Gap Fill Research Articles

On Being a Closer.

On Being a Closer.

Abstract 4744: Solving genomic assay trade-offs with an optimized, extended cancer gene panel for research and clinical applications

Abstract Choosing a genomic assay for cancer research is complicated by trade-offs. Cancer gene panels are a common choice, but they target mutational hotspots in a relatively small number of genes, often for cancers that are most commonly tested and that have common genetic etiologies. A common alternative is exome sequencing, which includes all the coding genes but, due to its larger genomic footprint, cannot reach the same depths as panels and therefore is less able to deal with low tumor purity and heterogeneity. Whole genome sequencing trades off very shallow depth and coverage over vast regions of uninterpretable genomic sequence in exchange for the identification of intergenic variants and structural variant breakpoints. All of these assays can be supplemented with RNA sequencing in order to capture gene fusions, allelic expression, splice isoforms, and gene expression. RNAseq comes with its own costs: the need to extract RNA from the same tissue, the need to perform a second assay, and the need to analyze a very different type of data from DNA sequencing. The trade-offs generally come down to three major issues: depth of sequencing, specific genes targeted, and cost. To solve these, we designed an extended, optimized cancer gene panel facilitating high depth sequencing at low cost. We started by identifying a comprehensive list of over 1,300 cancer genes. These genes were chosen through exhaustive cancer gene database and literature curation, and include genes from all major cancer pathways and from the Cancer Gene Census. We then took this gene list and applied an augmented targeting design strategy that we have previously used to create an augmented exome enrichment platform which fills in gaps that standard technical exomes miss. To validate the panel and analysis, we identified test samples including well-described cancer cell lines, cell line mixtures with engineered cancer variations, and formalin-fixed neoplastic tissues. We then performed a series of tests with these samples to measure the panel's small variant sensitivity and specificity, gauge its limits of detection, validate the detection of gene fusions, and demonstrate its ability to identify copy number alterations and loss of heterozygosity. In engineered cell lines, we detected 100% of small variants down to 5% allele frequency. We also mixed the cancer cell lines in various ratios and found similarly high sensitivity as well as very high specificity for small variant detection. We further compared our structural variation calls in the DNA and our fusion calls in the RNA with known data and found that we had very high concordance with known variations. These studies demonstrate that an extended, augmented cancer gene panel strategy solves many genomic assay trade-offs and leads to high accuracy and variant yield for cancer research applications. Citation Format: Michael J. Clark, Sean M. Boyle, Elena Helman, Shujun Luo, Gabor Bartha, Massimo Morra, Anil Patwardhan, Christian Haudenschild, Mirian Karbelashvili, Parin Sripakdeevong, Jason Harris, Deanna Church, Stephen Chervitz, John West, Richard Chen. Solving genomic assay trade-offs with an optimized, extended cancer gene panel for research and clinical applications. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4744. doi:10.1158/1538-7445.AM2015-4744

The Inflated Invocation of Inherent Jurisdiction and Powers by International and Internationalized Criminal Courts and Tribunals: Between Gap Filling and the Erosion of Core Values

Inherent jurisdiction and or inherent powers, although their true source remains unclear, have frequently been invoked in decisions by International, internationalized and mixed Tribunals and Courts in order to vindicate certain authority and prerogatives and also to overcome gaps and even limits set by statutes and rules of procedure and evidence. The strings of court decisions usually quoted by international criminal courts and tribunals shows to be, to some extent, out of focus if not distorted. The invocation of inherent powers may also impact on core principles. Claim by International Courts and Tribunals of inherent jurisdiction and power determine the temptation to recall the concept of a "Grotian moment," a shift in paradigms and the emergence of new values with unusual rapidity and equally unusual acceptance. For some stances the “Grotian moment” seems to be over, as in the case of the vindication of the power to review United Nations Security Council Resolutions underlying the original assertion of Kompetenz Kompetenz by the ICTY, which has been recently resized.

