for more widespread use of this allele in rice breeding.
Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70
S
Ribosome
Authors: Blaha Gregor , Stanley Robin E. , Steitz Thomas A.
Published: August 2009

Protein Synthesis Initiation Complex

The final step in the initiation phase of protein synthesis is the formation of the first peptide bond, which requires initiator transfer RNA (tRNA) to be bound at the ribosomal P site. Elongation factor P (EF-P) is a protein conserved in all eubacteria that stimulates this initial bond formation. Insight into how this is achieved comes from a structure of
Thermus thermophilus
70
S
ribosome bound to EF-P, initiator tRNA, and a short piece of messenger RNA presented by

Blaha
et al.

(p.
966
). EF-P binds between the P and E sites and facilitates proper positioning of initiator tRNA in the P site. A similar mechanism is likely to apply to structurally homologous initiation factors in archea and eukarya.
Energy and Technology Policies for Managing Carbon Risk
Authors: Patrinos Aristides A. N. , Bradley Richard A.
Published: August 2009

Elements of a global carbon management strategy have been defined, paving the way to increased international actions to reduce global emissions starting this year.
U.S. Energy Agency Stumbles Out of the Blocks
Authors: Mervis Jeffrey
Published: August 2009

Researchers are grumbling about the way the new U.S. Advanced Research Projects Agency–Energy (ARPA-E), which is part of the Department of Energy, is handling its first round of grant proposals.
Rejecting ‘Big Science’ Tag, Collins Sets Five Themes for NIH
Authors: Kaiser Jocelyn
Published: August 2009

Physician-geneticist Francis Collins, the new director of the U.S. National Institutes of Health (NIH), laid out his priorities this week, spending his 1st day on the job speaking to his staff and reporters.
Beyond the Yellow River: How China Became China
Authors: Lawler Andrew
Published: August 2009

The cradle of Chinese civilization was long considered to be the region around the middle Yellow River. But older and complex cultures from far-flung corners of the modern nation are now telling a different story about the origin of Chinese culture.
Founding Dynasty or Myth?
Authors: Lawler Andrew
Published: August 2009

A new crop of archaeologists, less willing to take ancient texts at face value, are challenging the existence of a legendary dynasty.
Spiramycin Treatment of
Toxoplasma gondii
Infection in Pregnant Women Impairs the Production and the Avidity Maturation of
T. gondii
-Specific Immunoglobulin G Antibodies
Authors: Meroni V. , Genco F. , Tinelli C. , Lanzarini P. , Bollani L. , Stronati M. , Petersen E.
Published: August 2009

The aim of the study was to evaluate the influence of treatment with spiramycin on the increase of immunoglobulin G (IgG) titers and IgG avidity indexes (AI) in pregnant women with seroconversion from the beginning of therapy until delivery and after delivery. This group was compared with adult patients with recently acquired untreated toxoplasmosis. One hundred four samples from 32 pregnant women with seroconversion for toxoplasmosis and/or very low IgG AI were followed from the beginning of therapy with spiramycin until delivery. Twenty-nine women were further followed some months after delivery and interruption of therapy. Thirty-eight samples from 16 untreated, nonpregnant patients were evaluated as the control group. The
Toxoplasma gondii
-specific IgG antibody and the
T. gondii
-specific IgG AI were significantly delayed in pregnant women receiving therapy compared to nonpregnant, untreated controls, and the findings were consistent with the results of assays from two different manufacturers. The
T. gondii
-specific IgG AI increased in pregnant women after they gave birth. Avidity maturation is delayed during pregnancy and treatment, and low-avidity antibodies in pregnant women within 3 to 4 months cannot be taken as a sign of infection.
Two Cases of Peritonitis Caused byKocuria marinain Patients Undergoing Continuous Ambulatory Peritoneal Dialysis
Authors: Lee Ja Young , Kim Si Hyun , Jeong Haeng Soon , Oh Seung Hwan , Kim Hye Ran , Kim Yeong Hoon , Lee Jeong Nyeo , Kook Joong-Ki , Kho Weon-Gyu , Bae Il Kwon , Shin Jeong Hwan
Published: August 2009

Kocuriaspp. are members of theMicrococcaceaefamily that are frequently found in the environment and on human skin. Few human infections have been reported. We describe what appear to be the first two cases ofKocuria marinaperitonitis in patients undergoing continuous ambulatory peritoneal dialysis.
Hepatitis C Virus RNA Quantitation in Venous and Capillary Small-Volume Whole-Blood Samples
Authors: Bruns Tony , Steinmetzer Katrin , Ermantraut Eugen , Stallmach Andreas
Published: August 2009

