bluuebunny/crossref_metadata_2025 huggingface dataset:
Host‐range studies, genetic diversity and evolutionary relationships of ACLSV isolates from ornamental, wild and cultivated Rosaceous species
Authors: Katsiani A.T. , Maliogka V. I. , Candresse T. , Katis N. I.
Published: April 2013

A large‐scale survey was carried out to study the host range and genetic diversity of Apple chlorotic leaf spot virus (ACLSV) in various Rosaceae species, with a special emphasis on ornamentals and wild shrubs. Samples were tested by DAS‐ELISA using two different antisera, and RT‐PCR amplification of part of the CP gene. There was generally a poor correlation between the results obtained with the two sets of serological reagents and between serological and molecular detection assays. Using a nested RT‐PCR assay developed here, ACLSV was found to be widespread among cultivated, ornamental and wild species of the Rosaceae. The virus was detected for the first time in plum, wild cherry, Crataegus monogyna, Prunus spinosa and Prunus cerasifera in Greece. Sequences of a part of the CP encoding gene and the 3′ untranslated region from ACLSV isolates originating from various wild species and ornamentals were compared to those of isolates from cultivated hosts, showing similar divergence levels. Further phylogenetic analysis using the sequenced region indicated that the isolates from wild or ornamental hosts were not more closely related to each other than to isolates from cultivated hosts. The possible role of different factors in the spread of ACLSV on cultivated, ornamental and wild species is discussed.
The Immediate Impact of the Fukushima Daiichi Accident on Local Property Values
Authors: Yamane Fumihiro , Ohgaki Hideaki , Asano Kota
Published: April 2013

The Fukushima Daiichi accident released huge amounts of radioactive material over a wide area. We can appreciate the geographical extent of radioactive contamination from the information published online by the Japanese government. Historically, this is an unprecedented situation, which allows “natural experimentation” to estimate the causal effects of radioactive contamination on our society. This study focused on property value losses caused by the accident and analyzed changes in land appraisals around the Fukushima Daiichi plant from July 2010 to July 2011 within the framework of hedonic approach. Thus, we estimated the short‐run impact of the contamination or the change in marginal value of proximity to the plant. The results suggest that the appraisals significantly and monotonically depreciated with increasing contamination levels. However, there was no evidence to suggest changes in the marginal value of proximity to the plant. A comparison between the appraisals and transaction prices indicates that this result could be interpreted as an underestimate of actual property value losses.
“Tractorettes” or Partners? Farmers' Views on Women in Kansas Farming Households
Authors: Beach Sarah S.
Published: April 2013

In the United States, for various reasons, fewer farm families rely solely on their farming operations for their livelihoods. As the structure of agriculture changes and farm families adjust their livelihood strategies, do the discourses around gender relations in households also change? This article analyzes the portrayal of women's roles in farming households by drawing on interviews with Kansas field crop farmers, primarily regarding their land‐use decisions, but also inquiring about their farms and communities. The article addresses the following question: How do farmers' discourses compare to Brandth's (2002a) categorizations of three dominant discourses in the literature on gender in European family farming—the discourse of the family farm, the discourse of masculinization, and the discourse of detraditionalization and diversity? While Brandth finds the discourse of the family farm prevalent in the literature, overall, the discourse apparent from 30 farmer interviews is more characteristic of detraditionalization and diversity. Although men are primarily the principal operators in farming, overall, women were not portrayed simply as helpers. Rather, their roles are depicted as diverse and important to farm operations.
The internal migration between public and faith‐based health providers: a cross‐sectional, retrospective and multicentre study from southern Tanzania
Authors: Tabatabai Patrik , Prytherch Helen , Baumgarten Inge , Kisanga Oberlin M. E. , Schmidt‐Ehry Bergis , Marx Michael
Published: April 2013

Objective

To assess the magnitude, direction and underlying dynamics of internal health worker migration between public and faith‐based health providers from a hospital perspective.

Methods

Two complementary tools were implemented in 10 public and six faith‐based hospitals in southern Tanzania. A hospital questionnaire assessed magnitude and direction of staff migration between January 2006 and June 2009. Interviews with 42 public and 20 faith‐based maternity nurses evaluated differences in staff perspectives and motives for the observed migration patterns.

Results

The predominant direction of staff movement was from the faith‐based to the public sector: 69.1% (n = 105/152) of hospital staff exits and 60.6% (n = 60/99) of hospital staff gains. Nurses were the largest group among the migrating health workforce. Faith‐based hospitals lost 59.3% (n = 86/145) of nurses and 90.6% (n = 77/85) of registered nurses to the public sector, whereby public hospitals reported 13.5% (n = 59/436) of nurses and 24.4% (n = 41/168) of registered nurses being former faith‐based employees. Interviews revealed significantly inferior staff perspectives among faith‐based respondents than their public colleagues. Main differences were identified regarding career development and training, management support, employee engagement and workload.

Conclusion

This study revealed considerable internal health worker migration from the faith‐based to the public sector. Staff retention and motivation within faith‐based hospitals are not restricted to financial considerations, and salary gaps can no longer uniquely explain this movement pattern. The consequences for the catchment area of faith‐based hospitals are potentially severe and erode cooperation potential between the public and private health sector.
Parvalbumin tunes spike‐timing and efferent short‐term plasticity in striatal fast spiking interneurons
Authors: Orduz David , Bischop Don Patrick , Schwaller Beat , Schiffmann Serge N. , Gall David
Published: April 2013

Key points

Fast spiking interneurons (FSIs) modulate output of the striatum and are implicated in severe motor disorders.

