Effect of Preanalytical Processing of ThinPrep Specimens on Detection of High-Risk Human Papillomavirus by the Aptima HPV Assay

Two important preanalytical protocols performed on liquid-based cytological specimens, namely, automated cytology processing and glacial acetic acid (GAA) treatment, may occur prior to the arrival of specimens in a molecular diagnostics laboratory. Ninety-two ThinPrep vials previously positive for high-risk human papillomavirus (HPV) via the Cervista HPV HR test were preselected and alternated with 92 previously negative ThinPrep vials. The specimen set was processed in a consecutive fashion by an automated cytology processor without fastidious decontamination precautions. Carryover potential was subsequently assessed by performance of the Aptima HPV assay on aliquots from reprocessed ThinPrep vials. All previously negative ThinPrep vials yielded a negative result following routine automated cytology processing, despite close proximity to known-positive ThinPrep vials. In separate experiments, aliquots from 236 ThinPrep vials were forwarded for tandem analysis with and without GAA treatment. Data from GAA- and mock-treated specimens generated by Aptima HPV were compared to correlate data generated by Cervista. A 99.2% concordance of Aptima HPV results from GAA-treated and mock-treated specimens was noted. This result differed from the concordance result derived from Cervista (91.5%; P \u3c 0.0002). Of the initially positive Cervista results, 21.9% reverted to negative following GAA treatment; the correlate value was 2.7% for Aptima HPV (P = 0.01). While deleterious effects of GAA treatment on genomic DNA were noted with Cervista (P = 0.0015), GAA treatment had no significant effects on Aptima HPV specimen signal/cutoff ratios or amplification of internal control RNA (P ≥ 0.07). The validity of an Aptima HPV result is independent of GAA treatment and routine automated cytology processing

Nitrogen cycle disruption through the application of de-icing salts on upland highways

It is hypothesized that episodic introductions of road salt severely disrupt the soil nitrogen cycle at a range of spatial and temporal scales. A field-scale study has confirmed impacts on the nitrogen cycle in soil, soil solution and river samples. There is evidence that ammonium-N retention on cation exchange sites has been reduced by the presence of sodium ions, and that ammonium-N has been flushed from the exchange sites. Increases in soil pH have been caused in naturally acidic uplands. These have enhanced mineralization of organic-N, especially nitrification, leading to a reduction in the mineralizable-N pool of roadside soils. There is evidence to support the hypothesis that organic matter content has been lowered over decades either through desorption or dispersal processes. Multiple drivers are identified that contribute to the disruption of nitrogen cycling processes, but their relative importance is difficult to quantify unequivocally. The influence of road salt on soil and soil solution declines with distance from the highway, but impacts on water chemistry in a local stream are still strongly evident at some distance from the road

Atomic scale switches based on self-assembled surface magic clusters

Atomic scale switches working at room temperature represent the ultimate level of device miniaturization. Using scanning tunneling microscopy, we find a bistable switching between two mirror-symmetric configurations of self-assembled magic rare earth silicide clusters on the Si(111) 7 X 7 surface. Density functional theory reveals an energy barrier of 1.3 eV between the two cluster configurations, suppressing the switching even at room temperature. However, intentional switch- ing between the two states is possible in the presence of a close tunneling tip due to a tip-induced lowering of the energy barrier

Characterizing driver–response relationships in marine pelagic ecosystems for improved ocean management

Scientists and resources managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressor. However, a growing body of literature demonstrates that many relationships are non-linear, where small changes in a driver prompt a disproportionately large ecological response. Here we aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focus our analyses on one of the best-studied marine systems, pelagic ecosystems, which allowed us to apply robust statistical techniques on a large pool of previously published studies. In this synthesis, we (1) conduct a wide literature review on single driver-response relationships in pelagic systems, (2) use statistical models to identify the degree of non-linearity in these relationships, and (3) assess whether general patterns exist in the strengths and shapes of non-linear relationships across drivers. Overall we found that non-linearities are common in pelagic ecosystems, comprising at least 52% of all driver-response relationships. This is likely an underestimate, as papers with higher quality data and analytical approaches reported non-linear relationships at a higher frequency - on average 11% more. Consequently, in the absence of evidence for a linear relationship, it is safer to assume a relationship is non-linear. Strong non-linearities can lead to greater ecological and socio-economic consequences if they are unknown (and/or unanticipated), but if known they may provide clear thresholds to inform management targets. In pelagic systems, strongly non-linear relationships are often driven by climate and trophodynamic variables, but are also associated with local stressors such as overfishing and pollution that can be more easily controlled by managers. Even when marine resource managers cannot influence ecosystem change, they can use information about threshold responses to guide how other stressors are managed and to adapt to new ocean conditions. As methods to detect and reduce uncertainty around threshold values improve, managers will be able to better understand and account for ubiquitous non-linear relationships

