A dynamic sampling methodology for plasma etch processes using Gaussian process regression

Plasma etch is a key process in modern semiconductor manufacturing facilities as it offers process simplification and yet greater dimensional tolerances compared to wet chemical etch technology. The main challenge of operating plasma etchers is to maintain a consistent etch rate spatially and temporally for a given wafer and for successive wafers processed in the same etch tool. Etch rate measurements require expensive metrology steps and therefore in general only limited sampling is performed. Furthermore, the results of measurements are not accessible in real-time, limiting the options for run-to-run control. This paper investigates a Virtual Metrology (VM) enabled Dynamic Sampling (DS) methodology as an alternative paradigm for balancing the need to reduce costly metrology with the need to measure more frequently and in a timely fashion to enable wafer-to-wafer control. Using a Gaussian Process Regression (GPR) VM model for etch rate estimation of a plasma etch process, the proposed dynamic sampling methodology is demonstrated and evaluated for a number of different predictive dynamic sampling rules. © 2013 IEEE.

Down-regulation of PERK enhances resistance to ionizing radiation

Although, ionizing radiation (IR) has been implicated to cause stress in endoplasmic reticulum (ER), how ER stress signaling and major ER stress sensors modulate cellular response to IR is unclear. Protein kinase RNA-like endoplasmic reticulum kinase (PERK) is an ER transmembrane protein which initiates unfolded protein response (UPR) or ER stress signaling when ER homeostasis is disturbed. Here, we report that down-regulation of PERK resulted in increased clonogenic survival, enhanced DNA repair and reduced apoptosis in irradiated cancer cells. Our study demonstrated that PERK has a role in sensitizing cancer cells to IR. 

Pharmacological interventions for dementia in people with Down Syndrome (Protocol).

Background: People with Down syndrome are vulnerable to developing dementia at an earlier age than the general population. Alzheimer’s disease and cognitive decline in people with Down syndrome can place a significant burden on both the person with Down syndrome and their family and carers. Various pharmacological interventions, including donepezil, galantamine, memantine and rivastigmine, appear to have some effect in treating cognitive decline in people without Down syndrome, but their effectiveness for those with Down syndrome remains unclear. Objectives: To assess the effectiveness of anti-dementia pharmacological interventions and nutritional supplements for treating cognitive decline in people with Down syndrome. Search methods In January 2015, we searched CENTRAL, ALOIS (the Specialised Register of the Cochrane Dementia and Cognitive Improvement Group), Ovid MEDLINE, Embase, PsycINFO, seven other databases, and two trials registers. In addition, we checked the references of relevant reviews and studies and contacted study authors, other researchers and relevant drug manufacturers to identify additional studies. Selection criteria: Randomised controlled trials (RCTs) of anti-dementia pharmacological interventions or nutritional supplements for adults (aged 18 years and older) with Down syndrome, in which treatment was administered and compared with either placebo or no treatment. Data collection and analysis Two review authors independently assessed the risk of bias of included trials and extracted the relevant data. Review authors contacted study authors to obtain missing information where necessaryMain results Only nine studies (427 participants) met the inclusion criteria for this review. Four of these (192 participants) assessed the effectiveness of donepezil, two (139 participants) assessed memantine, one (21 participants) assessed simvastatin, one study (35 participants) assessed antioxidants, and one study (40 participants) assessed acetyl-L-carnitine. Five studies focused on adults aged 45 to 55 years, while the remaining four studies focused on adults aged 20 to 29 years. Seven studies were conducted in either the USA or UK, one between Norway and the UK, and one in Japan. Follow-up periods in studies ranged from four weeks to two years. The reviewers judged all included studies to be at low or unclear risk of bias. Analyses indicate that for participants who received donepezil, scores in measures of cognitive functioning (standardised mean difference (SMD) 0.52, 95% confidence interval (CI) -0.27 to 1.13) and measures of behaviour (SMD 0.42, 95% CI -0.06 to 0.89) were similar to those who received placebo. However, participants who received donepezil were significantly more likely to experience an adverse event (odds ratio (OR) 0.32, 95% CI 0.16 to 0.62). The quality of this body of evidence was low. None of the included donepezil studies reported data for carer stress, institutional/home care, or death. For participants who received memantine, scores in measures of cognitive functioning (SMD 0.05, 95% CI -0.43 to 0.52), behaviour (SMD -0.17, 95% CI -0.46 to 0.11), and occurrence of adverse events (OR 0.45, 95% CI 0.18 to 1.17) were similar to those who received placebo. The quality of this body of evidence was low. None of the included memantine studies reported data for carer stress, institutional/home care, or death. Due to insufficient data, it was possible to provide a narrative account only of the outcomes for simvastatin, antioxidants, and acetylL-carnitine. Results from one pilot study suggest that participants who received simvastatin may have shown a slight improvement in cognitive measures. Authors’ conclusions Due to the low quality of the body of evidence in this review, it is difficult to draw conclusions about the effectiveness of any pharmacological intervention for cognitive decline in people with Down syndrome.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

Parents' perceptions of microneedle-mediated monitoring as an alternative to blood sampling in the monitoring of their infants

OBJECTIVES: Microneedle (MN) arrays could offer a pain-free, minimally invasive approach to monitoring. This is envisaged to be particularly beneficial for younger patients, but parents' views to date are unknown. The aim of this study was to explore parental perceptions of MN-mediated ISF monitoring, as an alternative to the use of conventional blood sampling, and to understand the important factors for technique approval.

METHODS: Semi-structured interviews were conducted with parents with recent experience of a premature birth. Recruitment was through the Northern Ireland premature infant charity, Tinylife. Interviews progressed until data saturation was reached and thematic analysis employed.