Getting noticed is half the battle.

The hiring game starts early. Well before a faculty position even opens, department members and administrators tend to observe the available pool of candidates and shortlist the ones they consider most promising. Savvy candidates work this preselection process to their advantage. Some ways of doing this are obvious: Be an excellent scholar. Publish well. Work hard. Communicate with the public and your peers. But a well-planned, long-range effort to ensure your visibility among those who have hiring responsibilities can be the deciding factor. Here's how it worked for me. I arrived at the University of Toronto in 1982 as a postdoctoral diploma candidate in clinical biochemistry. Coming from a rather poor country—Greece—was a disadvantage, so I did all I could to adapt to the new environment, fill in my knowledge gaps, and make a good impression with hard work and dedication. When I finished the diploma training in 1984, the chair of the department showed interest in finding a job for me. But I had to go back to Greece first to complete my medical degree. I finished it in 1986. ![Figure][1] “I made myself visible by participating in every research seminar.” ILLUSTRATION: ROBERT NEUBECKER When I returned to Toronto, I was hired as the director of research and development at a small biotechnology company spun off from the university; I also had an adjunct position in clinical biochemistry at the University of Toronto. I had no special training or experience in business management, but I found myself directing eight Ph.D. scientists, working together to develop a commercial product. Working at a company was not my first choice, but I gave it everything I had, and the work I did there laid a cornerstone for my future success. I learned to appreciate the difficulties associated with developing and commercializing a system, which we succeeded in doing toward the end of my time there. I learned how to manage people and how to keep them focused on a single task. I met with potential customers and investors and learned how to negotiate and promote products and ideas. The job was good and challenging, but it was not what I was aiming for in the long term. Meanwhile, a new chair had taken over in the department, and I set out to persuade him to hire me as an academic clinician-scientist. I worked 16 to 17 hours a day, not just to make progress on the technology but also to publish our results in high-impact journals. How did I manage it? My wife—also a Ph.D. scientist—worked far less than I did; she took on the bulk of the domestic responsibilities. Our children spent many Saturdays and some Sundays playing in the company lobby. We made lunch in the break room microwave. My colleagues and I managed to publish numerous papers, and I was invited repeatedly to present at national and international conferences. I was able to demonstrate, in the department's annual report, scientific productivity comparable in quantity and quality to the full-time academics in the department. I made sure these activities were noticed. I made myself visible by participating in every research seminar—not easy, considering the hour-long drive and how busy I was at the company. Each time I entered the lecture room, I made a point of passing in front of the department chair before sitting down. At the end of every seminar, I made sure to ask a carefully crafted question or two. After 18 months of this, the chair paid me an unexpected visit at the company and invited me to become his deputy in the department and at the teaching hospital. Ten years later, I succeeded him. Our daughter, by the way, is now a Ph.D. scientist working as a clinical chemist, and our son is in training to become an M.D.-Ph.D. neuropathologist. My wife is a senior scientist at a major teaching hospital. Making sure you are noticed can give you the edge you need over your silent competition. [1]: pending:yes

Quantifying a Threshold of Missing Values for Gap Filling Processes in Daily Precipitation Series

Multiple missing levels are explored to quantify a threshold of missing values during gap filling processes in daily precipitation series. An autoregressive model was used to generate rainfall estimates and subsets of data are selected with four sampling windows (whole data, front, middle, and rear section) at different missing levels, including 5, 10, 15, 16, 17, and 18 %. The proposed threshold was found and evaluated based on statistical criteria, including coefficient of determination (R2) and its associated index termed “the R2 difference index (RDI).” The result indicates that about 15 % missing level of data is plausible to construct daily precipitation series for further hydrological analysis when the Gamma distribution function (GDF) is used as an estimation method. The threshold determined from this study will contribute to gap filling guidelines, especially for water managers and hydrologists to take advantage of skillful estimates for missing daily precipitation data.

