bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypic plasticity and similarity among gall morphotypes on a superhost, Baccharis reticularia (Asteraceae)
Authors: Formiga A. T. , Silveira F. A. O. , Fernandes G. W. , Isaias R. M. S.
Published: August 2014

Understanding factors that modulate plant development is still a challenging task in plant biology. Although research has highlighted the role of abiotic and biotic factors in determining final plant structure, we know little of how these factors combine to produce specific developmental patterns. Here, we studied patterns of cell and tissue organisation in galled and non‐galled organs of Baccharis reticularia, a Neotropical shrub that hosts over ten species of galling insects. We employed qualitative and quantitative approaches to understand patterns of growth and differentiation in its four most abundant gall morphotypes. We compared two leaf galls induced by sap‐sucking Hemiptera and stem galls induced by a Lepidopteran and a Dipteran, Cecidomyiidae. The hypotheses tested were: (i) the more complex the galls, the more distinct they are from their non‐galled host; (ii) galls induced on less plastic host organs, e.g. stems, develop under more morphogenetic constraints and, therefore, should be more similar among themselves than galls induced on more plastic organs. We also evaluated the plant sex preference of gall‐inducing insects for oviposition. Simple galls were qualitative and quantitatively more similar to non‐galled organs than complex galls, thereby supporting the first hypothesis. Unexpectedly, stem galls had more similarities between them than to their host organ, hence only partially supporting the second hypothesis. Similarity among stem galls may be caused by the restrictive pattern of host stems. The opposite trend was observed for host leaves, which generate either similar or distinct gall morphotypes due to their higher phenotypic plasticity. The Relative Distance of Plasticity Index for non‐galled stems and stem galls ranged from 0.02 to 0.42. Our results strongly suggest that both tissue plasticity and gall inducer identity interact to determine plant developmental patterns, and therefore, final gall structure.
Horizontal bone augmentation by means of guided bone regeneration
Authors: Benic Goran I. , Hämmerle Christoph H. F.
Published: August 2014

The development of bone augmentation procedures has allowed placement of dental implants into jaw bone areas lacking an amount of bone sufficient for standard implant placement. Thus, the indications for implants have broadened to include jaw regions with bone defects and those with a bone anatomy that is unfavorable for implant anchorage. Of the different techniques, the best documented and the most widely used method to augment bone in localized alveolar defects is guided bone regeneration. A large body of evidence has demonstrated the successful use of guided bone regeneration to regenerate missing bone at implant sites with insufficient bone volume and the long‐term success of implants placed simultaneously with, or after, guided bone regeneration. However, the influence of guided bone regeneration on implant survival and success rates, and the long‐term stability of the augmented bone, remain unknown. Many of the materials and techniques currently available for bone regeneration of alveolar ridge defects were developed many years ago. Recently, various new materials and techniques have been introduced. Many of them have, however, not been sufficiently documented in clinical studies. The aim of this review was to present the scientific basis of guided bone regeneration and the accepted clinical procedures. A classification of bone defects has been presented, aiming at simplifying the decision‐making process regarding the choice of strategy for bone augmentation. Finally, an outlook into actual research and the possible future options related to bone augmentation has been provided.
Guided surgery: accuracy and efficacy
Authors: Vercruyssen Marjolein , Hultin Margareta , Van Assche Nele , Svensson Krister , Naert Ignace , Quirynen Marc
Published: August 2014

Different computer‐assisted implant‐placement procedures are currently available. These differ in software, template manufacture, guiding device, stabilization and fixation. The literature seems to indicate that one has to accept a certain inaccuracy of ±2.0 mm, which seems large initially but is clearly smaller than for nonguided surgery. A reduction of accuracy to below 0.5 mm seems extremely difficult. A common shortcoming identified in the studies included in this review is inconsistency in how clinical data and outcome variables are reported. Another limitation is the small number of comparative clinical studies. In order to find the best guiding system or the most important parameters for optimal accuracy, more randomized clinical trials are necessary. Information on cost‐effectiveness and patient‐centered evaluations (i.e. questionnaires and interviews) must also be included.
Dental cone beam computed tomography: justification for use in planning oral implant placement
Authors: Jacobs Reinhilde , Quirynen Marc
Published: August 2014

Intra‐oral and panoramic radiographs are most frequently used in oral health care. Yet, the inherent nature of jaws and teeth renders three‐dimensional diagnosis essential, especially in relation to oral surgery. Nowadays, this can be accomplished by dental cone beam computed tomography, which provides high‐quality images at low radiation doses and low costs. Nonetheless, the effective dose ranges of cone beam computed tomography machines may easily vary from 10 to 1000 μSv, this being equivalent to two to 200 panoramic radiographs, even for similar presurgical indications. Moreover, the diagnostic image quality varies massively among available machines and parameter settings. Apart from the radiodiagnostic possibilities, dental cone beam computed tomography may offer a vast therapeutic potential, including opportunities for surgical guidance and further prosthetic rehabilitation via computer‐aided design/computer‐aided manufacturing solutions. These additional options may definitely explain part of the success of cone beam computed tomography for oral implant placement. In conclusion, dental cone beam computed tomography imaging could be justified for oral implant‐related diagnosis, planning and transfer to surgical and further prosthetic treatment, but guidelines for justification and cone beam computed tomography optimization remain mandatory.
Foreign Exchange Intervention and Monetary Policy: A Tale of Two Agencies with Conflicting Objectives
Authors: Lambson Val , Takagi Shinji , Kozuru Issei
Published: August 2014