Selective expression of the calcium‐binding protein parvalbumin (PV) in FSIs raises questions about how PV controls FSI Ca2+ dynamics.

Here we report a novel mechanism linking PV‐Ca2+ buffering and FSI spiking as a result of the activation of small conductance (SK) Ca2+‐dependent K+ channels.

We also show that, at the presynaptic terminals, PV prevents synaptic facilitation at narrow frequencies at FSI to striatal output neuron synapses.

Our data establish that PV is a key element in providing rhythm generation in FSIs as well as filtering striatal output. Thus, FSI neuromodulation via PV and/or SK channels is an interesting target for controlling the establishment of oscillatory frequencies related to the induction or worsening of pathology‐related motor rhythms.

Abstract  Striatal fast spiking interneurons (FSIs) modulate output of the striatum by synchronizing medium‐sized spiny neurons (MSNs). Recent studies have broadened our understanding of FSIs, showing that they are implicated in severe motor disorders such as parkinsonism, dystonia and Tourette syndrome. FSIs are the only striatal neurons to express the calcium‐binding protein parvalbumin (PV). This selective expression of PV raises questions about the functional role of this Ca2+ buffer in controlling FSI Ca2+ dynamics and, consequently, FSI spiking mode and neurotransmission. To study the functional involvement of FSIs in striatal microcircuit activity and the role of PV in FSI function, we performed perforated patch recordings on enhanced green fluorescent protein‐expressing FSIs in brain slices from control and PV−/− mice. Our results revealed that PV−/− FSIs fired more regularly and were more excitable than control FSIs by a mechanism in which Ca2+ buffering is linked to spiking activity as a result of the activation of small conductance Ca2+‐dependent K+ channels. A modelling approach of striatal FSIs supports our experimental results. Furthermore, PV deletion modified frequency‐specific short‐term plasticity at inhibitory FSI to MSN synapses. Our results therefore reinforce the hypothesis that in FSIs, PV is crucial for fine‐tuning of the temporal responses of the FSI network and for the orchestration of MSN populations. This, in turn, may play a direct role in the generation and pathology‐related worsening of motor rhythms.
Fabrication of large-area, high-density Ni nanopillar arrays on GaAs substrates using diblock copolymer lithography and electrodeposition
Authors: Chang Chun-Chieh , Botez Dan , Wan Lei , Nealey Paul F. , Ruder Steven , Kuech Thomas F.
Published: April 2013

Large-area, ultradense Ni nanopillar arrays were fabricated directly on bare n-GaAs substrates using diblock copolymer lithography and electrodeposition. The Ni nanopillar arrays are hexagonally arranged, exhibiting an average pillar diameter of ∼24 nm, and an areal density of ∼1011/cm2 over an entire surface area of 1 cm × 1 cm. These arrays represent large-scale, highly dense, sub-30 nm metal-nanopillar arrays made on III-V semiconductor substrates suitable as pattern masks. The fabrication method offers a simple and effective route to manufacturing large-area, highly dense, sub-30 nm metal nanostructures for III-V optoelectronic devices, in order to enhance their performance and functionalities.
Study of hydrogen detection response time with Pt-gated diodes fabricated on AlGaN/GaN heterostructure
Authors: Xi Yuyin , Liu Lu , Hwang Ya-Hsi , Phillips Oluwadamilola , Ren Fan , Pearton Stephen J. , Kim Jihyun , Hsu Chien-Hsing , Lo Chien-Fong , Wayne Johnson Jerry
Published: April 2013

The hydrogen detection response time of Pt-gated diode sensors fabricated on AlGaN/GaN heterostructure as a function of the hydrogen concentration was investigated. A new method to extract the response time, taking the derivative of diode current, was proposed and shown to reduce the response time of detecting 1% hydrogen by about 60% as compared to the response time defined as the diode current reaching 90% of its total changes, t90. Hydrogen-sensing experiments were conducted at different temperatures, and an Arrhenius plot of the data determined an activation energy of 17.7 kJ/mole for the sensing process.
Glancing angle deposition on a roll: Towards high-throughput nanostructured thin films
Authors: Krause Kathleen M. , Taschuk Michael T. , Brett Michael J.
Published: April 2013

Increasing the throughput of the powerful single-step glancing angle deposition (GLAD) method using a prototype simplified roll-to-roll (R2R) system has been explored. While the conventional GLAD technique is popular for fabricating nanostructured devices in a single deposition step, it is not a high-output process. To evaluate the feasibility of large area GLAD deposition, the authors examined the geometrical considerations required to eventually achieve GLAD in a roll-to-roll manufacturing system. Nominal deposition and rotation angles were mathematically translated to their effective R2R counterparts, allowing for deposition recipes of the archetype GLAD nanostructures (slanted posts, vertical posts, and square spirals) and the mechanics of the phi-sweep technique to be converted to this space. Representative structures were then deposited, and the phi-sweep technique successfully applied, in a prototype single barrel roller R2R experimental system. This prototype system provides a foundation for moving GLAD from the laboratory to mass production.
Cascaded‐systems analyses and the detective quantum efficiency of single‐Z x‐ray detectors including photoelectric, coherent and incoherent interactions
Authors: Yun Seungman , Tanguay Jesse , Kim Ho Kyung , Cunningham Ian A.
Published: April 2013

Purpose:

Theoretical models of the detective quantum efficiency (DQE) of x‐ray detectors are an important step in new detector development by providing an understanding of performance limitations and benchmarks. Previous cascaded‐systems analysis (CSA) models accounted for photoelectric interactions only. This paper describes an extension of the CSA approach to incorporate coherent and incoherent interactions, important for low‐Z detectors such as silicon and selenium.

