bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of small field output factor measurements on IMRT dosimetry
Authors: Azimi Rezvan , Alaei Parham , Higgins Patrick
Published: July 2012

Purpose:

To evaluate how changes in the measured small field output factors affect the doses in intensity‐modulated treatment planning.

Methods:

IMRT plans were created using Philips Pinnacle treatment planning system. The plans were optimized to treat a cylindrical target 2 cm in diameter and 2 cm in length. Output factors for 2 × 2 and 3 × 3 cm2 field sizes were changed by ±5%, ±10%, and ±20% increments from the baseline measurements and entered into the planning system. The treatment units were recommissioned in the treatment planning system after each modification of the output factors and treatment plans were reoptimized. All plans were delivered to a solid water phantom and dose measurements were made using an ionization chamber. The percentage differences between measured and computed doses were calculated. An Elekta Synergy and a Varian 2300CD linear accelerator were separately evaluated.

Results:

For the Elekta unit, decreasing the output factors resulted in higher measured than computed doses by 0.8% for −5%, 3.6% for −10%, and 8.7% for −20% steps. Increasing the output factors resulted in lower doses by 2.9% for +5%, 5.4% for +10%, and 8.3% for +20% steps. For the Varian unit no changes were observed for either increased or decreased output factors.

Conclusions:

The measurement accuracy of small field output factors are of importance especially when the treatment plan consists of small segments as in IMRT. The method proposed here could be used to verify the accuracy of the measured small field output factors for certain linear accelerators as well as to test the beam model. The Pinnacle treatment planning system model uses output factors as a function of jaw setting. Consequently, plans using the Elekta unit, which conforms the jaws to the segments, are sensitive to small field measurement accuracy. On the other hand, for the Varian unit, jaws are fixed and segments are modeled as blocked fields hence, the impact of small field output factors on IMRT monitor unit calculation is not evaluable by this method.
Improvements in dose calculation accuracy for small off‐axis targets in high dose per fraction tomotherapy
Authors: Hardcastle Nicholas , Bayliss Adam , Wong Jeannie Hsiu Ding , Rosenfeld Anatoly B. , Tomé Wolfgang A.
Published: July 2012

Purpose:

A recent field safety notice from TomoTherapy detailed the underdosing of small, off‐axis targets when receiving high doses per fraction. This is due to angular undersampling in the dose calculation gantry angles. This study evaluates a correction method to reduce the underdosing, to be implemented in the current version (v4.1) of the TomoTherapy treatment planning software.

Methods:

The correction method, termed “Super Sampling” involved the tripling of the number of gantry angles from which the dose is calculated during optimization and dose calculation. Radiochromic film was used to measure the dose to small targets at various off‐axis distances receiving a minimum of 21 Gy in one fraction. Measurements were also performed for single small targets at the center of the Lucy phantom, using radiochromic film and the dose magnifying glass (DMG).

Results:

Without super sampling, the peak dose deficit increased from 0% to 18% for a 10 mm target and 0% to 30% for a 5 mm target as off‐axis target distances increased from 0 to 16.5 cm. When super sampling was turned on, the dose deficit trend was removed and all peak doses were within 5% of the planned dose. For measurements in the Lucy phantom at 9.7 cm off‐axis, the positional and dose magnitude accuracy using super sampling was verified using radiochromic film and the DMG.

Conclusions:

A correction method implemented in the TomoTherapy treatment planning system which triples the angular sampling of the gantry angles used during optimization and dose calculation removes the underdosing for targets as small as 5 mm diameter, up to 16.5 cm off‐axis receiving up to 21 Gy.
Fast DRR generation for 2D to 3D registration on GPUs
Authors: Tornai Gábor János , Cserey György , Pappas Ion
Published: July 2012

Purpose

: The generation of digitally reconstructed radiographs (DRRs) is the most time consuming step on the CPU in intensity based two‐dimensional x‐ray to three‐dimensional (CT or 3D rotational x‐ray) medical image registration, which has application in several image guided interventions. This work presents optimized DRR rendering on graphical processor units (GPUs) and compares performance achievable on four commercially available devices.

Methods

: A ray‐cast based DRR rendering was implemented for a 512 × 512 × 72 CT volume. The block size parameter was optimized for four different GPUs for a region of interest (ROI) of 400 × 225 pixels with different sampling ratios (1.1%–9.1% and 100%). Performance was statistically evaluated and compared for the four GPUs. The method and the block size dependence were validated on the latest GPU for several parameter settings with a public gold standard dataset (512 × 512 × 825 CT) for registration purposes.

Results

: Depending on the GPU, the full ROI is rendered in 2.7–5.2 ms. If sampling ratio of 1.1%–9.1% is applied, execution time is in the range of 0.3–7.3 ms. On all GPUs, the mean of the execution time increased linearly with respect to the number of pixels if sampling was used.