In several industrial countries, the government is responsible for foreign exchange intervention while the central bank is given operational independence in conducting domestic monetary policy. We model the interaction between the two agencies when their views differ and generate empirical implications using lattice‐theoretic techniques. Japanese data from 2001–2004 support the model's predictions with respect to central bank behavior. The evidence is less conclusive as to whether the massive intervention of 2001–2004 by the Ministry of Finance caused the Bank of Japan to raise the monetary target.
The Relationship Between the Alternative exon 7 Splice Variant of the BF Gene and MHC‐Related Marek's Disease Resistance in Chickens
Authors: Jin Y.‐C. , Huang L. , Wei X.‐X. , Zhao Z.‐Y. , Li Y. , Wei P.
Published: August 2014

The study was to analyse the relationship between the alternative exon 7 splice variant of the BF gene and MHC‐related Marek's disease (MD) resistance in chickens. The experiment first determined whether or not the cocks of Xiayan chickens have alternative splicing‐out of the exon 7 of the BF gene from peripheral blood leucocytes (PBLs). Then, selected two groups: Group K included the offspring of the selected cocks which have no alternative splicing‐out of the exon 7 of the BF gene; Group Y included the offspring of the selected cocks which have alternative splicing‐out of the exon 7 of the BF gene. All hens used in the cross‐breeding were non‐selected. The experimental chickens were challenged with a very virulent strain of Marek's disease virus (MDV) at 4 days old and were raised for 12 weeks. At this time, all the surviving chickens were killed and necropsy was also performed during the experiment whenever chickens died from the infection. Tumour incidence and mortality were calculated using SPSS, and the tissues were collected to detect MDV by PCR. The results showed that the mortalities of Group K and Y were 52.75% and 70.65%, respectively; and that the tumour incidences of non‐alternative splicing‐out of the exon 7 of the BF for Groups K and Y were 15.38% and 38.89%, respectively; the tumour incidences for the alternative splicing‐out of the exon 7 were 46.15% and 56.76%, respectively. The results demonstrated the tumour incidence was highly related with the alternative exon 7 splice variant of the BF gene (P < 0.05).
Inhibition of Neutrophil‐Dependent Cytotoxicity for Human Endothelial Cells by ACE Inhibitors
Authors: Andersson P. , Bratt J. , Heimbürger M. , Cederholm T. , Palmblad J.
Published: August 2014

Angiotensin‐converting enzyme inhibitors (ACEi) have immunomodulating properties and have been suggested to protect against endothelial injury, for example myocardial infarction and reperfusion injury. We tested whether two ACEi (captopril and enalapril), differing in a thiol group, protected human umbilical vein endothelial cells (HUVEC) from cytotoxicity induced by polymorphonuclear neutrophils (PMN) in vitro, when cells were activated by tumour necrosis factor‐α (TNFα) or the arachidonate derivative lipoxin‐A4 (LXA4), using separate cytotoxicity pathways. When 51Cr labelled HUVEC were treated with captopril (0–500 μm) or enalapril (0–100 μm) for 2 h and then activated by TNFα (100 ng/ml) for 24 h, a significant, dose‐dependent reduction of 51Cr release was observed. Similarly, captopril reduced 51Cr release when LXA4 (0.1 μm) was used to stimulate PMN for 4 h. Among previously defined mechanisms of significance for the cytotoxic reaction, expression of ICAM‐1, but not intracellular Ca2+ changes in PMN or PMN adherence to HUVEC, were reduced by ACEi treatment. Moreover, both ACEi inhibited HUVEC surface expression of TNFα receptor I (but not II). Thus, these ACEi, particularly captopril, interfere with PMN‐induced cytotoxicity for endothelial cells by modulating pro‐inflammatory surface receptors, which is a novel effect that might be explored for further therapeutic approaches.
Modification of a melanoma discrimination index derived from hyperspectral data: a clinical trial conducted in 2 centers between March 2011 and December 2013
Authors: Nagaoka T. , Kiyohara Y. , Koga H. , Nakamura A. , Saida T. , Sota T.
Published: August 2014

Background

The morphology of pigmented skin lesions (PSLs) is predominantly a result of varying concentrations and distributions of pigmented molecules such as melanin and hemoglobin. Based on these differences and the fact that their information is contained in cutaneous spectra, a hyperspectral imager (HSI) for pigmented melanoma and a single discrimination index derived from the resultant hyperspectral data are proposed.

Objective

To develop and evaluate a new discrimination index for melanomas, compared to the previous index.

Methods

A HSI, which is convenient for both patients and clinicians, was newly developed and used in a clinical trial conducted in 2 centers with 80 patients with primary lesions and 17 volunteers between March 2011 and December 2013. There were 24 melanomas and 110 other PSLs. A previously proposed discrimination index was used without modifications. A new index, which emphasized the essential features of melanoma, was proposed, and its performance was examined. For each index, a threshold value was set to minimize the average value of the false positive and false negative fractions. The performances of both indices were compared.

Results

The sensitivity and specificity of the old index were 75% and 97%, respectively, while those of the new index were 96% and 87%.