Methods:

A parallel‐cascade approach is used to describe the three types of x‐ray interactions. The description of incoherent scatter required developing expressions for signal and noise transfer through an “energy‐labeled reabsorption” process where the parameters describing reabsorption are random functions of the scatter photon energy. The description of coherent scatter requires the use of scatter form factors that may not be accurate for some crystalline detector materials. The model includes the effects of scatter reabsorption and escape, charge collection, secondary quantum sinks, noise aliasing, and additive noise. Model results are validated by Monte Carlo calculations for Si and Se detectors assuming free‐atom atomic form factors.

Results:

The new signal and noise transfer expressions were validated by showing agreement with Monte Carlo results. Coherent and incoherent scatter can degrade the DQE of Si and sometimes Se detectors depending on detector thickness and incident‐photon energy. Incoherent scatter can produce a substantial low‐frequency drop in the modulation transfer function and DQE.

Conclusions:

A generally useful CSA model of the DQE is described that is believed valid for any single‐Z material up to 10 cycles/mm at both mammographic and radiographic energies within the limitations of Fourier‐based linear‐systems models and the use of coherent‐scatter form factors. The model describes a substantial low‐frequency drop in the DQE of Si systems due to incoherent scatter above 20–40 keV.
Underwater radiated noise levels of a research icebreaker in the central Arctic Ocean
Authors: Roth Ethan H , Schmidt Val , Hildebrand John A. , Wiggins Sean M.
Published: April 2013

U.S. Coast Guard Cutter Healy's underwater radiated noise signature was characterized in the central Arctic Ocean during different types of ice-breaking operations. Propulsion modes included transit in variable ice cover, breaking heavy ice with backing-and-ramming maneuvers, and dynamic positioning with the bow thruster in operation. Compared to open-water transit, Healy's noise signature increased approximately 10 dB between 20 Hz and 2 kHz when breaking ice. The highest noise levels resulted while the ship was engaged in backing-and-ramming maneuvers, owing to cavitation when operating the propellers astern or in opposing directions. In frequency bands centered near 10, 50, and 100 Hz, source levels reached 190–200 dB re: 1 μPa at 1 m (full octave band) during ice-breaking operations.
Impact of polydispersity on multipolar resonant scattering in emulsions
Authors: Mascaro Benoit , Brunet Thomas , Poncelet Olivier , Aristégui Christophe , Raffy Simon , Mondain-Monval Olivier , Leng Jacques
Published: April 2013

The influence of size polydispersity on the resonant acoustic properties of dilute emulsions, made of fluorinated-oil droplets, is quantitatively investigated. Ultrasound attenuation and dispersion measurements on various samples with controlled size polydispersities, ranging from 1% to 13%, are found to be in excellent agreement with predictions based on the independent scattering approximation. By relating the particle-size distribution of the synthesized emulsions to the quality factor of the predicted multipolar resonances, the number of observable acoustic resonances is shown to be imposed by the sample polydispersity. These results are briefly discussed into the context of metamaterials for which scattering resonances are central to their effective properties.
Sparse-representation algorithms for blind estimation of acoustic-multipath channels
Authors: Zeng Wen-Jun , Jiang Xue , So Hing Cheung
Published: April 2013

Acoustic channel estimation is an important problem in various applications. Unlike many existing channel estimation techniques that need known probe or training signals, this paper develops a blind multipath channel identification algorithm. The proposed approach is based on the single-input multiple-output model and exploits the sparse multichannel structure. Three sparse representation algorithms, namely, matching pursuit, orthogonal matching pursuit, and basis pursuit, are applied to the blind sparse identification problem. Compared with the classical least squares approach to blind multichannel estimation, the proposed scheme does not require that the channel order be exactly determined and it is robust to channel order selection. Moreover, the ill-conditioning induced by the large delay spread is overcome by the sparse constraint. Simulation results for deconvolution of both underwater and room acoustic channels confirm the effectiveness of the proposed approach.
Similarity spectra analysis of high-performance jet aircraft noise
Authors: Neilsen Tracianne B. , Gee Kent L. , Wall Alan T. , James Michael M.
Published: April 2013