Conclusions

: The presented results outperform other results from the literature. This indicates that automatic 2D to 3D registration, which typically requires a couple of hundred DRR renderings to converge, can be performed quasi on‐line, in less than a second or depending on the application and hardware in less than a couple of seconds. Accordingly, a whole new field of applications is opened for image guided interventions, where the registration is continuously performed to match the real‐time x‐ray.
Design, construction, and evaluation of a dynamic MR compatible cardiac left ventricle model
Authors: Dieringer Matthias A. , Hentschel Jan , de Quadros Thiago , von Knobelsdorff‐Brenkenhoff Florian , Hoffmann Werner , Niendorf Thoralf , Schulz‐Menger Jeanette
Published: July 2012

Purpose:

Development of magnetic resonance (MR) sequences is important to answer clinical questions and to overcome current limitations. To meet the challenges of cardiac MR, dynamic and reproducible testing conditions are required. We aimed at developing a dynamic MR‐compatible cardiac left ventricle model that imitates myocardial tissue properties and simulates dynamic motion.

Methods:

A dynamic left ventricle silicone model was designed to match myocardial T1 and T2 relaxation times. Silicone mixtures were explored to replicate T2 values of myocardial edema. A controllable piston pump was constructed to produce pulsatile flow paradigms. They were validated against flow sensors and MR data, including SSFP‐based and phase‐contrast‐based sequences. A dedicated software interface was developed for the control.

Results:

Model dimensions represented cardiac left ventricle dimensions of healthy men. The range of end diastolic volumes was 85–175 ml, depending on the driven stroke volume. Stroke volume quantification for flow paradigms of 30/60/90/120 ml resulted in 29.2/57.6/88.8/118.4 ml by MR volumetry, 29.6/59.9/89.4/119.0 ml by phase contrast measurements, and 29.9/60.4/91.1/120.9 ml by flow meter revealing consistency. The system accurately replicated physiological and pathophysiological flow paradigms. The silicon model exhibited T1 of 1002 ± 8 ms, T2 of 58 ± 1 ms. Signal intensities (a.u.) of the ventricle model were 128 ± 23 for FGRE (vs 138 ± 17 in vivo) and 1156 ± 37 for b‐SSFP (vs 991 ± 96 in vivo). T2 of 75 ± 2 ms was achieved for the myocardial pathology.

Conclusions:

We developed a controllable left ventricle model resembling MR signal characteristics of human myocardium, including pathological conditions, and allowing for the replication of contraction and flow paradigms.
Auditory brainstem responses to chirps delivered by an insert earphone with equalized frequency response
Authors: Elberling Claus , Don Manuel , Kristensen Sinnet G. B.
Published: July 2012

Recently it has been demonstrated that auditory brainstem responses, ABRs, to chirps are larger with the ER-2 than with the ER-3A insert earphone due to differences between the corresponding amplitude-frequency responses. Therefore a modified chirp, which equalizes the amplitude-frequency response of the ER-3A, is constructed and subsequently compared to the unmodified chirp. ABRs are recorded from 20 normal-hearing subjects in response to the two chirps delivered by the ER-3A earphone at a wide range of levels. The results confirm that the modified chirp generates significantly larger ABRs than the unmodified chirp at levels below 60 dB nHL.
Finding Their Place In the World
Nature's Compass: The Mystery of Animal Navigation.
James L. Gould and Carol Grant Gould. Princeton University Press, Princeton, NJ, 2012. 310 pp. $29.95, £19.95. ISBN 9780691140452.
Authors: Yamahachi Homare
Published: July 2012

The Goulds survey the means by which animals navigate around their neighborhoods and across the globe.
The Ingredients for a 4000-Year-Old Proto-Curry
Authors: Lawler Andrew
Published: July 2012

Recent studies presented at the meeting found a surprisingly diverse Indus diet that incorporated spices, beans, and grains commonly eaten today, and even bananas.
Diving Into the Indian Ocean's Past
Authors: Lawler Andrew
Published: July 2012

Researchers studying what appears to be the oldest known shipwreck in the Indian Ocean say it promises to remake our understanding of the region and era.
Cardiac Glycosides Exert Anticancer Effects by Inducing Immunogenic Cell Death
Authors: Menger Laurie , Vacchelli Erika , Adjemian Sandy , Martins Isabelle , Ma Yuting , Shen Shensi , Yamazaki Takahiro , Sukkurwala Abdul Qader , Michaud Mickaël , Mignot Grégoire , Schlemmer Frederic , Sulpice Eric , Locher Clara , Gidrol Xavier , Ghiringhelli François , Modjtahedi Nazanine , Galluzzi Lorenzo , André Fabrice , Zitvogel Laurence , Kepp Oliver , Kroemer Guido
Published: July 2012

Cardiac glycosides kill cancer cells in a way that stimulates the immune response.
Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment
Authors: Zhao Yu , Caspers Martien P. , Abee Tjakko , Siezen Roland J. , Kort Remco
Published: July 2012

Thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain
Geobacillus thermoglucosidans
TNO-09.020 from a milk processing plant and report the complete genome of a dairy plant isolate consisting of a single chromosome of 3.75 Mb.
The Breadth and Titer of Maternal HIV-1-Specific Heterologous Neutralizing Antibodies Are Not Associated with a Lower Rate of Mother-to-Child Transmission of HIV-1
Authors: Chaillon Antoine , Wack Thierry , Braibant Martine , Mandelbrot Laurent , Blanche Stéphane , Warszawski Josiane , Barin Francis
Published: July 2012