Conclusion

The new index had a higher sensitivity and adequate specificity, indicating that it is more useful than the old index.
The movement of the non‐cell‐autonomous transcription factor, SHORT‐ROOT relies on the endomembrane system
Authors: Wu Shuang , Gallagher Kimberly L.
Published: August 2014

Plant cells are able to convey positional and developmental information between cells through the direct transfer of transcription factors. One well studied example of this is the SHORT‐ROOT (SHR) protein, which moves from the stele into the neighboring ground tissue layer to specify endodermis. While it has been shown that SHR trafficking relies on plasmodesmata (PD), and interaction with the SHR INTERACTING EMBRYONIC LETHAL (SIEL) protein, little information is known about how SHR trafficking is controlled or how SIEL promotes the movement of SHR. Here we show that SHR can move from multiple different cell types in the root. Analysis of subcellular localization indicates that in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL‐dependent manner. Interference of early and late endosomes disrupts intercellular movement of SHR. Our findings reveal an essential role for the plant endomembrane, independent of secretion, in the intercellular trafficking of SHR.
The effect of immunoadsorption with the Immusorba TR‐350 column on coagulation compared to plasma exchange
Authors: Koessler J. , Kobsar A. , Kuhn S. , Koessler A. , Yilmaz P. , Weinig E. , Putz E. , Boeck M. , Klinker E.
Published: August 2014

Background and Objectives

Plasma exchange (PE) and immunoadsorption with the Immusorba TR‐350 column (IA) are used to remove autoantibodies from plasma in acute neurological autoimmune disorders. The impact of IA on coagulation and on low molecular weight heparin (LMWH) levels in comparison with PE was investigated.

Patients and Methods

In five patients with neurological autoimmune disorders, coagulation parameters (global tests, coagulation factors) were measured before and after PE or IA (Part A). In five other patients under anticoagulation with LMWH, anti‐Xa activity and global tests were measured before and after the treatments (Part B).

Results

After PE, coagulation factors were significantly reduced by 50–70%. After IA, a distinct reduction was observed for fibrinogen, but not for antithrombin and most of the other coagulation factors. Anti‐Xa activity was reduced after PE (from 0·57 ± 0·10 to 0·13 ± 0·05 IU/ml) and almost unchanged after IA.

Conclusion

It is advisable to discontinue or to reduce LMWH doses and to monitor coagulation parameters and anti‐Xa activity after PE or IA to decide about further LMWH dosing.
The constructive membership problem for discrete free subgroups of rank 2 of
Authors: Eick B. , Kirschmer M. , Leedham-Green C.
Published: August 2014

We exhibit a practical algorithm for solving the constructive membership problem for discrete free subgroups of rank $2$ in $\mathrm{PSL}_2(\mathbb{R})$ or $\mathrm{SL}_2(\mathbb{R})$. This algorithm, together with methods for checking whether a two-generator subgroup of $\mathrm{PSL}_2(\mathbb{R})$ or $\mathrm{SL}_2(\mathbb{R})$ is discrete and free, have been implemented in Magma for groups defined over real algebraic number fields.

Supplementary materials are available with this article.
A system to detect cerebral aneurysms in multimodality angiographic data sets
Authors: Hentschke Clemens M. , Beuing Oliver , Paukisch Harald , Scherlach Cordula , Skalej Martin , Tönnies Klaus D.
Published: August 2014

Purpose:

The early detection of cerebral aneurysms plays a major role in preventing subarachnoid hemorrhage. The authors present a system to automatically detect cerebral aneurysms in multimodal 3D angiographic data sets. The authors’ system is parametrizable for contrast‐enhanced magnetic resonance angiography (CE‐MRA), time‐of‐flight magnetic resonance angiography (TOF‐MRA), and computed tomography angiography (CTA).

Methods:

Initial volumes of interest are found by applying a multiscale sphere‐enhancing filter. Several features are combined in a linear discriminant function (LDF) to distinguish between true aneurysms and false positives. The features include shape information, spatial information, and probability information. The LDF can either be parametrized by domain experts or automatically by training. Vessel segmentation is avoided as it could heavily influence the detection algorithm.

Results:

The authors tested their method with 151 clinical angiographic data sets containing 112 aneurysms. The authors reach a sensitivity of 95% with CE‐MRA data sets at an average false positive rate per data set (FPDS) of 8.2. For TOF‐MRA, we achieve 95% sensitivity at 11.3 FPDS. For CTA, we reach a sensitivity of 95% at 22.8 FPDS. For all modalities, the expert parametrization led to similar or better results than the trained parametrization eliminating the need for training. 93% of aneurysms that were smaller than 5 mm were found. The authors also showed that their algorithm is capable of detecting aneurysms that were previously overlooked by radiologists.

Conclusions:

The authors present an automatic system to detect cerebral aneurysms in multimodal angiographic data sets. The system proved as a suitable computer‐aided detection tool to help radiologists find cerebral aneurysms.
Image‐guided transorbital procedures with endoscopic video augmentation
Authors: DeLisi Michael P. , Mawn Louise A. , Galloway Robert L.
Published: August 2014

Purpose:

Surgical interventions to the orbital space behind the eyeball are limited to highly invasive procedures due to the confined nature of the region along with the presence of several intricate soft tissue structures. A minimally invasive approach to orbital surgery would enable several therapeutic options, particularly new treatment protocols for optic neuropathies such as glaucoma. The authors have developed an image‐guided system for the purpose of navigating a thin flexible endoscope to a specified target region behind the eyeball. Navigation within the orbit is particularly challenging despite its small volume, as the presence of fat tissue occludes the endoscopic visual field while the surgeon must constantly be aware of optic nerve position. This research investigates the impact of endoscopic video augmentation to targeted image‐guided navigation in a series of anthropomorphic phantom experiments.