Noise measured in the vicinity of an F-22A Raptor has been compared to similarity spectra found previously to represent mixing noise from large-scale and fine-scale turbulent structures in laboratory-scale jet plumes. Comparisons have been made for three engine conditions using ground-based sideline microphones, which covered a large angular aperture. Even though the nozzle geometry is complex and the jet is nonideally expanded, the similarity spectra do agree with large portions of the measured spectra. Toward the sideline, the fine-scale similarity spectrum is used, while the large-scale similarity spectrum provides a good fit to the area of maximum radiation. Combinations of the two similarity spectra are shown to match the data in between those regions. Surprisingly, a combination of the two is also shown to match the data at the farthest aft angle. However, at high frequencies the degree of congruity between the similarity and the measured spectra changes with engine condition and angle. At the higher engine conditions, there is a systematically shallower measured high-frequency slope, with the largest discrepancy occurring in the regions of maximum radiation.
Acoustic methods for measuring the porosities of porous materials incorporating dead-end pores
Authors: Dupont Thomas , Leclaire Philippe , Panneton Raymond
Published: April 2013

The acoustic properties of porous materials containing dead-end (DE) pores have been proposed by Dupont et al. [J. Appl. Phys. 110, 094903 (2011)]. In the theoretical description, two physical parameters were defined (the dead-end porosity and the average length of the dead-end pores). With the knowledge of the open porosity (measured with non-acoustic methods), and the measurement of kinematic porosity (also called the Biot porosity in this article), it is possible to deduce the dead-end porosity. Two acoustic methods for measuring the Biot porosity for a wide range of porosities are proposed. These methods are based on acoustic transmission and on the low and high frequency behaviors of acoustic indicators. The low frequency method is valid for high porosities. It involves measurements in a transmission tube and the knowledge of the theoretical asymptotic behavior of the phase velocity at high frequencies. The high frequency method is based on ultrasonic measurements and on the high frequency asymptotic behavior of the transmission coefficient. It is well adapted for material with relatively low values of porosity. Good precision was found for both methods and materials containing dead end porosity were tested.
Factors affecting the use of envelope interaural time differences in reverberation
Authors: Monaghan Jessica J. M. , Krumbholz Katrin , Seeber Bernhard U.
Published: April 2013

At high frequencies, interaural time differences (ITDs) are conveyed by the sound envelope. Sensitivity to envelope ITDs depends crucially on the envelope shape. Reverberation degrades the envelope shape, reducing the modulation depth of the envelope and the slope of its flanks. Reverberation also reduces the envelope interaural coherence (i.e., the similarity of the envelopes at two ears). The current study investigates the extent to which these changes affect sensitivity to envelope ITDs. The first experiment measured ITD discrimination thresholds at low and high frequencies in a simulated room. The stimulus was either a low-frequency narrowband noise or the same noise transposed to a higher frequency. The results suggest that the effect of reverberation on ITD thresholds was multiplicative. Given that the threshold without reverberation was larger for the transposed than for the low-frequency stimulus, this meant that, in absolute terms, the thresholds for the transposed stimulus showed a much greater increase due to reverberation than those for the low-frequency stimulus. Three further experiments indicated that the effect of reverberation on the envelope ITD thresholds was due to the combined effect of the reduction in the envelope modulation depth and slopes, as well as the decrease in the envelope interaural coherence.
Listening to speech in a background of other talkers: Effects of talker number and noise vocoding
Authors: Rosen Stuart , Souza Pamela , Ekelund Caroline , Majeed Arooj A
Published: April 2013

Some of the most common interfering background sounds a listener experiences are the sounds of other talkers. In Experiment 1, recognition for natural Institute of Electrical and Electronics Engineers (IEEE) sentences was measured in normal-hearing adults at two fixed signal-to-noise ratios (SNRs) in 16 backgrounds with the same long-term spectrum: unprocessed speech babble (1, 2, 4, 8, and 16 talkers), noise-vocoded versions of the babbles (12 channels), noise modulated with the wide-band envelope of the speech babbles, and unmodulated noise. All talkers were adult males. For a given number of talkers, natural speech was always the most effective masker. The greatest changes in performance occurred as the number of talkers in the maskers increased from 1 to 2 or 4, with small changes thereafter. In Experiment 2, the same targets and maskers (1, 2, and 16 talkers) were used to measure speech reception thresholds (SRTs) adaptively. Periodicity in the target was also manipulated by noise-vocoding, which led to considerably higher SRTs. The greatest masking effect always occurred for the masker type most similar to the target, while the effects of the number of talkers were generally small. Implications are drawn with reference to glimpsing, informational vs energetic masking, overall SNR, and aspects of periodicity.
Effects of dynamic range compression on spatial selective auditory attention in normal-hearing listeners
Authors: Schwartz Andrew H. , Shinn-Cunningham Barbara G.
Published: April 2013

Many hearing aids introduce compressive gain to accommodate the reduced dynamic range that often accompanies hearing loss. However, natural sounds produce complicated temporal dynamics in hearing aid compression, as gain is driven by whichever source dominates at a given moment. Moreover, independent compression at the two ears can introduce fluctuations in interaural level differences (ILDs) important for spatial perception. While independent compression can interfere with spatial perception of sound, it does not always interfere with localization accuracy or speech identification. Here, normal-hearing listeners reported a target message played simultaneously with two spatially separated masker messages. We measured the amount of spatial separation required between the target and maskers for subjects to perform at threshold in this task. Fast, syllabic compression that was independent at the two ears increased the required spatial separation, but linking the compressors to provide identical gain to both ears (preserving ILDs) restored much of the deficit caused by fast, independent compression. Effects were less clear for slower compression. Percent-correct performance was lower with independent compression, but only for small spatial separations. These results may help explain differences in previous reports of the effect of compression on spatial perception of sound.
Exact solutions for sound radiation from a moving monopole above an impedance plane
Authors: Ochmann Martin
Published: April 2013