Evaluation of statistical gap fillings for continuous energy flux (evapotranspiration) measurements for two different land cover types

Over the past few decades, energy and water fluxes have been directly measured by a global flux network, which was established by regional and continental network sites based on an eddy covariance (EC) method. Although, the EC method possesses many advantages, its typical data coverage could not exceed 65 % due to various environmental factors including micrometeorological conditions and systematic malfunctions. In this study, four different methodologies were used to fill the gap in latent heat flux (LE) data. These methods were Food and Agriculture Organization Penman–Monteith (FAO_PM) equation, mean diurnal variation (MDV), Kalman filter, and dynamic linear regression (DLR). We used these methods to evaluate two flux towers at different land cover types located at Seolmacheon (SMC) and Cheongmicheon (CMC) in Korea. The LE estimated by four different approaches was a fairly close match to the observed LE, with the root mean square error ranging from 4.81 to 61.88 W m−2 at SMC and from 0.89 to 60.27 W m−2 at CMC. At both sites, the LE estimated by DLR showed the best result with the value of the coefficient of correlation (R), equal to 0.99. Cost-effectiveness analysis for evaluating four different gap-filling methods also confirmed that DLR showed the best cost effectiveness ratio (C/R). The Kalman filter showed the second highest C/R rank except in the winter season at SMC followed by MDV and FAO_PM. Energy closures with estimated LE led to further improved compare to the energy closure of the observed LE. The results showed that the estimated LE at CMC was a better fit with the observed LE than the estimated LE at SMC due to the more complicated topography and land cover at the SMC site. This caused more complex interactions between the surface and the atmosphere. The estimated LE with all approaches used in this study showed improvement in energy closure at both sites. The results of this study suggest that each method can be used as a gap-filling model for LE. However, it is important to consider the strengths and weaknesses of each method, the purpose of research, characteristics of the study site, study period and data availability.

An Analysis of Gap Fill Items in Achievement Tests

This article revives the discussion over measurements of validity in criterion referenced (CR) tests. It presents how the principles of Classical Testing Theory (CTT), normally associated with norm-referenced tests, were applied to the Business English achievement tests at the University of Economics, Prague, Czech Republic. Firstly, measures of validity in criterion-referenced tests, test purpose, and test specifications are discussed. Next, a 10-item vocabulary gap fill subtest is subjected to a detailed analysis through the use of facility and discrimination indices. Key and distractor analyses of each item are then performed. The insights gained from such analyses are examined in relation to the cyclical test design process of constant review of items so that a high level of standardization is achieved. This paper thus provides teachers with simple tools to build valid language gap fill tests which reflect the criteria of accurate and equitable testing.

Multisensor and multitemporal data from Landsat images to detect damage to coral reefs, small islands in the Spermonde archipelago, Indonesia

Coral reefs are important because of their high biodiversity and their key role in the tropical marine biosphere. Furthermore, coral reefs are very valuable as a socioeconomic resource as they make important contributions to the gross domestic product of many countries. Thus, it is very important to monitor dynamic spatial distributions of coral reefs and related habitats dominated by coral rubble, dead coral, and bleached corals. Despite these natural and socio-economic advantages, many factors are threatening coral reefs. The study site was selected in Spermonde archipelago, South Sulawesi, Indonesia because this area is included in the Coral Triangle, recognized as the epicenter of coral diversity and a priority for conservation. Images of Landsat MSS, Landsat TM, Landsat ETM, Landsat ETM+, and Landsat 8 data were used to examine changes in the coral reefs of Suranti Island in the Spermonde Archipelago during forty one years from 1972 to 2013. The image processing includes gap fills, atmospheric corrections, geometric corrections, image composites, water column corrections, unsupervised classifications, and reclassifications. Fill Gap processing was done on Landsat ETM+ SLC-off. Subsequently, a multi-component change detection procedure was applied to define changes. Shallow water bottom types classification was divided into live coral, rubble and sand habitats, dead coral with algae, rubble, and sand. Preliminary results showed significant changes during the period 1972–2013 as well as changes in coral reefs, likely explained partly by destructive fishing practices.