It has been hypothesized that neutralizing antibodies (NAbs) should have broad specificity to be effective in protection against diverse HIV-1 variants. The mother-to-child transmission model of HIV-1 provides the opportunity to examine whether the breadth of maternal NAbs is associated with protection of infants from infection. Samples were obtained at delivery from 57 transmitting mothers (T) matched with 57 nontransmitting mothers (NT) enrolled in the multicenter French perinatal cohort (ANRS EPF CO1) between 1990 and 1996. Sixty-eight (59.6%) and 46 (40.4%) women were infected by B and non-B viruses, respectively. Neutralization assays were carried out with TZM-bl cells, using a panel of 10 primary isolates of 6 clades (A, B, C, F, CRF01_AE, and CRF02_AG), selected for their moderate or low sensitivity to neutralization. Neutralization breadths were not statistically different between T and NT mothers. However, a few statistically significant differences were observed, with higher frequencies or titers of NAbs toward several individual strains for NT mothers when the clade B-infected or non-clade B-infected mothers were analyzed separately. Our study confirms that the breadth of maternal NAbs is not associated with protection of infants from infection.
Selective Modification of Adenovirus Replication Can Be Achieved through Rational Mutagenesis of the Adenovirus Type 5 DNA Polymerase
Authors: Capella Cristina , Beltejar Michael-John , Brown Caitlin , Fong Vincent , Daddacha Waaqo , Kim Baek , Dewhurst Stephen
Published: July 2012

Mutations that reduce the efficiency of deoxynucleoside (dN) triphosphate (dNTP) substrate utilization by the HIV-1 DNA polymerase prevent viral replication in resting cells, which contain low dNTP concentrations, but not in rapidly dividing cells such as cancer cells, which contain high levels of dNTPs. We therefore tested whether mutations in regions of the adenovirus type 5 (Ad5) DNA polymerase that interact with the dNTP substrate or DNA template could alter virus replication. The majority of the mutations created, including conservative substitutions, were incompatible with virus replication. Five replication-competent mutants were recovered from 293 cells, but four of these mutants failed to replicate in A549 lung carcinoma cells and Wi38 normal lung cells. Purified polymerase proteins from these viruses exhibited only a 2- to 4-fold reduction in their dNTP utilization efficiency but nonetheless could not be rescued, even when intracellular dNTP concentrations were artificially raised by the addition of exogenous dNs to virus-infected A549 cells. The fifth mutation (I664V) reduced biochemical dNTP utilization by the viral polymerase by 2.5-fold. The corresponding virus replicated to wild-type levels in three different cancer cell lines but was significantly impaired in all normal cell lines in which it was tested. Efficient replication and virus-mediated cell killing were rescued by the addition of exogenous dNs to normal lung fibroblasts (MRC5 cells), confirming the dNTP-dependent nature of the polymerase defect. Collectively, these data provide proof-of-concept support for the notion that conditionally replicating, tumor-selective adenovirus vectors can be created by modifying the efficiency with which the viral DNA polymerase utilizes dNTP substrates.
Observational evidence that urbanisation and neighbourhood deprivation are associated with escalation in chronic pharmacological pain treatment: a longitudinal population-based study in the Netherlands
Authors: Leue Carsten , Buijs Servaas , Strik Jacqueline , Lousberg Richel , Smit Jasper , van Kleef Maarten , van Os Jim
Published: July 2012

Objective

To examine, in the light of the association between urban environment and poor mental health, whether urbanisation and neighbourhood deprivation are associated with analgesic escalation in chronic pharmacological pain treatment and whether escalation is associated with prescriptions of psychotropic medication.

Design

Longitudinal analysis of a population-based routine dispensing database in the Netherlands.

Setting

Representative sample of pharmacies, covering 73% of the Dutch nationwide medication consumption in the primary care and hospital outpatient settings.

Participants

449 410 patients aged 15–85 years were included, of whom 166 374 were in theStarter groupand 283 036 in theContinuation groupof chronic analgesic treatment.

Main outcome measure

Escalation of analgesics (ie, change to a higher level of analgesic potency, classified across five levels) in association with urbanisation (five levels) and dichotomous neighbourhood deprivation was analysed over a 6-month observation period.

Methods

Ordered logistic multivariate model evaluating analgesic treatment.

Results

In bothStarterandContinuationgroups, escalation was positively associated with urbanisation in a dose–response fashion (Starter group: OR (urbanisation level 1 compared with level 5): 1.24, 95% CI 1.18 to 1.30; Continuation group: OR 1.18, 95% CI 1.14 to 1.23). An additional association was apparent with neighbourhood deprivation (Starter group: OR 1.07, 95% CI 1.02 to 1.11; Continuation group: OR 1.04, 95% CI 1.01 to 1.08). Use of somatic and particularly psychotropic co-medication was associated with escalation in both groups.

Conclusions

Escalation of chronic analgesic treatment is associated with urban and deprived environments and occurs in a context of adding psychotropic medication prescriptions. These findings suggest that pain outcomes and mental health outcomes share factors that increase risk and remedy suffering.
An evaluation of overnight fixation to facilitate neuropathological examination in Coroner's autopsies: our experience of over 200 cases
Authors: Scott Ian Stuart , MacDonald Alastair Wray
Published: July 2012

Aims

Following recent changes in Coroner's Rules, there has been a desire to examine brains at the time of autopsy, rather than after a prolonged period of immersion fixation. Examination of the fresh brain at postmortem can yield unsatisfactory results where detailed histological examination is required. We aim to provide a compromise, where detailed examination of the brain is possible, without the requirement for prolonged fixation, interference with funeral arrangements and delay in the Coronial process.