Methods:

A group of 16 surgeons performed a target identification task within the orbits of four skull phantoms. The task consisted of identifying the correct target, indicated by the augmented video and the preoperative imaging frames, out of four possibilities. For each skull, one orbital intervention was performed with video augmentation, while the other was done with the standard image guidance technique, in random order.

Results:

The authors measured a target identification accuracy of 95.3% and 85.9% for the augmented and standard cases, respectively, with statistically significant improvement in procedure time (Z = −2.044, p = 0.041) and intraoperator mean procedure time (Z = 2.456, p = 0.014) when augmentation was used.

Conclusions:

Improvements in both target identification accuracy and interventional procedure time suggest that endoscopic video augmentation provides valuable additional orientation and trajectory information in an image‐guided procedure. Utilization of video augmentation in transorbital interventions could further minimize complication risk and enhance surgeon comfort and confidence in the procedure.
A Raman cell based on hollow core photonic crystal fiber for human breath analysis
Authors: Chow Kam Kong , Short Michael , Lam Stephen , McWilliams Annette , Zeng Haishan
Published: August 2014

Purpose:

Breath analysis has a potential prospect to benefit the medical field based on its perceived advantages to become a point‐of‐care, easy to use, and cost‐effective technology. Early studies done by mass spectrometry show that volatile organic compounds from human breath can represent certain disease states of our bodies, such as lung cancer, and revealed the potential of breath analysis. But mass spectrometry is costly and has slow‐turnaround time. The authors’ goal is to develop a more portable and cost effective device based on Raman spectroscopy and hollow core‐photonic crystal fiber (HC‐PCF) for breath analysis.

Methods:

Raman scattering is a photon‐molecular interaction based on the kinetic modes of an analyte which offers unique fingerprint type signals that allow molecular identification. HC‐PCF is a novel light guide which allows light to be confined in a hollow core and it can be filled with a gaseous sample. Raman signals generated by the gaseous sample (i.e., human breath) can be guided and collected effectively for spectral analysis.

Results:

A Raman‐cell based on HC‐PCF in the near infrared wavelength range was developed and tested in a single pass forward‐scattering mode for different gaseous samples. Raman spectra were obtained successfully from reference gases (hydrogen, oxygen, carbon dioxide gases), ambient air, and a human breath sample. The calculated minimum detectable concentration of this system was ∼15 parts per million by volume, determined by measuring the carbon dioxide concentration in ambient air via the characteristic Raman peaks at 1286 and 1388 cm−1.

Conclusions:

The results of this study were compared to a previous study using HC‐PCF to trap industrial gases and backward‐scatter 514.5 nm light from them. The authors found that the method presented in this paper has an advantage to enhance the signal‐to‐noise ratio (SNR). This SNR advantage, coupled with the better transmission of HC‐PCF in the near‐IR than in the visible wavelengths led to an estimated seven times improvement in the detection sensitivity. The authors’ prototype device also demonstrated a 100‐fold improvement over a recently reported detection limit of a reflective capillary fiber‐based Raman cell for breath analysis. Continued development is underway to increase the detection sensitivity further to reach practical clinical applications.
Amorphous In–Ga–Zn–O thin‐film transistor active pixel sensor x‐ray imager for digital breast tomosynthesis
Authors: Zhao Chumin , Kanicki Jerzy
Published: August 2014

Purpose:

The breast cancer detection rate for digital breast tomosynthesis (DBT) is limited by the x‐ray image quality. The limiting Nyquist frequency for current DBT systems is around 5 lp/mm, while the fine image details contained in the high spatial frequency region (>5 lp/mm) are lost. Also today the tomosynthesis patient dose is high (0.67–3.52 mGy). To address current issues, in this paper, for the first time, a high‐resolution low‐dose organic photodetector/amorphous In–Ga–Zn–O thin‐film transistor (a‐IGZO TFT) active pixel sensor (APS) x‐ray imager is proposed for next generation DBT systems.

Methods:

The indirect x‐ray detector is based on a combination of a novel low‐cost organic photodiode (OPD) and a cesium iodide‐based (CsI:Tl) scintillator. The proposed APS x‐ray imager overcomes the difficulty of weak signal detection, when small pixel size and low exposure conditions are used, by an on‐pixel signal amplification with a significant charge gain. The electrical performance of a‐IGZO TFT APS pixel circuit is investigated by SPICE simulation using modified Rensselaer Polytechnic Institute amorphous silicon (a‐Si:H) TFT model. Finally, the noise, detective quantum efficiency (DQE), and resolvability of the complete system are modeled using the cascaded system formalism.

Results:

The result demonstrates that a large charge gain of 31–122 is achieved for the proposed high‐mobility (5–20 cm2/V s) amorphous metal‐oxide TFT APS. The charge gain is sufficient to eliminate the TFT thermal noise, flicker noise as well as the external readout circuit noise. Moreover, the low TFT (<10−13 A) and OPD (<10−8 A/cm2) leakage currents can further reduce the APS noise. Cascaded system analysis shows that the proposed APS imager with a 75 μm pixel pitch can effectively resolve the Nyquist frequency of 6.67 lp/mm, which can be further improved to ∼10 lp/mm if the pixel pitch is reduced to 50 μm. Moreover, the detector entrance exposure per projection can be reduced from 1 to 0.3 mR without a significant reduction of DQE. The signal‐to‐noise ratio of the a‐IGZO APS imager under 0.3 mR x‐ray exposure is comparable to that of a‐Si:H passive pixel sensor imager under 1 mR, indicating good image quality under low dose. A threefold reduction of current tomosynthesis dose is expected if proposed technology is combined with an advanced DBT image reconstruction method.