Challenges in Laboratory Coding 2015

1. Kathleen Hansen, MLS(ASCP)CM[⇑][1] 1. Advisor, ASCLS Government Affairs Committee, Laboratory Administration Consultant, Fairview Health Services, Minneapolis, MN 1. Address for Correspondence: Kathleen Hansen, MLS(ASCP)CM, 2309 Beverly Road, St. Paul, MN 55104, 651-983-8613 khansen3{at}fairview.org INTRODUCTION Laboratory managers and others have long been familiar with the use of Current Procedural Terminology (CPT) codes to identify services provided by the laboratory for billing and reporting purposes. The CPT manual is the property of the American Medical Association (AMA) and is updated annually, including the laboratory section, which encompasses CPT codes 80047-89398. Until recently, the typical year's update consisted of 10-15 new or modified codes. Updates are announced in early summer, and the Center for Medicare and Medicaid Services (CMS) holds a mid-July meeting each year at which stakeholders present testimony about the new codes and make suggestions as to how they should be priced by CMS. ASCLS Executive Vice President Elissa Passiment attends this meeting to present our views, or alternatively ASCLS submits testimony in writing. Final codes and instructions for their use are published in the fall. Reimbursement amounts are published near the end of the year with the new Clinical Laboratory Fee Schedule (CLFS). Reimbursement amounts for the CLFS are determined using one of two methodologies: crosswalk or gap fill. Crosswalk matches the new code with an existing code that is deemed to be of similar cost to perform, and assigns that same reimbursement to the new code. Gap fill assumes that the new code is sufficiently different from existing codes to need its own reimbursement determination. Each Medicare contractor decides what its reimbursement will be based on its determination of the cost to perform the test. These different amounts are used for a… ABBREVIATIONS: CLFS – Clinical Laboratory Fee Schedule, CPT - Current Procedural Terminology, AMA - American Medical Association, CMS - Center for Medicare and Medicaid Services, HCPCS – Healthcare Common Procedure Coding System, NGS - Next Generation Sequencing, MAC - Medicare Administrative Contractor, Mopath – molecular pathology, MUE - Medically Unlikely Edit [1]: #corresp-1