The acoustic field of a monopole source moving with constant velocity at constant height above an infinite locally reacting plane can be expressed in analytical form by combining the Lorentz transformation with the method of superimposing complex or real point sources. For a plane with masslike response, the solution in Lorentz space consists of a superposition of monopoles only and therefore, does not differ in principle from the solution for the corresponding stationary boundary value problem. However, by considering a frequency independent surface impedance, e.g., with pure absorbing behavior, the half-space Green's function is now comprised of not only a line of monopoles but also of dipoles. For certain field points at a special line g, this solution can be written explicitly by using an exponential integral. For arbitrary field points, the method of stationary phase leads to an asymptotic solution for the reflection coefficient which agrees with prior results from the literature.
Whistle characteristics of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in Sanniang Bay, China
Authors: Wang Zhitao , Fang Liang , Shi Wenjing , Wang Kexiong , Wang Ding
Published: April 2013

Broadband recording systems were adapted to characterize the whistle characteristics of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in Sanniang Bay, China. A total of 4630 whistles were recorded, of which 2651 with legible contours and relatively good signal-to-noise ratios were selected for statistical analysis. Of the six tonal types (i.e., flat, down, rise, convex, U-shaped, and sine), flat (N = 1426; 39.45%) was the most predominant, followed by down (N = 754; 23.35%) and rise (N = 489; 12.34%). The whistles showed a short duration (mean ± SD: 370.19 ± 285.61 ms; range: 29–2923 ms), a broad frequency range (fundamental contour ranged from 0.52 to 33 kHz), and two harmonics (mean ± SD: 1.90 ± 2.74, with the maximum frequency of harmonics beyond 96 kHz). Whistles without gaps and stairs accounted for 76.7% and 86.4%, respectively. No significant interspecies differences in frequency parameters were observed compared with S. teuszii, which is inconsistent with morphological taxonomies but confirms phylogenetic results, thus suggesting a close relation between Chinese S. chinensis and Atlantic S. teuszii. Significant intra- and interspecific differences in the genus Sousa were also observed, indicating that animal vocalization may not be limited by genetically determined traits but could also be a function of local habitat adaptation.
Optogenetic Dissection of Entorhinal-Hippocampal Functional Connectivity
Authors: Zhang Sheng-Jia , Ye Jing , Miao Chenglin , Tsao Albert , Cerniauskas Ignas , Ledergerber Debora , Moser May-Britt , Moser Edvard I.
Published: April 2013

From Grid to Place

Grid cells are considered one of the key sources for place-cell signals in the hippocampus. The entorhinal circuit also contains other functional cell types, but it is unclear which project to the place cells of the hippocampus.

Zhang
et al.

(10.1126/science.1232627, see the Perspective by

Poucet and Sargolini

) addressed this question using optogenetics and in vivo multi-electrode electrophysiology. Hippocampal cells received input from a broad spectrum of entorhinal neuronal cell types. Grid cells represented the biggest group of spatial inputs, but border cells, head-direction cells, and a large fraction of nonspatial cells also provided inputs. Thus, hippocampal circuits have local mechanisms for processing specific types of functional input from the entorhinal cortex to generate place-specific signals.
Influence of HLA-C Expression Level on HIV Control
Authors: Apps Richard , Qi Ying , Carlson Jonathan M. , Chen Haoyan , Gao Xiaojiang , Thomas Rasmi , Yuki Yuko , Del Prete Greg Q. , Goulder Philip , Brumme Zabrina L. , Brumme Chanson J. , John Mina , Mallal Simon , Nelson George , Bosch Ronald , Heckerman David , Stein Judy L. , Soderberg Kelly A. , Moody M. Anthony , Denny Thomas N. , Zeng Xue , Fang Jingyuan , Moffett Ashley , Lifson Jeffrey D. , Goedert James J. , Buchbinder Susan , Kirk Gregory D. , Fellay Jacques , McLaren Paul , Deeks Steven G. , Pereyra Florencia , Walker Bruce , Michael Nelson L. , Weintrob Amy , Wolinsky Steven , Liao Wilson , Carrington Mary
Published: April 2013

Thwarting HIV

Multiple genome-wide association studies have revealed that human leukocyte antigen (HLA) genes of the major histocompatibility complex locus have the strongest impact on HIV. In particular, a single-nucleotide polymorphism 35 base pairs upstream of HLA-C shows significant association with viral load and protection against HIV. How HLA-C mediates these effects is unknown.

Apps
et al.

(p.
87
) now demonstrate that increasing surface expression of HLA-C is associated with reduced viral load and reduced rate of progression to low CD4
+
T cell counts in African and European Americans. High HLA-C expression likely promoted improved HIV control through a more effective cytotoxic CD8
+
T cell response. In contrast to HIV infection, high HLA-C expression was associated with a higher risk of the inflammatory bowel disease, Crohn's disease.
Dynamics of Coral Reef Recovery
Authors: Polidoro Beth , Carpenter Kent
Published: April 2013

Coral reefs can better recover from bleaching events when stresses resulting from human activities are minimized.