Conclusions:

The proposed a‐IGZO APS x‐ray imager with a pixel pitch <75 μm is capable to achieve a high spatial frequency (>6.67 lp/mm) and a low dose (<0.4 mGy) in next generation DBT systems.
Neural control of maternal and paternal behaviors
Authors: Dulac Catherine , O’Connell Lauren A. , Wu Zheng
Published: August 2014

Parental care, including feeding and protection of young, is essential for the survival as well as mental and physical well-being of the offspring. A large variety of parental behaviors has been described across species and sexes, raising fascinating questions about how animals identify the young and how brain circuits drive and modulate parental displays in males and females. Recent studies have begun to uncover a striking antagonistic interplay between brain systems underlying parental care and infant-directed aggression in both males and females, as well as a large range of intrinsic and environmentally driven neural modulation and plasticity. Improved understanding of the neural control of parental interactions in animals should provide novel insights into the complex issue of human parental care in both health and disease.
A single-stranded architecture for cotranscriptional folding of RNA nanostructures
Authors: Geary Cody , Rothemund Paul W. K. , Andersen Ebbe S.
Published: August 2014

The future of RNA origami writ large

Researchers have long fabricated intricate nanostructures from carefully linked DNA strands. Now they can use RNA made by gene expression, which avoids the costly strand synthesis and lengthy annealing steps necessary with DNA origami. Geary
et al.
used molecular modeling to extend the size of folded RNA origami structures (see the Perspective by Leontis and Westhof). The modeling revealed assembly patterns for linking single-stranded RNA into A-form helices. The authors created two-dimensional structures as large as 660 nucleotides on mica surfaces.

Science
, this issue p.
799
; see also p.
732
Parenting from before conception
Authors: Lane Michelle , Robker Rebecca L. , Robertson Sarah A.
Published: August 2014

At fertilization, the gametes endow the embryo with a genomic blueprint, the integrity of which is affected by the age and environmental exposures of both parents. Recent studies reveal that parental history and experiences also exert effects through epigenomic information not contained in the DNA sequence, including variations in sperm and oocyte cytosine methylation and chromatin patterning, noncoding RNAs, and mitochondria. Transgenerational epigenetic effects interact with conditions at conception to program the developmental trajectory of the embryo and fetus, ultimately affecting the lifetime health of the child. These insights compel us to revise generally held notions to accommodate the prospect that biological parenting commences well before birth, even prior to conception.
Programmable on-chip DNA compartments as artificial cells
Authors: Karzbrun Eyal , Tayar Alexandra M. , Noireaux Vincent , Bar-Ziv Roy H.
Published: August 2014

Toward an “artificial cell” on a chip

Cell-free systems that reconstitute biochemical pathways have been critical for unraveling the inner workings of the cell. Karzbrun
et al.
created a highly miniaturized cell-free system on a silicon chip. A series of tiny linked compartments were fabricated on the chip, in which DNA-driven reactions occurred, with materials flowing into and diffusing between the compartments. The system recreated oscillating protein expression patterns and protein gradients, and provides a stepping stone to creating “artificial cells” on a chip.

Science
, this issue p.
829
Self-assembled RNA nanostructures
Authors: Leontis Neocles B. , Westhof Eric
Published: August 2014

RNA structures have been designed that self-assemble and are programmable and scalable

[Also see Report by

Geary
et al.

]
You are what you eat, but what about your DNA?
Authors: Susiarjo Martha , Bartolomei Marisa S.
Published: August 2014

Parental nutrition influences the health of subsequent generations through epigenetic changes in germ cells

[Also see Research Article by

Radford
et al.

]
The rising toll
Authors: Bohannon John
Published: August 2014

Newly released data reveal that the war in Afghanistan is becoming more dangerous for civilians.
Unsettled questions trail IVF's success
Authors: Servick Kelly
Published: August 2014

Researchers are still struggling to understand the potential long-term effects of assisted reproduction.
Decorin Binding Proteins A and B in the Serodiagnosis of Lyme Disease in North America
Authors: Arnaboldi Paul M. , Sambir Mariya , Dattwyler Raymond J.
Published: August 2014

The laboratory diagnosis of Lyme disease is based upon the detection of antibodies generated against
Borrelia burgdorferi
using a two-tier assay, typically consisting of an enzyme-linked immunosorbent assay (ELISA), followed by a Western blot. This system, put into place to address the nonspecificity associated with standalone first-tier assays, is insensitive for diagnosing early infection, when most people seek care. The use of bacterial lysates or whole-protein antigens as first-tier assay targets contributes to nonspecificity due, in part, to the presence of cross-reactive epitopes that are also found in other bacteria. This precludes their use as sensitive standalone assays. The use of peptides containing linear epitopes that are highly specific for
B. burgdorferi
offers a method for reducing this cross-reactivity. In the present study, we mapped the linear epitopes of the prominently expressed
Borrelia
adhesins decorin binding protein A (DbpA) and DbpB. We identified several epitopes in each protein that were highly conserved among North American strains of
B. burgdorferi
, and we screened peptides containing specific epitopes using serum panels from early and late Lyme disease patients. The individual peptides primarily detected IgM but not IgG, while the proteins efficiently detected both IgM and IgG. While no individual peptide demonstrated better utility for antibody detection than its respective whole protein, an assay containing a combination of a DbpA and a DbpB peptide adequately detected both IgM and IgG, accurately identifying 87.5% (84/96) of the early Lyme disease patients and 80.0% (16/20) of the late Lyme disease patients.
Laboratory Detection of Clostridium difficile in Piglets in Australia
Authors: Knight Daniel R. , Squire Michele M. , Riley Thomas V.
Published: August 2014