고준위폐기물처분장 공학적방벽의 갭채움재 기술현황

고준위폐기물처분장에서 갭채움재는 완충재와 뒷채움재의 성능을 좌우하는 중요한 공학적방벽의 구성요소이다. 본 논문에서는 갭채움재에 대한 해외 기술현황을 조사하고, 이를 통하여 갭채움재의 개념, 제조기술, 성형특성, 설치기술에 대한 연구결과들을 정리하였다. 갭채움재 개념은 처분방식과 처분개념에 따라서 나라마다 약간씩 차이가 있었다. 갭채움재 물질로는 대부분 벤토나이트를 사용하였고, 충전제로 점토를 사용하였다. 갭채움재는 펠렛, 과립상, 또는 펠렛-과립상 혼합물의 형태로 사용되었다. 갭채움재 펠렛 제조에는 정압축, 롤러압축, 압출-컷팅 방법 등이 사용되었으며, 이 중, 실험과 실제 현장에서의 펠렛 소요량을 감안하여 많은 나라들이 롤러압축방법과 압출-컷팅방법에 대한 기술 확보에 집중하였다. 펠렛 성형특성 실험결과, 펠렛의 건조밀도와 건전성은 수분함량, 구성물질, 제조방법, 펠렛 크기에 민감하였고, 제작 시 압축하중에는 상대적으로 덜 민감하였다. 갭채움재의 설치방법으로는 수직처분공 완충재 갭에서는 부어넣기(pouring) 방법, 붓고 다지기(pouring and tamping) 방법, 진동을 주며 부어넣기(pouring with vibration) 방법 등이 시도되었으며, 수평처분공 완충재와 처분터널의 뒷채움재 갭에서는 숏크리트 기술을 이용한 불어넣기(blowing by use of shotcrete technology) 방법과 오거를 이용한 정치 및 다지기(auger placement and compaction) 방법 등이 시도되었다. 그러나 이 방법들은 아직 기술적으로 초기단계에 있어 앞으로도 계속적인 연구가 이루어질 것으로 예상되었다. In a high-level waste repository, the gap fill of the engineered barrier is an important component that influences the performance of the buffer and backfill. This paper reviewed the overseas status of R&D on the gap fill used engineered barriers, through which the concept of the gap fill, manufacturing techniques, pellet-molding characteristics, and emplacement techniques were summarized. The concept of a gap fill differs for each country depending on its disposal type and concept. Bentonite has been considered a major material of a gap fill, and clay as an inert filler. Gap fill was used in the form of pellets, granules, or a pellet-granule blend. Pellets are manufactured through one of the following techniques: static compaction, roller compression, or extrusion-cutting. Among these techniques, countries have focused on developing advanced technologies of roller compression and extrusion-cutting techniques for industrial pellet production. The dry density and integrity of the pellet are sensitive to water content, constituent material, manufacturing technique, and pellet size, and are less sensitive to the pressure applied during the manufacturing. For the emplacement of the gap fill, pouring, pouring and tamping, and pouring with vibration techniques were used in the buffer gap of the vertical deposition hole; blowing through the use of shotcrete technology and auger placement and compaction techniques have been used in the gap of horizontal deposition hole and tunnel. However, these emplacement techniques are still technically at the beginning stage, and thus additional research and development are expected to be needed.

Reducing Bias and Filling in Spatial Gaps in Fishery‐Dependent Catch‐per‐Unit‐Effort Data by Geostatistical Prediction, I. Methodology and Simulation

AbstractGeostatistical prediction can address two difficult issues in interpreting fishery‐dependent catch per unit effort (CPUE): the lack of a sampling design and the need to fill spatial gaps. In this paper we demonstrate the spatial weighting properties of geostatistics for treating data collected without a sampling design or with a selection bias, two basic traits of fishery‐dependent data. We then examine the bias and precision of geostatistical prediction of CPUE based on fishery‐dependent data through simulation. We create data sets with known variograms, sample them with a preference for sites with high abundance, and then estimate variograms and CPUE as the geostatistical mean relative abundance. The variograms obtained from the simulated fishery samples correctly estimated the range but underestimated the sill, and the geostatistical mean substantially improved the estimation of CPUE over the arithmetic mean. Though the geostatistical mean still overestimated the true value, the error was primarily due to prediction into unsampled locations, where predictions revert toward the arithmetic mean. The geostatistical variance at a point, which is a function of spatial autocorrelation and the location of adjacent samples, provides a measure of uncertainty. This variance measures the degree to which predictions are derived from nearby data versus distant observations, which translates the spatial extent of extrapolation into probabilistic terms. In conjunction with conventional standardization methods that account for factors affecting catchability, geostatistical prediction provides an additional tool that reduces but does not eliminate biases inherent in fishery‐dependent data and supports the need to predict CPUE in unsampled areas.Received July 26, 2013; accepted June 2, 2014

Reducing Bias and Filling in Spatial Gaps in Fishery‐Dependent Catch‐per‐Unit‐Effort Data by Geostatistical Prediction, II. Application to a Scallop Fishery