Quantitation of hepatitis C virus (HCV) RNA in plasma and serum samples is a costly procedure in both time and reagents. Additionally, cell-associated viral RNA may not be detected. This study evaluated the accuracy of HCV RNA quantitation in small-volume whole-blood (WB) samples, which would be appropriate for point-of-care diagnostic devices. HCV RNA was extracted from 222 clinical plasma and WB samples of 82 patients with chronic hepatitis C by a specific locked nucleic acid-mediated capture method and quantified by real-time reverse transcription-PCR. The results were compared to the reference plasma viral load determined with the COBAS AmpliPrep/TaqMan (CAP/CTM) HCV test. This assay had an analytical sensitivity of 9 IU per 10-μl sample (95% limit of detection [95% LOD]), a linearity range of 500 to 5 × 10
6
IU/ml, and was accurate in testing 10 HCV subtypes (<0.22 log
10
unit) in plasma. The assay was matrix equivalent for plasma and WB samples (coefficient of determination [
R
2
] of 0.943) and had a specificity of 100% (
n
= 20) in WB samples. The HCV RNA concentration in clinical WB samples exceeded the estimated hematocrit-corrected plasma viral loads by 0.22 log
10
unit, but absolute quantitation results in plasma and WB samples were identical (95% confidence interval, −0.06 to 0.04 log
10
unit). The sensitivity in WB samples was 100% (
n
= 141) for plasma concentrations above the 95% LOD. Quantitation results in 10-μl WB samples correlated linearly with the CAP/CTM HCV plasma test results (
R
2
= 0.919;
n
= 140) and did not differ between capillary and venous samples (
R
2
= 0.960;
n
= 40). This study shows that HCV RNA quantitation in 10-μl WB samples is appropriate for monitoring viral loads of >900 IU/ml, although the use of WB does not increase the diagnostic sensitivity.
Wild-Type MIC Distribution and Epidemiological Cutoff Values for
Aspergillus fumigatus
and Three Triazoles as Determined by the Clinical and Laboratory Standards Institute Broth Microdilution Methods
Authors: Pfaller M. A. , Diekema D. J. , Ghannoum M. A. , Rex J. H. , Alexander B. D. , Andes D. , Brown S. D. , Chaturvedi V. , Espinel-Ingroff A. , Fowler C. L. , Johnson E. M. , Knapp C. C. , Motyl M. R. , Ostrosky-Zeichner L. , Sheehan D. J. , Walsh T. J.
Published: August 2009

Antifungal susceptibility testing of
Aspergillus
species has been standardized by both the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Recent studies suggest the emergence of strains of
A
spergillus fumigatus
with acquired resistance to azoles. The mechanisms of resistance involve mutations in the
cyp51A
(sterol demethylase) gene, and patterns of azole cross-resistance have been linked to specific mutations. Studies using the EUCAST broth microdilution (BMD) method have defined wild-type (WT) MIC distributions, epidemiological cutoff values (ECVs), and cross-resistance among the azoles. We tested a collection of 637 clinical isolates of
A. fumigatus
for which itraconazole MICs were ≤2 μg/ml against posaconazole and voriconazole using the CLSI BMD method. An ECV of ≤1 μg/ml encompassed the WT population of
A. fumigatus
for itraconazole and voriconazole, whereas an ECV of ≤0.25 μg/ml was established for posaconazole. Our results demonstrate that the WT distribution and ECVs for
A. fumigatus
and the mold-active triazoles were the same when determined by the CLSI or the EUCAST BMD method. A collection of 43 isolates for which itraconazole MICs fell outside of the ECV were used to assess cross-resistance. Cross-resistance between itraconazole and posaconazole was seen for 53.5% of the isolates, whereas cross-resistance between itraconazole and voriconazole was apparent in only 7% of the isolates. The establishment of the WT MIC distribution and ECVs for the azoles and
A. fumigatus
will be useful in resistance surveillance and is an important step toward the development of clinical breakpoints.
Differentiating Culture Samples Representing Coagulase-Negative Staphylococcal Bacteremia from Those Representing Contamination by Use of Time-to-Positivity and Quantitative Blood Culture Methods
Authors: Kassis Christelle , Rangaraj Gopi , Jiang Ying , Hachem Ray Y. , Raad Issam
Published: August 2009