Inhibition of Golgi function causes plastid starch accumulation

Little is known about possible interactions between chloroplasts and the Golgi apparatus, although there is increasing evidence for a direct Golgi to chloroplast transport pathway targeting proteins to their destinations within the membranes and stroma of plastids. Here data are presented showing that a blockage of secretion results in a significant increase of starch within plastids. Golgi disassembly promoted either by the secretory inhibitor brefeldin A or through an inducible Sar1-GTP system leads to dramatic starch accumulation in plastids, thus providing evidence for a direct interaction between plastids and Golgi activity. The possibility that starch accumulation is due either to elevated levels of cytosolic sugars because of loss of secretory Golgi activity or even to a blockage of amylase transport from the Golgi to the chloroplast is discussed

Optical control of 4f orbital state in rare-earth metals

Information technology demands continuous increase of data-storage density. In high-density magnetic recording media, the large magneto-crystalline anisotropy (MCA) stabilizes the stored information against decay through thermal fluctuations. In the latest generation storage media, MCA is so large that magnetic order needs to be transiently destroyed by heat to enable bit writing. Here we show an alternative approach to control high-anisotropy magnets: With ultrashort laser pulses the anisotropy itself can be manipulated via electronic state excitations. In rare-earth materials like terbium metal, magnetic moment and high MCA both originate from the 4f electronic state. Following infrared laser excitation 5d-4f electron-electron scattering processes lead to selective orbital excitations that change the 4f orbital occupation and significantly alter the MCA. Besides these excitations within the 4f multiplet, 5d-4f electron transfer causes a transient change of the 4f occupation number, which, too, strongly alters the MCA. Such MCA change cannot be achieved by heating: The material would rather be damaged than the 4f configuration modified. Our results show a way to overcome this limitation for a new type of efficient magnetic storage medium. Besides potential technological relevance, the observation of MCA-changing excitations also has implications for a general understanding of magnetic dynamics processes on ultrashort time scales, where the 4f electronic state affects the angular momentum transfer between spin system and lattice.Comment: Manuscript (14 pages, 3 figures) and Supplementary Information (22 pages, 9 figures

Memory recall in arousing situations – an emotional von Restorff effect?

BACKGROUND: Previous research has demonstrated a relationship between memory recall and P300 amplitude in list learning tasks, but the variables mediating this P300-recall relationship are not well understood. In the present study, subjects were required to recall items from lists consisting of 12 words, which were presented in front of pictures taken from the IAPS collection. One word per list is made distinct either by font color or by a highly arousing background IAPS picture. This isolation procedure was first used by von Restorff. Brain potentials were recorded during list presentation. RESULTS: Recall performance was enhanced for color but not for emotional isolates. Event-related brain potentials (ERP) showed a more positive P300-component for recalled non-isolated words and color-isolated words, compared to the respective non-remembered words, but not for words isolated by arousing background. CONCLUSION: Our findings indicate that it is crucial to take emotional mediator variables into account, when using the P300 to predict later recall. Highly arousing environments might force the cognitive system to interrupt rehearsal processes in working memory, which might benefit transfer into other, more stable memory systems. The impact of attention-capturing properties of arousing background stimuli is also discussed

From research to practice: Lay adherence counsellors' fidelity to an evidence-based intervention for promoting adherence to antiretroviral treatment in the Western Cape, South Africa

In the Western Cape, lay counsellors are tasked with supporting antiretroviral (ARV) adherence in public healthcare clinics. Thirty-nine counsellors in 21 Cape Town clinics were trained in Options for Health (Options), an evidence-based intervention based on motivational interviewing (MI). We evaluated counsellors’ ability to deliver Options for addressing poor adherence following 5 days training. Audio-recordings of counselling sessions collected following training were transcribed and translated into English. Thirty-five transcripts of sessions conducted by 35 counsellors were analysed for fidelity to the Options protocol, and using the Motivational Interviewing Treatment and Integrity (MITI) code. Counsellors struggled with some of the strategies associated with MI, such as assessing readiness-to-change and facilitating change talk. Overall, counsellors failed to achieve proficiency in the approach of MI according to the MITI. Counsellors were able to negotiate realistic plans for addressing patients’ barriers to adherence. Further efforts aimed at strengthening the ARV adherence counselling programme are needed.Department of HE and Training approved lis

A limited-size ensemble of homogeneous CNN/LSTMs for high-performance word classification

The strength of long short-term memory neural networks (LSTMs) that have been applied is more located in handling sequences of variable length than in handling geometric variability of the image patterns. In this paper, an end-to-end convolutional LSTM neural network is used to handle both geometric variation and sequence variability. The best results for LSTMs are often based on large-scale training of an ensemble of network instances. We show that high performances can be reached on a common benchmark set by using proper data augmentation for just five such networks using a proper coding scheme and a proper voting scheme. The networks have similar architectures (convolutional neural network (CNN): five layers, bidirectional LSTM (BiLSTM): three layers followed by a connectionist temporal classification (CTC) processing step). The approach assumes differently scaled input images and different feature map sizes. Three datasets are used: the standard benchmark RIMES dataset (French); a historical handwritten dataset KdK (Dutch); the standard benchmark George Washington (GW) dataset (English). Final performance obtained for the word-recognition test of RIMES was 96.6%, a clear improvement over other state-of-the-art approaches which did not use a pre-trained network. On the KdK and GW datasets, our approach also shows good results. The proposed approach is deployed in the Monk search engine for historical-handwriting collections