AbstractFishery‐dependent catch per unit effort (CPUE) comprises critical input for many stock assessments. Construction of CPUE indices usually employs some method of data standardization. However, conventional methods based on linear models do not effectively deal with the fact that samples are collected with a selection bias or with the problem of filling spatial gaps. Geostatistical interpolation methods can ameliorate some of the biases caused by both of these problems while remaining complementary to traditional linear model‐based CPUE standardization. In this paper we present geostatistical estimates of sea scallop Placopecten magellanicus CPUE from tows recorded by onboard observers during an opening of Georges Bank Closed Area II in 1999. By selecting tows for which there was little prior effort (on the basis of accumulated effort measured by vessel monitoring systems), we obtained tows that reflected initial abundance as closely as possible. These tows were used to obtain a variogram which was used in geostatistical prediction of sea scallop CPUE. The kriged mean was substantially lower than the arithmetic sample mean, indicating that a geostatistical approach reduced the influence of repeated sampling in locations of extremely high CPUE and increased the weight of isolated observations in areas of low CPUE. The results produced a map that was qualitatively similar to that obtained from a preseason fishery‐independent survey. Overall differences between the two approaches were driven by the extension of predictions into areas at the edges of spatial autocorrelation where kriging predictions approached the grand mean of the data set.Received July 26, 2013; accepted June 2, 2014

Smoking and Unstable Hinge Fractures Cause Delayed Gap Filling Irrespective of Early Weight Bearing After Open Wedge Osteotomy

The purpose of this study was to examine the osteotomy gap filling rate with new bone after open wedge high tibial osteotomy (HTO) without bone graft and the effects of smoking, lateral hinge fracture, and early full weight bearing. A prospective series (N= 70) of open wedge HTOs with the TomoFix plate (DePuy Synthes, Umkirch, Germany) was performed. Radiologic follow-up examinations took place postoperatively, after 6 and 12 weeks, and after 6, 12, and 18 months to measure osteotomy gap filling at each follow-up. Bone healing was compared in smokers versus nonsmokers who underwent open wedge HTOs with intact lateral hinges. Fractured lateral hinges were classified according to the Takeuchi classification and separately analyzed regarding bone healing. Patients were randomly assigned to undergo early (11 days) or standard (6 weeks) full-weight-bearing rehabilitation. A delay in the osteotomy gap filling rate between smokers and nonsmokers could be observed at all follow-up periods, but differences were not significant. A fracture of the lateral hinge was found in 39% of the patients. A type I fracture was observed in 14% of patients, a type II fracture was observed in 13%, and a type III fracture was found in 6%. The highest increase in the osteotomy gap filling rate was observed between 12 weeks and 6 months after surgery in patients with intact lateral hinges. For patients with unstable type II fractures, the highest increase in the gap filling rate was delayed until 6 to 12 months. Early full weight bearing had no effect on the gap filling rate in any of the patient groups evaluated. This study shows that osteotomy gap filling after open wedge HTO is delayed in smokers and in patients in whom opening of the gap resulted in unstable lateral hinge fractures. Early full weight bearing did not have a significant effect on the gap filling rate. Level III, prognostic study.

Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models.

Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights. With exponentially increasing sequencing capacity, there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame. Current methods for automated metabolic network reconstruction rely on gene and reaction annotations to build draft metabolic networks and algorithms to fill gaps in these networks. However, automated reconstruction is hampered by database inconsistencies, incorrect annotations, and gap filling largely without considering genomic information. Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. We show that computed likelihood values were significantly higher for annotations found in manually curated metabolic networks than those that were not. We then apply these alternative functional predictions to estimate reaction likelihoods, which are used in a new gap filling approach called likelihood-based gap filling to predict more genomically consistent solutions. To validate the likelihood-based gap filling approach, we applied it to models where essential pathways were removed, finding that likelihood-based gap filling identified more biologically relevant solutions than parsimony-based gap filling approaches. We also demonstrate that models gap filled using likelihood-based gap filling provide greater coverage and genomic consistency with metabolic gene functions compared to parsimony-based approaches. Interestingly, despite these findings, we found that likelihoods did not significantly affect consistency of gap filled models with Biolog and knockout lethality data. This indicates that the phenotype data alone cannot necessarily be used to discriminate between alternative solutions for gap filling and therefore, that the use of other information is necessary to obtain a more accurate network. All described workflows are implemented as part of the DOE Systems Biology Knowledgebase (KBase) and are publicly available via API or command-line web interface.