Clostridium difficile
is a well-known enteric pathogen of humans and the causative agent of high-morbidity enteritis in piglets aged 1 to 7 days.
C. difficile
prevalence in Australian piglets is as high as 70%. The current diagnostic assays have been validated only for human infections, and there are no published studies assessing their performance in Australian piglets. We evaluated the suitability of five assays for detecting
C. difficile
in 157 specimens of piglet feces. The assays included a loop-mediated isothermal amplification (LMIA)-PCR for
tcdA
(illumigene
C. difficile
; Meridian), a real-time PCR for
tcdB
(GeneOhm Cdiff; Becton Dickinson), two-component enzyme immunoassays (EIA) for
C. difficile
glutamate dehydrogenase (GDH) (EIA-GDH) and TcdA/TcdB (EIA-TcdA/TcdB) (C. diff Quik Chek; Alere), and direct culture (DC) (
C. difficile
chromID agar; bioMérieux). The assays for detection of the organism were compared against enrichment culture (EC), and assays for detection of toxins/toxin genes were compared against EC followed by PCR for toxin genes (toxigenic EC [TEC]). The recovery of
C. difficile
by EC was 39.5% (
n
= 62/157), and TEC revealed that 58.1% (
n
= 36/62) of isolates were positive for at least one toxin gene (
tcdA
/
tcdB
). Compared with those for EC/TEC, the sensitivities, specificities, positive predictive values, and negative predictive values were, respectively, as follows: DC, 91.9, 100.0, 100.0, and 95.0%; EIA-GDH, 41.9, 92.6, 78.8, and 71.0%; EIA-TcdA/TcdB, 5.6, 99.2, 66.7, and 77.9%; real-time PCR, 42.9, 96.7, 78.9, and 85.4% and LMIA-PCR, 25.0, 95.9, 64.3, and 81.1%. The performance of the molecular methods was poor, suggesting that the current commercially available assays for diagnosis of
C. difficile
in humans are not suitable for use in piglets.
C. difficile
recovery by the DC provides a cost-effective alternative.
PCR in Diagnosis of Invasive Aspergillosis: a Meta-Analysis of Diagnostic Performance
Authors: Arvanitis Marios , Ziakas Panayiotis D. , Zacharioudakis Ioannis M. , Zervou Fainareti N. , Caliendo Angela M. , Mylonakis Eleftherios
Published: August 2014

Invasive aspergillosis is a difficult-to-diagnose infection with a high mortality rate that affects high-risk groups such as patients with neutropenia and hematologic malignancies. We performed a bivariate meta-analysis of diagnostic data for an
Aspergillus
sp. PCR assay with blood specimens from high-risk hematology patients. We included all studies involving human subjects that assessed the performance of any PCR assay for invasive aspergillosis in whole blood or serum and that used the European Organization for the treatment of Cancer/Mycoses Study Group criteria as a reference standard. Three investigators independently searched the literature for eligible studies and extracted the data. Out of a total of 37 studies, 25 met strict quality criteria and were included in our evidence synthesis. Twenty-five studies with 2,595 patients were analyzed. The pooled diagnostic performance of whole-blood and serum PCR assays was moderate, with a sensitivity and specificity of 84% (95% confidence interval [CI], 75 to 91%) and 76% (95% CI, 65 to 84%), respectively, suggesting that a positive or negative result is unable, on its own, to confirm or exclude a suspected infection. The performance of a PCR assay of serum was not significantly different from that of whole blood. Notably, at least two positive PCR test results were found to have a specificity of 95% and a sensitivity of 64% for invasive infection, achieving a high positive likelihood ratio of 12.8. Importantly, the European
Aspergillus
PCR Initiative (EAPCRI) recommendations improved the performance of the PCR even further when at least two positive specimens were used to define PCR positivity. In conclusion, two positive PCR results should be considered highly indicative of an active
Aspergillus
sp. infection. Use of the EAPCRI recommendations by clinical laboratories can further enhance PCR performance.
Comparative Evaluation of Three Commercial Systems for Detection of High-Risk Human Papillomavirus in Cervical and Vaginal ThinPrep PreservCyt Samples and Correlation with Biopsy Results
Authors: Binnicker M. J. , Pritt B. S. , Duresko B. J. , Espy M. J. , Grys T. E. , Zarka M. A. , Kerr S. E. , Henry M. R.
Published: August 2014