Methods

A retrospective audit of over 200 neuropathology cases requested by HM Coroner for the East Riding of Yorkshire between 2007 and 2010 was performed. The cases consisted of full neuropathology autopsies (n=212) and brains referred by general pathology colleagues (n=26).

Results

Of the 238 brains examined, approximately half (n=109) of the brains were sectioned fresh in the mortuary. The remaining brains (n=129) were immersion fixed overnight in 20% formalin prior to cutting and sampling for histology (n=127). The median time for reporting was 31 days (range 1–167; n=101) for brains requiring histology. This equates to a median turnaround time of 1 month for a neuropathological autopsy requiring detailed histology. In all cases, the report was prepared and available to HM Coroner in advance of the Inquest.

Conclusions

This method provides reliable histological diagnoses in neuropathological autopsies and does not interfere with funeral arrangements for bereaved families following deaths falling under Coronial jurisdiction. In all cases, the body could be released to relatives, at Coroner's discretion, within two working days of the autopsy.
Efficacy of intranasal vaccination of field buffaloes against haemorrhagic septicaemia with a live gdhA derivative Pasteurella multocida B:2
Authors: Rafidah O. , Zamri‐Saad M. , Shahirudin S. , Nasip E.
Published: July 2012

The efficacy of an intranasal haemorrhagic septicaemia vaccine containing live gdhA derivative Pasteurella multocida B:2 was tested in buffaloes in Sabah. Sixty buffaloes, kept grazing in the field with minimal human intervention were devided into three groups of 20 buffaloes per group. Buffaloes of group 1 were exposed intranasal to 5 ml vaccine containing 106 CFU/ml of live gdhA derivative P multocida B:2. Buffaloes of group 2 were not exposed to the vaccine but exposed to PBS and were allowed to commingle and graze in the same field as the buffaloes of group 1 while buffaloes of group 3 were similarly exposed to PBS and were grazing separately. Booster was on group 1, two weeks later. Twelve months after the first vaccination, three buffaloes from each group were brought into the experimental house and challenged subcutaneously with 109 CFU/ml of live wild‐type P multocida B:2. All challenged buffaloes of groups 1 and 2 survived with only mild, transient signs while all control unvaccinated buffaloes developed severe signs of haemorrhagic septicaemia and were euthanased between 28 hours and 38 hours postchallenge with signs and lesions typical of haemorrhagic septicaemia. These data showed that the gdhA mutant strain, given intranasally as two doses two weeks apart, successfully induced systemic immunity in exposed buffaloes and also led to spread of vaccine strain to the in‐contact animals, where it acted as an effective live vaccine to protect both exposed buffaloes and in‐contact buffaloes against challenge with the virulent parent strain.
Variations and classification of toxic epitopes related to celiac disease among α-gliadin genes from four Aegilops genomes
Authors: Li Jie , Wang Shunli , Li Shanshan , Ge Pei , Li Xiaohui , Ma Wujun , Zeller F.J. , Hsam Sai L.K. , Yan Yueming
Published: July 2012

The α-gliadins are associated with human celiac disease. A total of 23 noninterrupted full open reading frame α-gliadin genes and 19 pseudogenes were cloned and sequenced from C, M, N, and U genomes of four diploid Aegilops species. Sequence comparison of α-gliadin genes from Aegilops and Triticum species demonstrated an existence of extensive allelic variations in Gli-2 loci of the four Aegilops genomes. Specific structural features were found including the compositions and variations of two polyglutamine domains (QI and QII) and four T cell stimulatory toxic epitopes. The mean numbers of glutamine residues in the QI domain in C and N genomes and the QII domain in C, N, and U genomes were much higher than those in Triticum genomes, and the QI domain in C and N genomes and the QII domain in C, M, N, and U genomes displayed greater length variations. Interestingly, the types and numbers of four T cell stimulatory toxic epitopes in α-gliadins from the four Aegilops genomes were significantly less than those from Triticum A, B, D, and their progenitor genomes. Relationships between the structural variations of the two polyglutamine domains and the distributions of four T cell stimulatory toxic epitopes were found, resulting in the α-gliadin genes from the Aegilops and Triticum genomes to be classified into three groups.
Modelling volume growth response of young Scots pine (Pinus sylvetris) stands to N, P, and K fertilization in drained peatland sites in Finland
Authors: Hökkä Hannu , Repola Jaakko , Moilanen Mikko
Published: July 2012

Fertilizers are applied in drained peatland forests to correct nutrient imbalances, but few models have been developed for predicting the stand growth response. We used 10- to 34-year-long stem growth increment data from 51 fertilization experiments involving ash, PK, and NPK treatments (doses of P, K, and N varying between 35 and 45, 60 and 80, and 80 and 90 kg·ha–1, respectively) and controls to model the volume growth response of young Scots pine (Pinus sylvetris L.) stands to fertilization in drained peatland sites of middle and northern Finland. We used the linear mixed models method to express the stand-level growth response as a function of time (5-year periods), site type group, location, and the fertilization treatment (ash–PK combined and NPK). Different growth responses were obtained for nitrogen-rich sites with PK treatment and nitrogen-poor sites with NPK treatment. The PK fertilization in nitrogen-rich sites resulted in the largest volume growth response and longest temporal effect (1.0–2.0 m3·ha–1·a–1 higher mean growth for at least 35 years), with quicker and stronger effects in more southern conditions where average temperature sums were greater than 1000 degree-days (°C). NPK fertilization in nitrogen-poor sites gave a modest response (0.4–0.8 m3·ha–1·a–1 in 35 years).
Determining carrying capacity from foraminiferal time-series
Authors: Wilson Brent , Horton Benjamin P.
Published: July 2012