Conformational change of bovine serum albumin molecules at neutral pH in ultra-diluted aqueous solutions.

Surface chemical and electrochemical techniques were applied to reveal the unfolding of bovine serum albumin (BSA) molecules induced by concentrations in aqueous solution. Real-time surface pressures vs time (π-t) kinetic curves were recorded over an aqueous subphase (190 mL) by spreading BSA solutions of different concentrations but of the same amount (8.0 × 10(-4) mg) at the air/water (A/W) interface. A critical concentration (∼1.0 ppm) was discovered below which the surface pressure declines with time and the BSA is totally solubilized in the water subphase. Above this critical concentration (e.g., 8.0 ppm), the surface pressure goes up and the protein molecules assemble into a Langmuir monolayer at the A/W interface. These findings demonstrate that the BSA molecules have different conformations in the spreading protein solutions. The conformational transition in BSA molecules induced by concentrations was also confirmed by spectroscopy means and the catalytic hydrogen evolution reaction on a silver amalgam electrode by using constant current chronopotentiometric stripping. This discovery fills in gaps of Foster's N (normal) → F (fast) model, in which the unfolding of BSA molecules occurs at neutral pH values (8.0-4.3).

Noise Reduction and Gap Filling of fAPAR Time Series Using an Adapted Local Regression Filter

Time series of remotely sensed data are an important source of information for understanding land cover dynamics. In particular, the fraction of absorbed photosynthetic active radiation (fAPAR) is a key variable in the assessment of vegetation primary production over time. However, the fAPAR series derived from polar orbit satellites are not continuous and consistent in space and time. Filtering methods are thus required to fill in gaps and produce high-quality time series. This study proposes an adapted (iteratively reweighted) local regression filter (LOESS) and performs a benchmarking intercomparison with four popular and generally applicable smoothing methods: Double Logistic (DLOG), smoothing spline (SSP), Interpolation for Data Reconstruction (IDR) and adaptive Savitzky-Golay (ASG). This paper evaluates the main advantages and drawbacks of the considered techniques. The results have shown that ASG and the adapted LOESS perform better in recovering fAPAR time series over multiple controlled noisy scenarios. Both methods can robustly reconstruct the fAPAR trajectories, reducing the noise up to 80% in the worst simulation scenario, which might be attributed to the quality control (QC) MODIS information incorporated into these filtering algorithms, their flexibility and adaptation to the upper envelope. The adapted LOESS is particularly resistant to outliers. This method clearly outperforms the other considered methods to deal with the high presence of gaps and noise in satellite data records. The low RMSE and biases obtained with the LOESS method (|rMBE| < 8%; rRMSE < 20%) reveals an optimal reconstruction even in most extreme situations with long seasonal gaps. An example of application of the LOESS method to fill in invalid values in real MODIS images presenting persistent cloud and snow coverage is also shown. The LOESS approach is recommended in most remote sensing applications, such as gap-filling, cloud-replacement, and observing temporal dynamics in situ where rapid seasonal changes are produced.