Differentiating true coagulase-negative staphylococcal infection from contamination has an important impact on therapeutic implications. Time to positivity reflects bacterial density and may help in the interpretation of blood cultures. We retrospectively reviewed the records of 272 patients from June 2005 to January 2008 for clinical characteristics, microbiological data, and therapeutic outcome. Four groups were identified. The first three groups, as follows, included patients with one positive quantitative blood culture: the low-colony-count group (<10 CFU/ml), the moderate-colony-count group (30 to 100 CFU/ml), and the high-colony-count group (>100 CFU/ml). The control group included patients with two positive quantitative blood cultures and definite coagulase-negative staphylococcal bloodstream infection. The high-colony-count group had shorter time to positivity (≤16 h) than did the low-colony-count group (
P
< 0.0001). The low-colony-count group had a significantly longer time to positivity, >20 h (
P
= 0.001), than did the moderate-colony-count group. Even though antibiotics were not provided in 71% of cases and central venous catheter was retained in 83%, the low-colony-count group had a favorable outcome, suggesting that <10 CFU/ml represents contamination. The high-colony-count group, similar to the positive control group, required antibiotics in 81% of cases and central venous catheter removal in 51% (
P
= 0.001). A time to positivity of ≤16 h reflects high-grade bacteremia with CFU of >100. Similar to the positive control group, these patients required an active therapeutic approach. A time to positivity of >20 h indicates possible contamination with a CFU of <10, and active therapy may not be required.
Impaired Plasmacytoid Dendritic Cell (PDC)-NK Cell Activity in Viremic Human Immunodeficiency Virus Infection Attributable to Impairments in both PDC and NK Cell Function
Authors: Conry Sara J. , Milkovich Kimberly A. , Yonkers Nicole L. , Rodriguez Benigno , Bernstein Helene B. , Asaad Robert , Heinzel Frederick P. , Tary-Lehmann Magdalena , Lederman Michael M. , Anthony Donald D.
Published: August 2009

Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections impair plasmacytoid dendritic cell (PDC) and natural killer (NK) cell subset numbers and functions, though little is known about PDC-NK cell interactions during these infections. We evaluated PDC-dependent NK cell killing and gamma interferon (IFN-γ) and granzyme B production, using peripheral blood mononuclear cell (PBMC)-based and purified cell assays of samples from HCV- and HIV-infected subjects. CpG-enhanced PBMC killing and IFN-γ and granzyme B activity (dependent on PDC and NK cells) were impaired in viremic HIV infection. In purified PDC-NK cell culture experiments, CpG-enhanced, PDC-dependent NK cell activity was cell contact and IFN-α dependent, and this activity was impaired in viremic HIV infection but not in HCV infection. In heterologous PDC-NK cell assays, impaired PDC-NK cell killing activity was largely attributable to an NK cell defect, while impaired PDC-NK cell IFN-γ-producing activity was attributable to both PDC and NK cell defects. Additionally, the response of NK cells to direct IFN-α stimulation was defective in viremic HIV infection, and this defect was not attributable to diminished IFN-α receptor expression, though IFN-α receptor and NKP30 expression was closely associated with killer activity in viremic HIV infection but not in healthy controls. These data indicate that during uncontrolled HIV infection, PDC-dependent NK cell function is impaired, which is in large part attributable to defective IFN-α-induced NK cell activity and not to altered IFN-α receptor, NKP30, NKP44, NKP46, or NKG2D expression.
Extension of Flavivirus Protein C Differentially Affects Early RNA Synthesis and Growth in Mammalian and Arthropod Host Cells
Authors: Schrauf Sabrina , Mandl Christian W. , Bell-Sakyi Lesley , Skern Tim
Published: August 2009

The translation of flaviviral RNA genomes yields a single polyprotein that is processed into the mature proteins by viral and host cell proteases. Mature capsid protein C is freed from the polyprotein by the viral NS2B/3 protease, cleaving in the C-terminal region of protein C in front of the signal sequence for prM. Protein C has been shown to be involved in viral assembly and RNA packaging. To examine further the role of protein C and its production by proteolysis, we replaced the NS2B/3 capsid cleavage site in tick-borne encephalitis virus (TBEV) and West Nile virus (WNV) by the 2A protein of foot-and-mouth disease virus (TBEV-2A and WNV-2A). This obviated the need for NS2B/3 processing at the C terminus of mature protein C while simultaneously producing a 19-amino-acid extension on protein C. Infectious virions were generated with both viruses; the phenotype depended on the host cell. TBEV-2A replicated well in BHK-21 cells but was essentially incapable of replication in tick cells. In contrast, WNV-2A replicated well in mosquito cells but showed a small-plaque phenotype in Vero cells, with frequent production of larger plaques. Sequencing of viral RNA from the larger plaques showed substitutions in the signal sequence for prM, presumably improving coordinated protein processing at the C-prM junction. Furthermore, both TBEV-2A and WNV-2A were also defective in unpackaging and/or early RNA synthesis. Together, these results indicate a role for flavivirus protein C in both viral assembly and RNA replication, possibly by interacting with host cell factors required to set up the cell for RNA replication.
E1 Mutants Identify a Critical Region in the Trimer Interface of the Semliki Forest Virus Fusion Protein
Authors: Liu Catherine Y. , Kielian Margaret
Published: August 2009