Abstract. The carrying capacity K is the equilibrium population density of a species that an area can support while adequately meeting the needs of every individual. Although widely used in ecology, it has yet to be applied rigorously to living foraminifera. K is readily determined from time-series of population densities. Given that Nt+1 = Nt + RNt, in which Nt is the population densities at time t, Nt+1 is the density at a subsequent time t+1 and R is the per capita rate of change in population density, then linear regression gives Rt = Rm − sNt, in which Rt is the per capita rate of increase at time t, the constant Rm is the maximum possible individual rate of increase, and the negative slope s represents the strength of intraspecific interactions. Setting Rt = 0, so that Nt = K and Rm – sK = 0, gives K = Rm/s, which is applicable in aseasonal environments. There are two carrying capacities in seasonal environments, depending on whether the season is favourable (Kmax) or unfavourable (Kmin). Values of Kmax and Kmin are estimated for Nonion depressulus in the Exe estuary, UK (25 monthly samples), Quinqueloculina spp. in the Indian River Lagoon, USA (60 monthly samples) and Haynesina germanica in Cowpen Marsh, UK (25 fortnightly samples). The most precise estimate was for H. germanica, but it was unclear if this was due to the high rate of sampling or the large number of replicates used to erect this time-series.
Archaeometallurgy: The Study of Preindustrial Mining and Metallurgy
Authors: Killick David , Fenn Thomas
Published: July 2012

Archaeometallurgy is an interdisciplinary and international field of study that examines all aspects of the production, use, and consumption of metals from ∼8000 BCE to the present, although this review is restricted to mining and metallurgy in preindustrial societies. Most of this literature was not written with an anthropological readership in mind, but many of its central themes are relevant to some current debates in anthropology. Since the 1970s, archaeometallurgists have been concerned explicitly with the materiality of metals and also with the highly variable value of precious metals across time and space. Exacting criteria have been developed for distinguishing past technology transfers from independent inventions. Archaeometallurgists have also done important work on the social construction of technology in precapitalist economies. In short, archaeometallurgy offers much that is of interest to anthropologists who study the growth and spread of knowledge, and of systems of value, before the capitalist era.
Music, Language, and Texts: Sound and Semiotic Ethnography
Authors: Faudree Paja
Published: July 2012

This review surveys recent research on language-music: the unified expressive field comprising sounded and textual signs whose segmentation into “language” and “music” is culturally constructed. I argue that approaching language-music semiotically will promote—alongside the discipline's emergent “auditory turn”—greater holism in anthropological practice if coupled to the joint effort of attending to textuality while decentering its primacy. I discuss recent scholarship that demonstrates, if often implicitly, the merit of this approach. I organize this work into three overlapping themes of active research: scholarship on chronotopes and soundscapes exploring processes that reconfigure time and place; work on subject creation focusing on voice, emotion, intersubjectivity, and listening; and scholarship on the social dimensions of object creation, including technological mediation, authentication, and circulation. I conclude by discussing future directions in research on language-music and the promise such work offers of furthering the call to broaden anthropology's holism while loosening adherence to its text-centered practices.
Immigration, Crime, and Victimization: Rhetoric and Reality
Authors: Zatz Marjorie S. , Smith Hilary
Published: July 2012

Contrary to popular perceptions that immigration increases crime, the research literature demonstrates that immigration generally serves a protective function, reducing crime. This review takes as its starting point the contradiction between the rhetoric and the reality of immigration and crime in the United States. We begin by exploring the conditions under which immigration reduces crime and those under which it has less or no effect, with particular attention to traditional and new destination sites. We then demonstrate how the moral panic about immigration has contributed to unprecedented levels of new legislation and intensified enforcement practices. These new laws and policies, we suggest, are making immigrants and their communities less safe. We consider some of the ways in which immigrants have become more vulnerable and how that vulnerability is patterned and nuanced. We close by examining recent research in other parts of the world, finding some similarities but also differences in the relationships among immigration, crime, and victimization.
Vitamin A Metabolism in Rod and Cone Visual Cycles
Authors: Saari John C.
Published: July 2012

The chromophore of all known visual pigments consists of 11-cis-retinal (derived from either vitamin A1 or A2) or a hydroxylated derivative, bound to a protein (opsin) via a Schiff base. Absorption of a photon results in photoisomerization of the chromophore to all-trans-retinal and conversion of the visual pigment to the signaling form. Regeneration of the 11-cis-retinal occurs in an adjacent tissue and involves several enzymes, several water-soluble retinoid-binding proteins, and intra- and intercellular diffusional processes. Rod photoreceptor cells depend completely on the output of 11-cis-retinal from adjacent retinal pigment epithelial (RPE) cells. Cone photoreceptors cells can use 11-cis-retinal from the RPE and from a second more poorly characterized cycle, which appears to involve adjacent Müller (glial) cells. Recent progress in the characterization of rod and cone visual cycle components and reactions will result in the development of approaches to the amelioration of blinding eye diseases associated with visual cycle defects.
CCL2 and CCL3 are essential mediators of pelvic pain in experimental autoimmune prostatitis
Authors: Quick Marsha L. , Mukherjee Soumi , Rudick Charles N. , Done Joseph D. , Schaeffer Anthony J. , Thumbikat Praveen
Published: July 2012