[Also see Report by

Gilmour
et al.

]
The Deep Earth Machine Is Coming Together
Authors: Kerr Richard A.
Published: April 2013

Researchers studying how Earth's deep interior works are recognizing a new part connecting the depths to the surface, though the depths remain mysterious.
'Dead' Enzymes Show Signs of Life
Authors: Leslie Mitch
Published: April 2013

Pseudoenzymes can't catalyze chemical reactions, but researchers are discovering that they perform a variety of other cellular jobs.
Dead or Alive?
Authors: Leslie Mitch
Published: April 2013

The enzymatic competence of proteins can be difficult to judge, and some apparent pseudoenzymes have fooled researchers.
Conjugation of Polysaccharide 6B from Streptococcus pneumoniae with Pneumococcal Surface Protein A: PspA Conformation and Its Effect on the Immune Response
Authors: Perciani Catia T. , Barazzone Giovana C. , Goulart Cibelly , Carvalho Eneas , Cabrera-Crespo Joaquin , Gonçalves Viviane M. , Leite Luciana C. C. , Tanizaki Martha M.
Published: April 2013

Despite the substantial beneficial effects of incorporating the 7-valent pneumococcal conjugate vaccine (PCV7) into immunization programs, serotype replacement has been observed after its widespread use. As there are many serotypes currently documented, the use of a conjugate vaccine relying on protective pneumococcal proteins as active carriers is a promising alternative to expand PCV coverage. In this study, capsular polysaccharide serotype 6B (PS6B) and recombinant pneumococcal surface protein A (rPspA), a well-known protective antigen fromStreptococcus pneumoniae, were covalently attached by two conjugation methods. The conjugation methodology developed by our laboratory, employing 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM) as an activating agent through carboxamide formation, was compared with reductive amination, a classical methodology. DMT-MM-mediated conjugation was shown to be more efficient in coupling PS6B to rPspA clade 1 (rPspA1): 55.0% of PS6B was in the conjugate fraction, whereas 24% was observed in the conjugate fraction with reductive amination. The influence of the conjugation process on the rPspA1 structure was assessed by circular dichroism. According to our results, both conjugation processes reduced the alpha-helical content of rPspA; reduction was more pronounced when the reaction between the polysaccharide capsule and rPspA1 was promoted between the carboxyl groups than the amine groups (46% and 13%, respectively). Regarding the immune response, both conjugates induced functional anti-rPspA1 and anti-PS6B antibodies. These results suggest that the secondary structure of PspA1, as well as its reactive groups (amine or carboxyl) involved in the linkage to PS6B, may not play an important role in eliciting a protective immune response to the antigens.
Clostridium difficile Ribotype Diversity at Six Health Care Institutions in the United States
Authors: Waslawski Sheila , Lo Eugene S. , Ewing Sarah A. , Young Vincent B. , Aronoff David M. , Sharp Susan E. , Novak-Weekley Susan M. , Crist Arthur E. , Dunne W. Michael , Hoppe-Bauer Joan , Johnson Michelle , Brecher Stephen M. , Newton Duane W. , Walk Seth T.
Published: April 2013

Capillary-based PCR ribotyping was used to quantify the presence/absence and relative abundance of 98
Clostridium difficile
ribotypes from clinical cases of disease at health care institutions in six states of the United States. Regionally important ribotypes were identified, and institutions in close proximity did not necessarily share more ribotype diversity than institutions that were farther apart.
Detection of New Delhi Metallo-β-Lactamase (Encoded by
bla
NDM-1
) in Acinetobacter schindleri during Routine Surveillance
Authors: McGann Patrick , Milillo Michael , Clifford Robert J. , Snesrud Erik , Stevenson Lindsay , Backlund Michael G. , Viscount Helen B. , Quintero Reyes , Kwak Yoon I. , Zapor Michael J. , Waterman Paige E. , Lesho Emil P.
Published: April 2013

A carbapenem-resistant
Alcaligenes faecalis
strain was isolated from a surveillance swab of a service member injured in Afghanistan. The isolate was positive for
bla
NDM
by real-time PCR. Species identification was reevaluated on three identification systems but was inconclusive. Genome sequencing indicated that the closest relative was
Acinetobacter schindleri
and that
bla
NDM-1
was carried on a plasmid that shared >99% identity with one identified in an
Acinetobacter lwoffii
isolate. The isolate also carried a novel chromosomally encoded class D oxacillinase.
Identification and Characterization of a Peptide Affinity Reagent for Detection of Noroviruses in Clinical Samples
Authors: Rogers Jennifer D. , Ajami Nadim J. , Fryszczyn Bartlomiej G. , Estes Mary K. , Atmar Robert L. , Palzkill Timothy
Published: April 2013