Genital human papillomavirus (HPV) is the etiologic agent of more than 99% of all cervical cancers worldwide, with 14 genotypes being considered oncogenic or “high risk” because of their association with severe dysplasia and cervical carcinoma. Among these 14 high-risk types, HPV-16 and -18 account for approximately 70% of cervical cancers. The aim of this study was to evaluate three FDA-approved HPV nucleic acid-based tests for the ability to predict high-grade cervical intraepithelial neoplasias (CIN2 or worse) in corresponding tissue biopsy specimens. Residual specimens (total
n
= 793, cervical
n
= 743, vaginal
n
= 50) collected in ThinPrep PreservCyt medium with a cytologic result of ≥atypical squamous cells of undetermined significance were tested by the Hybrid Capture 2 (HC2) assay (Qiagen, Gaithersburg, MD), the cobas HPV test (Roche Diagnostics, Indianapolis, IN), and the APTIMA HPV assay (Hologic, San Diego, CA). Genotyping for HPV-16 and HPV-18 was simultaneously performed by the cobas HPV test. Results were compared to cervical or vaginal biopsy findings, when they were available (
n
= 350). Among the 350 patients with corresponding biopsy results, 81 (23.1%) showed ≥CIN2 by histopathology. The ≥CIN2 detection sensitivity was 91.4% by the cobas and APTIMA assays and 97.5% by HC2 assay. The specificities of the cobas, APTIMA, and HC2 assays were 31.2, 42.0, and 27.1%, respectively. When considering only positive HPV-16 and/or HPV-18 genotype results, the cobas test showed a sensitivity and a specificity of 51.9 and 86.6%, respectively. While the HC2, cobas, and APTIMA assays showed similar sensitivities for the detection of ≥CIN2 lesions, the specificities of the three tests varied, with the greatest specificity (86.6%) observed when the HPV-16 and/or HPV-18 genotypes were detected.
Cross-Clade Ultrasensitive PCR-Based Assays To Measure HIV Persistence in Large-Cohort Studies
Authors: Vandergeeten Claire , Fromentin Rémi , Merlini Esther , Lawani Mariam B. , DaFonseca Sandrina , Bakeman Wendy , McNulty Amanda , Ramgopal Moti , Michael Nelson , Kim Jerome H. , Ananworanich Jintanat , Chomont Nicolas
Published: August 2014

A small pool of infected cells persists in HIV-infected individuals receiving antiretroviral therapy (ART). Here, we developed ultrasensitive assays to precisely measure the frequency of cells harboring total HIV DNA, integrated HIV DNA, and two long terminal repeat (2-LTR) circles. These assays are performed on cell lysates, which circumvents the labor-intensive step of DNA extraction, and rely on the coquantification of each HIV molecular form together with CD3 gene sequences to precisely measure cell input. Using primary isolates from HIV subtypes A, B, C, D, and CRF01_A/E, we demonstrate that these assays can efficiently quantify low target copy numbers from diverse HIV subtypes. We further used these assays to measure total HIV DNA, integrated HIV DNA, and 2-LTR circles in CD4+T cells from HIV-infected subjects infected with subtype B. All samples obtained from ART-naive subjects were positive for the three HIV molecular forms (n= 15). Total HIV DNA, integrated HIV DNA, and 2-LTR circles were detected in, respectively, 100%, 94%, and 77% of the samples from individuals in which HIV was suppressed by ART. Higher levels of total HIV DNA and 2-LTR circles were detected in untreated subjects than individuals on ART (P= 0.0003 andP= 0.0004, respectively), while the frequency of CD4+T cells harboring integrated HIV DNA did not differ between the two groups. These results demonstrate that these novel assays have the ability to quantify very low levels of HIV DNA of multiple HIV subtypes without the need for nucleic acid extraction, making them well suited for the monitoring of viral persistence in large populations of HIV-infected individuals.

IMPORTANCESince the discovery of viral reservoirs in HIV-infected subjects receiving suppressive ART, measuring the degree of viral persistence has been one of the greatest challenges in the field of HIV research. Here, we report the development and validation of ultrasensitive assays to measure HIV persistence in HIV-infected individuals from multiple geographical regions. These assays are relatively inexpensive, do not require DNA extraction, and can be completed in a single day. Therefore, they are perfectly adapted to monitor HIV persistence in large cohorts of HIV-infected individuals and, given their sensitivity, can be used to monitor the efficacy of therapeutic strategies aimed at interfering with HIV persistence after prolonged ART.
Modulation of Hepatitis C Virus Genome Replication by Glycosphingolipids and Four-Phosphate Adaptor Protein 2
Authors: Khan Irfan , Katikaneni Divya S. , Han Qingxia , Sanchez-Felipe Lorena , Hanada Kentaro , Ambrose Rebecca L. , Mackenzie Jason M. , Konan Kouacou V.
Published: August 2014

Hepatitis C virus (HCV) assembles its replication complex on cytosolic membrane vesicles often clustered in a membranous web (MW). During infection, HCV NS5A protein activates PI4KIIIα enzyme, causing massive production and redistribution of phosphatidylinositol 4-phosphate (PI4P) lipid to the replication complex. However, the role of PI4P in the HCV life cycle is not well understood. We postulated that PI4P recruits host effectors to modulate HCV genome replication or virus particle production. To test this hypothesis, we generated cell lines for doxycycline-inducible expression of short hairpin RNAs (shRNAs) targeting the PI4P effector, four-phosphate adaptor protein 2 (FAPP2). FAPP2 depletion attenuated HCV infectivity and impeded HCV RNA synthesis. Indeed, FAPP2 has two functional lipid-binding domains specific for PI4P and glycosphingolipids. While expression of the PI4P-binding mutant protein was expected to inhibit HCV replication, a marked drop in replication efficiency was observed unexpectedly with the glycosphingolipid-binding mutant protein. These data suggest that both domains are crucial for the role of FAPP2 in HCV genome replication. We also found that HCV significantly increases the level of some glycosphingolipids, whereas adding these lipids to FAPP2-depleted cells partially rescued replication, further arguing for the importance of glycosphingolipids in HCV RNA synthesis. Interestingly, FAPP2 is redistributed to the replication complex (RC) characterized by HCV NS5A, NS4B, or double-stranded RNA (dsRNA) foci. Additionally, FAPP2 depletion disrupts the RC and alters the colocalization of HCV replicase proteins. Altogether, our study implies that HCV coopts FAPP2 for virus genome replication via PI4P binding and glycosphingolipid transport to the HCV RC.