The alphavirus Semliki Forest virus (SFV) uses a membrane fusion reaction to infect host cells. Fusion of the virus and cell membranes is triggered by low pH in the endosome and is mediated by the viral membrane protein E1. During fusion, E1 inserts into the target membrane, trimerizes, and refolds into a hairpin conformation. Formation of the E1 homotrimer is critical to membrane fusion, but the mechanism of trimerization is not understood. The crystal structure of the postfusion E1 trimer shows that an aspartate residue, D188, is positioned in the central core trimer interface. D188 is conserved in all reported alphavirus E1 sequences. We tested the contribution of this amino acid to trimerization and fusion by replacing D188 with alanine (D188A) or lysine (D188K) in an SFV infectious clone. These mutations were predicted to disrupt specific interactions at this position and/or change their pH dependence. Our results indicated that the D188K mutation blocked SFV fusion and infection. At low pH, D188K E1 inserted into target membranes but was trapped as a target membrane-inserted monomer that did not efficiently form the stable core trimer. In contrast, the D188A mutant was infectious, although trimerization and fusion required a lower pH. While there are extensive contacts between E1 subunits in the homotrimer, the D188K mutant identifies an important “hot spot” for protein-protein interactions within the core trimer.
Coinfection of Ugandan Red Colobus (
Procolobus
[
Piliocolobus
]
rufomitratus tephrosceles
) with Novel, Divergent Delta-, Lenti-, and Spumaretroviruses
Authors: Goldberg Tony L. , Sintasath David M. , Chapman Colin A. , Cameron Kenneth M. , Karesh William B. , Tang Shaohua , Wolfe Nathan D. , Rwego Innocent B. , Ting Nelson , Switzer William M.
Published: August 2009

Nonhuman primates host a plethora of potentially zoonotic microbes, with simian retroviruses receiving heightened attention due to their roles in the origins of human immunodeficiency viruses type 1 (HIV-1) and HIV-2. However, incomplete taxonomic and geographic sampling of potential hosts, especially the African colobines, has left the full range of primate retrovirus diversity unexplored. Blood samples collected from 31 wild-living red colobus monkeys (
Procolobus
[
Piliocolobus
]
rufomitratus tephrosceles
) from Kibale National Park, Uganda, were tested for antibodies to simian immunodeficiency virus (SIV), simian T-cell lymphotrophic virus (STLV), and simian foamy virus (SFV) and for nucleic acids of these same viruses using genus-specific PCRs. Of 31 red colobus tested, 22.6% were seroreactive to SIV, 6.4% were seroreactive to STLV, and 97% were seroreactive to SFV. Phylogenetic analyses of SIV polymerase (
pol
), STLV
tax
and long terminal repeat (LTR), and SFV
pol
and LTR sequences revealed unique SIV and SFV strains and a novel STLV lineage, each divergent from corresponding retroviral lineages previously described in Western red colobus (
Procolobus badius badius
) or black-and-white colobus (
Colobus guereza
). Phylogenetic analyses of host mitochondrial DNA sequences revealed that red colobus populations in East and West Africa diverged from one another approximately 4.25 million years ago. These results indicate that geographic subdivisions within the red colobus taxonomic complex exert a strong influence on retroviral phylogeny and that studying retroviral diversity in closely related primate taxa should be particularly informative for understanding host-virus coevolution.
Excited states of HI and DI and their negative ions between 10 and 20 eV
Authors: Marmet P. , Nasrallah Hamid
Published: August 2009

The ionization-efficiency curves of HI and DI, obtained by the impact of monoenergetic electrons between 10 and 20 eV, are presented with a very high signal-to-noise ratio. Several new Rydberg states between the 2Π(3/2) and 2Π(1/2) limits and also below the 2Σ+ limit have been identified. Also, the first two 6s and 6p Rydberg levels with configuration (5sσ)1(5pσ)2(5pπ)4nlλ have been observed at 17.3 and 18.6 eV, respectively. The results obtained in DI confirm the structures observed in HI.
Hyperfine-structure interactions: preliminary results
Authors: San-Fabian Emilio , Fraga Serafin
Published: August 2009