Norovirus (NoV) is the most common agent of nonbacterial epidemic gastroenteritis and is estimated to cause 21 million cases of the disease in the United States annually. The antigen enzyme-linked immunosorbent assays (ELISAs) currently available for NoV diagnosis detect only certain strains and are approved for use in the United States only in epidemics where NoV is suspected. There is a clear need for simpler, more rapid, and more reliable diagnostic tools for the detection of NoV. In this study, phage display technology was used to screen a library of phage displaying random 12-mer peptides for those that bind to Norwalk virus virus-like particles (NV VLPs). Three phage clones displaying unique peptides were identified, and both the peptide-displaying phages and the peptides were confirmed to bind specifically to NV VLPs. The peptide displayed on phage clone NV-N-R5-1 was determined to bind to the protruding domain of the VP1 capsid protein. This phage also bound to NV VLPs seeded into NoV-negative stool with a limit of detection of 1.56 ng NV VLP. This value was comparable to monoclonal antibody (MAb) 3912, which is currently used in commercially available assays. Furthermore, the NV-N-R5-1 phage exhibited high specificity by detecting NV only in previously characterized NV-positive stool samples in contrast to no detection in NV-negative stool samples. These data demonstrate that the further development of NV-N-R5-1 phage as a diagnostic reagent is possible and might offer several distinct advantages over antibodies, such as decreases in the time and cost of production and ease of isolating phage against other epidemic strains currently circulating as well as those that are emerging.
Analysis of the Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrum of Staphylococcus aureus Identifies Mutations That Allow Differentiation of the Main Clonal Lineages
Authors: Josten Michaele , Reif Marion , Szekat Christiane , Al-Sabti Nahed , Roemer Terry , Sparbier Katrin , Kostrzewa Markus , Rohde Holger , Sahl Hans-Georg , Bierbaum Gabriele
Published: April 2013

Nosocomial infections involving epidemic methicillin-resistant
Staphylococcus aureus
(MRSA) strains are a serious problem in many countries. In order to analyze outbreaks, the infectious isolates have to be typed; however, most molecular methods are expensive or labor-intensive. Here, we evaluated matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) of cell extracts for the molecular characterization of
S. aureus
strains. The peak patterns of 401 MRSA and methicillin-susceptible
S. aureus
(MSSA) strains, including clinical and laboratory strains, were analyzed. Database searches indicated the peptides that were represented by the corresponding peaks in the spectra. The identities of the peptides were confirmed by the sequencing of mutants, the expression of antisense RNA fragments that resulted in the knockdown of the peptide of interest and the concomitant loss of the signal, or tandem MALDI-TOF MS (MALDI-TOF/TOF MS). It was shown that the signals derive mainly from stress proteins and ribosomal proteins. Peak shifts that differentiate the main
S. aureus
clonal complexes CC5, CC22, CC8, CC45, CC30, and CC1 correlate to point mutations in the respective genes. Retrospective typing of an MRSA outbreak showed that it is possible to differentiate unrelated MSSA, MRSA, and borderline resistant
S. aureus
(BORSA) strains isolated from health care workers. In conclusion, this method allows for the detection of the epidemic lineages of
S. aureus
during species identification by MALDI-TOF MS analysis.
Septic Arthritis and Concern for Osteomyelitis in a Child with Rat Bite Fever
Authors: Flannery Dustin D. , Akinboyo Ibukunoluwa , Ty Jennifer M. , Averill Lauren W. , Freedman Abigail
Published: April 2013

Rat bite fever is a rare infection usually caused by
Streptobacillus moniliformis
. A case of septic arthritis and possible osteomyelitis as sequelae of rat bite fever in a pediatric patient is described.
Detection of non-
jejuni
and -coli Campylobacter Species from Stool Specimens with an Immunochromatographic Antigen Detection Assay
Authors: Couturier Brianne A. , Couturier Marc Roger , Kalp Kim J. , Fisher Mark A.
Published: April 2013

The STAT! Campy immunochromatographic assay for
Campylobacter
antigen was compared to culture for 500 clinical stool specimens. Antigen was detected in six culture-negative, PCR-positive specimens.
C. upsaliensis
, a pathogenic species that is traditionally difficult to recover in routine stool cultures, was detected in two of these culture-negative specimens. This study provides evidence that antigen testing may cross-react with at least one additional non-
jejuni
and -
coli Campylobacter
species that may be missed by routine culture for campylobacteriosis.
Microbiological Diagnosis of Severe Diarrhea in Kidney Transplant Recipients by Use of Multiplex PCR Assays
Authors: Coste Jean-François , Vuiblet Vincent , Moustapha Betoul , Bouin Alexis , Lavaud Sylvie , Toupance Olivier , de Rougemont Alexis , Benejat Lucie , Megraud Francis , Wolak-Thierry Aurore , Villena Isabelle , Chemla Cathy , Le Magrex Elisabeth , de Champs Christophe , Andreoletti Laurent , Rieu Philippe , Leveque Nicolas
Published: April 2013