Experimental autoimmune prostatitis (EAP) is a murine model of chronic prostatitis/chronic pelvic pain syndrome (CPPS) in men, a syndrome characterized by chronic pelvic pain. We have demonstrated that chemokine ligands CCL2 and CCL3 are biomarkers that correlate with pelvic pain symptoms. We postulated that CCL2 and CCL3 play a functional role in CPPS and therefore examined their expression in EAP. Upon examination of the prostate 5 days after induction of EAP, CCL2 mRNA was elevated 2- to 3-fold, CCL8 by 15-fold, CCL12 by 12- to 13-fold, and CXCL9 by 2- to 4-fold compared with control mice. At 10 days the major chemokines were CXCL13 and CXCL2; at 20 days CCL2 (1- to 2-fold), CCL3 (2- to 3-fold) and CCL11 (2- to 3-fold); and at 30 days, CCL12 (20- to 35-fold) and smaller increases in CCL2, CCL3, and XCL1. Chemokine elevations were accompanied by increases in mast cells and B cells at 5 days, monocytes and neutrophils at day 10, CD4+ T cells at day 20, and CD4+ and CD8+ T cells at day 30. Anti-CCL2 and anti-CCL3 neutralizing antibodies administered at EAP onset attenuated pelvic pain development, but only anti-CCL2 antibodies were effective therapeutically. CCL2- and its cognate receptor CCR2-deficient mice were completely protected from development of pain symptoms but assumed susceptibility after reconstitution with wild-type bone marrow. CCL3-deficient mice showed resistance to the maintenance of pelvic pain while CCR5-deficient mice did not show any lessening of pelvic pain severity. These results suggest that the CCL2-CCR2 axis and CCL3 are important mediators of chronic pelvic pain in EAP.
Age-dependent adrenergic actions in the main olfactory bulb that could underlie an olfactory-sensitive period
Authors: Pandipati Sruthi , Schoppa Nathan E.
Published: July 2012

Many sensory systems are endowed with mechanisms of neural plasticity that are restricted to a sensitive period in the young developing animal. In this study, we performed experiments in slices of the main olfactory bulb (OB) from rats to examine possible age-dependent cellular mechanisms of plasticity in the olfactory system. We focused on the neurotransmitter norepinephrine (NE), shown to be important in different forms of olfactory learning, examining whether two specific cellular effects of NE previously observed in rats less than P14 extended to older animals. These included an acute reduction in GABAergic synaptic transmission from granule cells (GCs) onto output mitral cells (MCs) and an enhancement in gamma frequency (30–70 Hz) oscillations that persists long after removal of NE. We found that NE failed to reduce GC-to-MC transmission or enhance gamma oscillations in older rats at P18–23. The loss of NE actions on both phenomena appeared to reflect an age-dependent loss of function of α2-adrenergic receptors. In addition, we found that NE induced an age-dependent enhancement of transient excitation in MCs, providing a mechanism to link the acute decrease in GC-to-MC inhibition to the long-term increase in gamma oscillations through increases in intracellular calcium. The age-dependent cellular mechanisms that we describe could underlie an olfactory-sensitive period in newborn rodents.
Comparison of latency and rate coding for the direction of whisker deflection in the subcortical somatosensory pathway
Authors: Storchi Riccardo , Bale Michael R. , Biella Gabriele E. M. , Petersen Rasmus S.
Published: July 2012

The response of many neurons in the whisker somatosensory system depends on the direction in which a whisker is deflected. Although it is known that the spike count conveys information about this parameter, it is not known how important spike timing might be. The aim of this study was to compare neural codes based on spike count and first-spike latency, respectively. We extracellularly recorded single units from either the rat trigeminal ganglion (primary sensory afferents) or ventroposteromedial (VPM) thalamic nucleus in response to deflection in different directions and quantified alternative neural codes using mutual information. We found that neurons were diverse: some (58% in ganglion, 32% in VPM) conveyed information only by spike count; others conveyed additional information by latency. An issue with latency coding is that latency is measured with respect to the time of stimulus onset, a quantity known to the experimenter but not directly to the subject's brain. We found a potential solution using the integrated population activity as an internal timing signal: in this way, 91% of the first-spike latency information could be recovered. Finally, we asked how well direction could be decoded. For large populations, spike count and latency codes performed similarly; for small ones, decoding was more accurate using the latency code. Our findings indicate that whisker deflection direction is more efficiently encoded by spike timing than by spike count. Spike timing decreases the population size necessary for reliable information transmission and may thereby bring significant advantages in both wiring and metabolic efficiency.
Transduction inDrosophilaolfactory receptor neurons is invariant to air speed
Authors: Zhou Yi , Wilson Rachel I.
Published: July 2012