Hyperfine-structure splittings have been evaluated for the SL ground states of some chosen atoms (11B, 11C, 13C, 14N, 17O, 19F, and 27Al) using a program developed at this laboratory. The program predicts the energy levels of many-electron atoms within the framework of a configuration-interaction treatment, using a Hamiltonian operator that includes the electrostatic interaction, the specific-mass correction, the SL nonsplitting terms, the fine-structure couplings, and the hyperfine-structure interactions. The agreement with experimental data is satisfactory.
Time violating amplitudes in the (3He, p) reactions
Authors: Khalil Ali E.
Published: August 2009

The difference between the polarization (P) of protons in the reaction (3He, [Formula: see text]) and the analyzing power (A) in the inverse reaction ([Formula: see text], 3He) has been calculated using a spin-independent isospin-independent, time reversal violating interaction in the form [α(r)[Formula: see text] + Hermitian conjugate]. The interaction strength is adjusted to be 1% of the time conserving optical potentials. A distorted-wave Born approximation (DWBA) calculation assuming a direct reaction mechanism has been performed. The relative values of the time violating amplitudes have no signatures for any measurable time violating effects.
Construction of nuclear potentials from phase shifts at different energies and angular momenta
Authors: Hooshyar M. A. , Razavy M.
Published: August 2009

This paper is concerned with an approximate method of construction of a central nuclear potential when [Formula: see text]-matrix elements or phase shifts for different partial waves are given at different energies. This is done by a generalization of the continued-fraction technique that was formulated for solving inverse problems at fixed energy.
Lattice dynamics of thallium iodide
Authors: Haridass C. , Sundararajan R. , Krishnamurthy N.
Published: August 2009

The long-wavelength optical phonons in orthorhombic TlI are calculated employing a shell model and transferring the potential parameters from cubic TlI and TlBr. Satisfactory agreement between experimental Raman and infrared phonons suggests that the change in the crystal structure alone is the main reason for the redistribution of phonons in the cubic to orthorhombic transition.
Temperature and pressure dependence of the optical gaps in Hf1−xZrxS2
Authors: Roubi Larbi , Carlone Cosmo
Published: August 2009

Mixed layered crystals of the type Hf1−xZrxS2, with x = 0.0, 0.1, 0.25, 0.5, 0.75, 0.90, and 1.0, have been grown by the iodine transport method. The direct (at the Γ points) and indirect (Γ to L) transitions have been measured (at T = 290 K) as a function of pressure from 0 to 30 kbar, and (at p = 0 kbar) as a function of the temperature (15–290 K). The phonon frequency assisting the indirect transition is 40 ± 2 MeV. The intrinsic (volume effect) and extrinsic (interaction effect) contributions to the change in electronic energy have been evaluated. We find that the electron–phonon interaction is more aptly described by a quasi-three-dimensional model than a purely two-dimensional one. From the shift of the indirect gap, we find that the electron–phonon coupling constant g varies linearly from 0.54 ± 0.03 (x = 0) to 0.44 ± 0.03 (x = 1.0).
Low-absorption measurement of optical thin films using the photothermal surface-deformation technique
Authors: Welsch E. , Walther H. G. , Eckardt P. , Lan Ton
Published: August 2009

The purpose of this paper is to show both theoretically and experimentally the feasibility of the photothermal surface-deformation (PTD) technique for a highly sensitive, completely contactless detection, as well as a lateral and depth-resolved localization, of absorption in optical thin films. Peculiarities in the interpretation of the measuring signal, such as the influence of the thermal-expansion coefficient of the substrate and the focal diameter of the heating beam, have been pointed out.As a relevant example, the absorption of evaporated ZrO2, single layers on BK 7 substrates has been measured at λ = 515 nm. Their bulk absorption is shown to be strongly influenced by both deposition parameters and the baking procedure.
Born and impact-parameter cross sections for the process H(1s) + H(1s) → H(2s) + H(1s)
Authors: Mayo R. , Rolston S. , Morgan T. J.
Published: August 2009

We report the results of a series of calculations of the cross section for the excitation of a neutral hydrogen atom to the 2s level, due to the collision of two neutral ground-state hydrogen atoms within the energy range 1–100 keV. Cross sections are presented for the first-Born approximation and for the straight-line impact-parameter method employing velocity truncation approximations. Electron exchange terms have been included in all calculations. Reported impact-parameter calculations are the best results of a series of calculations studying the inclusion, in the equation of motion, of terms that are zero- and first-order in the internuclear velocity. These results are compared with first- and second-order Born calculations neglecting exchange, recent infinite-order impact-parameter calculations, and experimental data.