Diarrhea is a frequent complication after kidney transplantation, ascribed to adverse effects of the immunosuppressive therapy in case of negative microbiological examination of the stools. The aim of this study was to improve the microbiological diagnosis by implementing molecular tests. Fifty-four severe diarrhea events that occurred in 49 adult kidney transplant recipients from September 2010 to November 2011 were investigated. One or several enteric pathogens were detected in 13 (23%) stool samples using classical microbiological methods versus 39 (72%) for the seven commercially available multiplex PCR assays used retrospectively (
P
= 0.006). Interestingly, molecular diagnosis identified 15 multiple infections compared to none using classical techniques. The primary pathogens detected were enteropathogenic
Escherichia coli
(EPEC) (
n
= 15; 38%),
Campylobacter
spp. (
n
= 15; 38%), and
Norovirus
(
n
= 14; 36%). Specificities for
Campylobacter
and
Norovirus
infection diagnosis were 75 and 100%, respectively, by comparison to reference methods. Based on molecular findings, a cyclosporine-mycophenolate mofetil combination was identified as a risk factor for developing
Norovirus
-induced diarrhea.
Norovirus
infections were also responsible for higher weight loss than all the other causes of diarrhea. In samples from asymptomatic immunocompromised and immunocompetent patients, EPEC but not
Norovirus
and
Campylobacter
infections were detected at a frequency similar to that observed in symptomatic kidney transplant recipients. In conclusion, molecular tools significantly improved the detection of single and multiple enteric infections by comparison to classical techniques and could quickly become the key element in the management of severe acute diarrhea in transplant recipients.
HIV-1 Vpu Does Not Degrade Interferon Regulatory Factor 3
Authors: Hotter Dominik , Kirchhoff Frank , Sauter Daniel
Published: April 2013

It has been reported that HIV-1 Vpu mediates the degradation of interferon regulatory factor 3 (IRF-3) to avoid innate immune sensing. Here, we show that Vpu does not deplete IRF-3 from transfected cell lines or HIV-1-infected primary cells. Furthermore, the Vpu-dependent suppression of beta interferon expression described in previous studies could be ascribed to inhibition of NF-κB activation. Thus, Vpu suppresses innate immune activation through inhibition of NF-κB rather than degradation of IRF-3.
Genome-Wide Analysis of Host mRNA Translation during Hepatitis C Virus Infection
Authors: Colman Hélène , Le Berre-Scoul Catherine , Hernandez Céline , Pierredon Sandra , Bihouée Audrey , Houlgatte Rémi , Vagner Stephan , Rosenberg Arielle R. , Féray Cyrille
Published: April 2013

In the model of Huh-7.5.1 hepatocyte cells infected by the JFH1 hepatitis C virus (HCV) strain, transcriptomic and proteomic studies have revealed modulations of pathways governing mainly apoptosis and cell cycling. Differences between transcriptomic and proteomic studies pointed to regulations occurring at the posttranscriptional level, including the control of mRNA translation. In this study, we investigated at the genome-wide level the translational regulation occurring during HCV infection. Sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells. Translationally regulated mRNAs were found to correspond to genes enriched in specific pathways, including vesicular transport and posttranscriptional regulation. Interestingly, the strongest translational regulation was found for mRNAs encoding proteins involved in pre-mRNA splicing, mRNA translation, and protein folding. Strikingly, these pathways were not previously identified, through transcriptomic studies, as being modulated following HCV infection. Importantly, the observed changes in host mRNA translation were directly due to HCV replication rather than to HCV entry, since they were not observed in JFH1-infected Huh-7.5.1 cells treated with a potent HCV NS3 protease inhibitor. Overall, this study highlights the need to consider, beyond transcriptomic or proteomic studies, the modulation of host mRNA translation as an important aspect of HCV infection.
Coal in Brazil
Authors: Machado Eurico Rômulo
Published: April 2013

Brazil has five coal-bearing regions: (1) Pliocene(?) coal in the Pébas Formation of the Upper Amazon basin; (2) Eopaleozoic coal in the Rio Fresco Formation of the Rio Fresco region; (3) Pennsylvanian coal in the Piauí Formation of the Tocantins-Araguaia region, western Parnaíba basin; (4) Mississippian coal in the Poti Formation, eastern Parnaíba basin; and (5) Late Carboniferous or Early Permian coal in the Paraná basin. The Paraná basin contains all of the country’s commercial coal, which is in the Rio Bonito Formation of the Gondwana sequence. Total blocked reserves are 3.2 billion metric tons, of which about 5.6 million tons of run-of-mine coal is extracted annually.
Coal deposits in Colombia
Authors: Suescún-Gomez Dario
Published: April 2013

Colombian coal deposits range in age from Maestrichtian-Paleocene in the Sabana de Bogotá and Boyacá basins to middle Oligocene in the Amagá-Titiribí basin in Antioquia. On the basis of age alone, these coal beds should be of lignitic rank, but because of the intense Andean tectonism (especially during Pliocene time) the rank has been increased to bituminous coal with high to medium volatile-matter content. In some areas, as a result of thermometa-morphic action by the intrusion of porphyritic andesite, the coal beds have been transformed to meta-anthracite. Chemical analyses of the best known coal deposits show a large range in rank.

The main basins studied are Amagá-Titiribí (middle Oligo-cene), Santander (Paleocene-Oligocene), Valle del Cauca (Eocene), Cerrejón and Jagua de Ibirico (Paleocene), and Boyacá-Sabana de Bogotá (Maestrichtian-Paleocene).

Evaluations made in Colombia in 1968 were 5 billion metric tons of exploitable coal, of which 5 percent is measured coal, 15 percent is indicated coal, and 80 percent is inferred coal. There are some basins yet to be explored and evaluated; when this is accomplished, total coal resources in Columbia may be as much as 10 billion metric tons.