In the vertebrate nose, increasing air speed tends to increase the magnitude of odor-evoked activity in olfactory receptor neurons (ORNs), given constant odor concentration and duration. It is often assumed that the same is true of insect olfactory organs, but this has not been directly tested. In this study, we examined the effect of air speed on ORN responses in Drosophila melanogaster. We constructed an odor delivery device that allowed us to independently vary concentration and air speed, and we used a fast photoionization detector to precisely measure the actual odor concentration at the antenna while simultaneously recording spikes from ORNs in vivo. Our results demonstrate that Drosophila ORN odor responses are invariant to air speed, as long as odor concentration is kept constant. This finding was true across a >100-fold range of air speeds. Because odor hydrophobicity has been proposed to affect the air speed dependence of olfactory transduction, we tested a >1,000-fold range of hydrophobicity values and found that ORN responses are invariant to air speed across this full range. These results have implications for the mechanisms of odor delivery to Drosophila ORNs. Our findings are also significant because flies have a limited ability to control air flow across their antennae, unlike terrestrial vertebrates, which can control air flow within their nasal cavity. Thus, for the fly, invariance to air speed may be adaptive because it confers robustness to changing wind conditions.
NPM-ALK: The Prototypic Member of a Family of Oncogenic Fusion Tyrosine Kinases
Authors: Pearson Joel D. , Lee Jason K. H. , Bacani Julinor T. C. , Lai Raymond , Ingham Robert J.
Published: July 2012

Anaplastic lymphoma kinase (ALK) was first identified in 1994 with the discovery that the gene encoding for this kinase was involved in the t(2;5)(p23;q35) chromosomal translocation observed in a subset of anaplastic large cell lymphoma (ALCL). The NPM-ALK fusion protein generated by this translocation is a constitutively active tyrosine kinase, and much research has focused on characterizing the signalling pathways and cellular activities this oncoprotein regulates in ALCL. We now know about the existence of nearly 20 distinct ALK translocation partners, and the fusion proteins resulting from these translocations play a critical role in the pathogenesis of a variety of cancers including subsets of large B-cell lymphomas, nonsmall cell lung carcinomas, and inflammatory myofibroblastic tumours. Moreover, the inhibition of ALK has been shown to be an effective treatment strategy in some of these malignancies. In this paper we will highlight malignancies where ALK translocations have been identified and discuss why ALK fusion proteins are constitutively active tyrosine kinases. Finally, using ALCL as an example, we will examine three key signalling pathways activated by NPM-ALK that contribute to proliferation and survival in ALCL.
Ischemic Preconditioning of Rat Livers from Non-Heart-Beating Donors Decreases Parenchymal Cell Killing and Increases Graft Survival after Transplantation
Authors: Currin Robert T. , Peng Xing-Xi , Lemasters John J.
Published: July 2012

A critical shortage of donors exists for liver transplantation, which non-heart-beating cadaver donors could help ease. This study evaluated ischemic preconditioning to improve graft viability after non-heart-beating liver donation in rats. Ischemic preconditioning was performed by clamping the portal vein and hepatic artery for 10 min followed by unclamping for 5 min. Subsequently, the aorta was cross-clamped for up to 120 min. After 2 h of storage, livers were either transplanted or perfused with warm buffer containing trypan blue. Aortic clamping for 60 and 120 min prior to liver harvest markedly decreased 30-day graft survival from 100% without aortic clamping to 50% and 0%, respectively, which ischemic preconditioning restored to 100 and 50%. After 60 min of aortic clamping, loss of viability of parenchymal and nonparenchymal cells was 22.6 and 5.6%, respectively, which preconditioning decreased to 3.0 and 1.5%. Cold storage after aortic clamping further increased parenchymal and non-parenchymal cell killing to 40.4 and 10.1%, respectively, which ischemic preconditioning decreased to 12.4 and 1.8%. In conclusion, ischemic preconditioning markedly decreased cell killing after subsequent sustained warm ischemia. Most importantly, ischemic preconditioning restored 100% graft survival of livers harvested from non-heart-beating donors after 60 min of aortic clamping.
Effects of Conjugate Heat Transfer on Steady MHD Mixed Convective Heat Transfer Flow over a Thin Vertical Plate Embedded in a Porous Medium with High Porosity
Authors: Kaya Ahmet
Published: July 2012

This study investigates mixed convection heat transfer about a thin vertical plate in
the presence of magneto and conjugate heat transfer effects in the porous medium
with high porosity. The fluid is assumed to be incompressible and dense. The
nonlinear coupled parabolic partial differential equations governing the flow are
transformed into the nonsimilar boundary layer equations, which are then solved
numerically using the Keller box method. The effects of the conjugate heat transfer
parameter p, the porous medium parameter k1, the Forchheimer parameter F*,
the mixed convection parameter Ri, the magnetic parameter Mn, and the electric
field parameter E1 on the velocity and temperature profiles as well as on the local
skin friction and local heat transfer are presented and analyzed. The validity of the
methodology and analysis is checked by comparing the results obtained for some
specific cases with those available in the literature.
Hepatitis C Variability, Patterns of Resistance, and Impact on Therapy
Authors: Strahotin Cristina Simona , Babich Michael
Published: July 2012