KEY FINDINGS: The study included 16 parents. Parental support for MN-mediated monitoring was evident, alongside the unpopularity of traditional blood sampling in neonates. Factors facilitating MN approval included the opportunity for pain reduction, the simplicity of the procedure, the potential for increased parental involvement and the more favourable appearance, owing to the minute size of MNs and similarities with a sticking plaster. Confirmation of correct application, a pain-free patch removal and endorsement from trusted healthcare professionals were important.

CONCLUSION: These findings will inform researchers in the field of MN development and enlighten practitioners regarding parental distress resulting from conventional blood sampling. Further work is necessary to understand MN acceptability among practitioners. This work should assist in the development of an acceptable MN device and facilitate the reduction of parental distress.

Pathways Project Final Report Volume 1: Field Investigation and Catchment Conceptual Models

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Executive Summary
The Pathways Project field studies were targeted at improving the understanding of contaminant transport along different hydrological pathways in Irish catchments, including their associated impacts on water quality and river ecology. The contaminants of interest were phosphorus, nitrogen and sediment. The working Pathways conceptual model included overland flow, interflow, shallow groundwater flow, and deep groundwater flow. This research informed the development of a set of Catchment Management Support Tools (CMSTs) comprising an Exploratory Tool, Catchment Characterization Tool (CCT) and Catchment Modelling Tool (CMT) as outlined in Pathways Project Final Reports Volumes 3 and 4.
In order to inform the CMST, four suitable study catchments were selected following an extensive selection process, namely the Mattock catchment, Co. Louth/Meath; Gortinlieve catchment, Co. Donegal; Nuenna catchment, Co. Kilkenny and the Glen Burn catchment, Co. Down. The Nuenna catchment is well drained as it is underlain by a regionally important karstified limestone aquifer with permeable limestone tills and gravels, while the other three catchments are underlain by poorly productive aquifers and low permeability clayey tills, and are poorly drained.
All catchments were instrumented, and groundwater, surface and near-surface water and aquatic ecology were monitored for a period of two years. Intensive water quality sampling during rainfall events was used to investigate the pathways delivering nutrients. The proportion of flow along each pathway was determined using chemical and physical hydrograph separation techniques, supported by numerical modelling.
The outcome of the field studies broadly supported the use of the initial four-pathway conceptual model used in the Pathways CMT (time-variant model). The artificial drainage network was found to be a significant contributing pathway in the poorly drained catchments, at low flows and during peak flows in wet antecedent conditions. The transition zone (TZ), i.e. the broken up weathered zone at the top of the bedrock, was also found to be an important pathway. It was observed to operate in two contrasting hydrogeological scenarios: in groundwater discharge zones the TZ can be regarded as being part of the shallow groundwater pathway, whereas in groundwater recharge zones it behaves more like interflow.
In the catchments overlying poorly productive aquifers, only a few fractures or fracture zones were found to be hydraulically active and the TZ, where present, was the main groundwater pathway. In the karstified Nuenna catchment, the springs, which are linked to conduits as well as to a diffuse fracture network, delivered the majority of the flow. These findings confirm the two-component groundwater contribution from bedrock but suggest that the size and nature of the hydraulically active fractures and the nature of the TZ are the dominant factors at the scale of a stream flow event.
Diffuse sources of nitrate were found to be typically delivered via the subsurface pathways, especially in the TZ and land drains in the poorly productive aquifer catchments, and via the bedrock groundwater in the Nuenna. Phosphorus was primarily transported via overland flow in both particulate and soluble forms. Where preferential flow paths existed in the soil and subsoil, soluble P, and to a lesser extent particulate P, were also transported via the TZ and in drains and ditches. Arable land was found to be the most important land use for
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the delivery of sediment, although channel bank and in-stream sources were the most significant in the Glen Burn catchment. Overland flow was found to be the predominant transport sediment pathway in the poorly productive catchments. These findings informed the development of the transport and attenuation equations used in the CCT and CMT. From an assessment of the relationship between physico-chemical and biological conditions, it is suggested that in the Nuenna, Glen Burn and Gortinlieve catchments, a relationship may exist between biological water quality and nitrogen concentrations, as well as with P. In the Nuenna, there was also a relationship between macroinvertebrate status and alkalinity.
Further research is recommended on the transport and delivery of phosphorus in groundwater, the transport and attenuation dynamics in the TZ in different hydrogeological settings and the relationship between macroinvertebrates and co-limiting factors. High resolution temporal and spatial sampling was found to be important for constraining the conceptual understanding of nutrient and sediment dynamics which should also be considered in future studies.

HPV16 Down-Regulates the Insulin-Like Growth Factor Binding Protein 2 to Promote Epithelial Invasion in Organotypic Cultures

Cervical cancer is a multi-stage disease caused by human papillomaviruses (HPV) infection of cervical epithelial cells, but the mechanisms regulating disease progression are not clearly defined. Using 3-dimensional organotypic cultures, we demonstrate that HPV16 E6 and E7 proteins alter the secretome of primary human keratinocytes resulting in local epithelial invasion. Mechanistically, absence of the IGF-binding protein 2 (IGFBP2) caused increases in IGFI/II signalling and through crosstalk with KGF/FGFR2b/AKT, cell invasion. Repression of IGFBP2 is mediated by histone deacetylation at the IGFBP2 promoter and was reversed by treatment with histone deacetylase (HDAC) inhibitors. Our in vitro findings were confirmed in 50 invasive cancers and 79 cervical intra-epithelial neoplastic lesions caused by HPV16 infection, where IGFBP2 levels were reduced with increasing disease severity. In summary, the loss of IGFBP2 is associated with progression of premalignant disease, and sensitises cells to pro-invasive IGF signalling, and together with stromal derived factors promotes epithelial invasion.