IMPORTANCE
Like most viruses with a positive-sense RNA genome, HCV replicates its RNA on remodeled host membranes composed of lipids hijacked from various internal membrane compartments. During infection, HCV induces massive production and retargeting of the PI4P lipid to its replication complex. However, the role of PI4P in HCV replication is not well understood. In this study, we have shown that FAPP2, a PI4P effector and glycosphingolipid-binding protein, is recruited to the HCV replication complex and is required for HCV genome replication and replication complex formation. More importantly, this study demonstrates, for the first time, the crucial role of glycosphingolipids in the HCV life cycle and suggests a link between PI4P and glycosphingolipids in HCV genome replication.
Polyomavirus Small t Antigen Interacts with Yes-Associated Protein To Regulate Cell Survival and Differentiation
Authors: Hwang Justin H. , Pores Fernando Arun T. , Faure Nathalie , Andrabi Shaida , Hahn William C. , Schaffhausen Brian S. , Roberts Thomas M.
Published: August 2014

Murine polyomavirus small t antigen (PyST) regulates cell cycle, cell survival, apoptosis, and differentiation and cooperates with middle T antigen (MT) to transform primary cells
in vitro
and
in vivo
. Like all polyomavirus T antigens, PyST functions largely via its interactions with host cell proteins. Here, we show that PyST binds both Yes-associated protein 1 (YAP1) and YAP2, integral parts of the Hippo signaling pathway, which is a subject of increasing interest in human cancer. The transcription factor TEAD, which is a known target of YAP, is also found in PyST complexes. PyST enhanced YAP association with protein phosphatase 2A (PP2A), leading to decreased YAP phosphorylation. PyST increased YAP levels by decreasing its degradation. This effect was mediated by a reduction in YAP association with β-transducin repeat protein (βTRCP), which is known to regulate YAP turnover in a phosphorylation-dependent manner. Genetic analysis has identified PyST mutants defective in YAP binding. These mutants demonstrated that YAP binding is important for PyST to block myoblast differentiation and to synergize with the phosphodiesterase inhibitor isobutylmethylxanthine (IBMX) to promote cell death in 3T3-L1 preadipocytes placed under differentiation conditions. In addition to YAP binding, both of these phenotypes require PyST binding to PP2A.

IMPORTANCE
The Hippo/YAP pathway is a highly conserved cascade important for tissue development and homeostasis. Defects in this pathway are increasingly being associated with cancer. Polyomavirus small t antigen is a viral oncogene that cooperates with middle T antigen in transformation. On its own, small t antigen controls cell survival and differentiation. By binding YAP, small t antigen brings it together with protein phosphatase 2A. This work shows how this association of small t antigen with YAP is important for its effects on cell phenotype. It also suggests that PyST can be used to characterize cellular processes that are regulated by YAP.
Visualization of Retroviral Envelope Spikes in Complex with the V3 Loop Antibody 447-52D on Intact Viruses by Cryo-Electron Tomography
Authors: Dutta Moumita , Liu Jun , Roux Kenneth H. , Taylor Kenneth A.
Published: August 2014

The gp120 portion of the envelope spike on human immunodeficiency virus type 1 (HIV-1) plays a critical role in viral entry into host cells and is a key target for the humoral immune response, and yet many structural details remain elusive. We have used cryoelectron tomography to visualize the binding of the broadly neutralizing monoclonal antibody (MAb) 447-52D to intact envelope spikes on virions of HIV-1 MN strain. Antibody 447-52D has previously been shown to bind to the tip of the V3 loop. Our results show antibody arms radiating from the sides of the gp120 protomers at a range of angles and place the antibody-bound V3 loop in an orientation that differs from that predicted by most current models but consistent with the idea that antibody binding dislodges the V3 loop from its location in the Env spike, making it flexible and disordered. These data reveal information on the position of the V3 loop and its relative flexibility and suggest that 447-52D neutralizes HIV-1 MN by capturing the V3 loop, blocking its interaction with the coreceptor and altering the structure of the envelope spike.

IMPORTANCEAntibody neutralization is one of the primary ways that the body fights infection with HIV. Because HIV is a highly mutable virus, the body must constantly produce new antibodies to counter new strains of HIV that the body itself is producing. Consequently, antibodies capable of neutralizing multiple HIV strains are comparatively few. An improved understanding of the mechanism of antibody neutralization might advance the development of immunogens. Most neutralizing antibodies target the Env glycoprotein spikes found on the virus surface. The broadly neutralizing antibody 447-52D targets the highly conserved β-turn of variable loop 3 (V3) of gp120. The importance of V3 lies in its contribution to the coreceptor binding site on the target cell. We show here that 447-52D binding to V3 converts the Env conformation from closed to open and makes the V3 loop highly flexible, implying disruption of coreceptor binding and attachment to the target cell.