Hepatitis C (HCV), a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma, is the most common indication for liver transplantation in the United States. Although annual incidence of infection has declined since the 1980s, aging of the currently infected population is expected to result in an increase in HCV burden. HCV is prone to develop resistance to antiviral drugs, and despite considerable efforts to understand the virus for effective treatments, our knowledge remains incomplete. This paper reviews HCV resistance mechanisms, the traditional treatment with and the new standard of care for hepatitis C treatment. Although these new treatments remain PEG-IFN-α- and ribavirin-based, they add one of the newly FDA approved direct antiviral agents, telaprevir or boceprevir. This new “triple therapy” has resulted in greater viral cure rates, although treatment failure remains a possibility. The future may belong to nucleoside/nucleotide analogues, non-nucleoside RNA-dependent RNA polymerase inhibitors, or cyclophilin inhibitors, and the treatment of HCV may ultimately parallel that of HIV. However, research should focus not only on effective treatments, but also on the development of a HCV vaccine, as this may prove to be the most cost-effective method of eradicating this disease.
Generalized -Type I Univex Functions in Multiobjective Optimization
Authors: Kharbanda Pallavi , Agarwal Divya , Sinha Deepa
Published: July 2012

A new class of generalized functions -type I univex is introduced for a nonsmooth multiobjective programming problem. Based upon these generalized functions, sufficient optimality conditions are established. Weak, strong, converse, and strict converse duality theorems are also derived for Mond-Weir-type multiobjective dual program.
Early Hearing-Impairment Results in Crossmodal Reorganization of Ferret Core Auditory Cortex
Authors: Meredith M. Alex , Allman Brian L.
Published: July 2012

Numerous investigations of cortical crossmodal plasticity, most often in congenital or early-deaf subjects, have indicated that secondary auditory cortical areas reorganize to exhibit visual responsiveness while the core auditory regions are largely spared. However, a recent study of adult-deafened ferrets demonstrated that core auditory cortex was reorganized by the somatosensory modality. Because adult animals have matured beyond their critical period of sensory development and plasticity, it was not known if adult-deafening and early-deafening would generate the same crossmodal results. The present study used young, ototoxically-lesioned ferrets (n=3) that, after maturation (avg. = 173 days old), showed significant hearing deficits (avg. threshold = 72 dB SPL). Recordings from single-units (n=132) in core auditory cortex showed that 72% were activated by somatosensory stimulation (compared to 1% in hearing controls). In addition, tracer injection into early hearing-impaired core auditory cortex labeled essentially the same auditory cortical and thalamic projection sources as seen for injections in the hearing controls, indicating that the functional reorganization was not the result of new or latent projections to the cortex. These data, along with similar observations from adult-deafened and adult hearing-impaired animals, support the recently proposed brainstem theory for crossmodal plasticity induced by hearing loss.
Lean Breed Landrace Pigs Harbor Fecal Methanogens at Higher Diversity and Density than Obese Breed Erhualian Pigs
Authors: Luo Yu-heng , Su Yong , Wright André-Denis G. , Zhang Ling-li , Smidt Hauke , Zhu Wei-yun
Published: July 2012

The diversity of fecal methanogens of Erhualian (obese type) and Landrace (lean type) pigs was examined using separate 16S rRNA gene libraries for each breed. A total of 763 clones were analyzed; 381 from the Erhualian library and 382 from the Landrace library were identified belonging to the genus Methanobrevibacter. Others were identified belonging to the genus Methanosphaera. The two libraries showed significant differences in diversity (P<0.05) and composition (P<0.0001). Only two operational taxonomic units (OTUs) were found in both libraries, whereas six OTUs were found only in the Erhualian library and 23 OTUs were found only in the Landrace library. Real-time PCR showed that the abundance of fecal methanogens in Landrace pigs was significantly higher than that in Erhualian pigs (P<0.05). Results showed that the Landrace pig (lean) harbored a greater diversity and higher numbers of methanogenmcrAgene copies than the Erhualian pig (obese). These differences may be related to the fatness or leanness in these two pig breeds. The results provide new leads for further investigations on the fat storage of pigs or even humans.
Suppression ofBromus tectorumL. by Established Perennial Grasses: Potential Mechanisms—Part One
Authors: Blank Robert R. , Morgan Tye
Published: July 2012

Bromus tectorumL. (cheatgrass) is an Eurasian annual grass that has invaded ecosystems throughout the Intermountain west of the United States. Our purpose was to examine mechanisms by which established perennial grasses suppress the growth ofB. tectorum. Using rhizotrons, the experiment was conducted over 5 growth cycles: (1)B. tectorumplanted between perennial grasses; (2) perennials clipped andB. tectorumplanted; (3) perennials clipped andB. tectorumplanted into soil mixed with activated carbon; (4) perennials clipped,B. tectorumplanted, and top-dressed with fertilizer, and; (5) perennial grasses killed andB. tectorumplanted. Water was not limiting in this study. Response variables measured at the end of each growth cycle included above-ground mass and tissue nutrient concentrations. Relative to controls (B. tectorumwithout competition), established perennial grasses significantly hindered the growth ofB. tectorum. Overall, biomass ofB. tectorum, grown between established perennials, increased considerably after fertilizer addition and dramatically upon death of the perennials. Potential mechanisms involved in the suppression ofB. tectoruminclude reduced nitrogen (possibly phosphorus) availability and coopting of biological soil space by perennial roots. Our data cannot confirm or reject allelopathic suppression. Understanding the mechanisms involved with suppression may lead to novel control strategies againstB. tectorum.