Stinking stones and rocks of gold: phosphate, fertilizer, and industrialization in postbellum South Carolina

A finely layered and important study that fills in gaps in the industrial history of the New South and especially low-country South Carolina.--Sidney Bland, author of Preserving Charleston's Past, Shaping Its Future: The Life and Times of Susan Pringle Frost Skillfully blurs the old, comfortable line between Old and New South economies and paints a nuanced picture of the new labor relations in the post-slavery era.--Charles Holden, author of In the Great Maelstrom In the first book ever written about the impact of phosphate mining on the South Carolina plantation economy, Shepherd McKinley explains how the convergence of the phosphate and fertilizer industries carried long-term impacts for America and the South.Fueling the rapid growth of lowcountry fertilizer companies, phosphate mining provided elite plantation owners a way to stem losses from emancipation. At the same time, mining created an autonomous alternative to sharecropping, enabling freed people to extract housing and labor concessions.Stinking Stones and Rocks of Gold develops an overarching view of what can be considered one of many key factors in the birth of southern industry. This top-down, bottom-up history (business, labor, social, and economic) analyzes an alternative path for all peoples in the post-emancipation South.

A new sediment type of coated grain: Oolitic sinter

As a special sedimentary grain type, the coated grain (with an ooid model) has been known for two centuries due to its fascinating special fabric and genesis developments. The leading factors in forming the coated grain consist mainly of: (1) microorganism movement field; (2) chemical sedimentary effect; (3) hydrodynamic force environment and topography condition; (4) abundant core material supply; (5) embedding condition; and (6) humic acids condition in water medium. With the development of the coated grain genesis, the single factor theory cannot reasonably explain the exact formation of the surface sediment of coated grain. Here, we find a new way to study the coated grain on the basis of traditional research methods. The Wenquan area on the northeast edge of the Qiangtang Basin is one of the few areas where the coated grain is developing, and is a rare “natural laboratory” for the study of the coated grain and the thermal spring sediment. The oolitic sinter of the area has the triaxiality modality of pea polymer, and is obviously different from the karst travertine and the normal lacustrine ooid. We found that the hot spring water in the Wenquan area has higher partial pressure of CO2 \(\left( {P_{CO_2 } } \right)\) and saturation index of the calcite (SIc) than normal. Macrocosmically, the oolitic sinter is shaped like a pea, and its grains and gap fillings are light yellow. Microcosmically, the sinter grain forms six types of fundamental lamina, and those six types are developed to be four grain types with different combinations. The C-axis of the mineral grain of sinter cement (calcite) is normal to the lamina face, and grows on it with distinct generation formations. In short, the grain type of oolitic sinter is the oncoid, with the grain development caused by the factors such as the shallow water of strong hydrodynamic force, the special hydrochemistry condition, and the extensive algae activities (diatom).

Memory and the body

Early psychoanalysis could be viewed as memory-centred. Emerging from the cathartic method of Breuer and Freud, Freud stated that the aim of the new treatment was to remove the amnesias, that is, fill in the memory gaps, thus making what was previously unconscious due to resistances accessible to consciousness. This was seen as the main curative factor. As we know, psychoanalysis developed in various directions during its first decades. With Reich and his followers, an increasing attention was paid to character, muscular tensions and bodily positions at the expense of working with psychological material like memories and phantasies. However, repetitions in transference and acting out may also be considered aspects of memory, and in that sense, their importance has been retained in all psychoanalytic developments. The aim in this article is to highlight various aspects of remembering and to make a plea for a differentiated view of memory in the current practice of psychoanalysis; in that respect, it is an example of returning to Freud.

Oral Corrective Feedback and Learning of English Modals

The study examines the effects of interactional corrective feedback (CF) in the form of recasts (i.e. teacher's reformulation) and metalinguistic information (i.e. provision of some grammatical information) in response to any erroneous utterance in English modals. Evidence regarding the relative effectiveness of these types is mixed (reviewed by Li [1]), and only few studies have isolated metalinguistic feedback from recasts. The current classroom study aims to address these issues, and focuses on learning of English modals, a structure which has been neglected in corrective feedback studies and is considered to be difficult for EFL/ESL learners (Celce- Murcia and Freeman [2]). Pre-intermediate L1 Arabic learners (n=36) in an ESL context were randomly assigned into two experimental groups; metalinguistic information (MI) and recast (R), and one task only (TO) group. Three hour oral communicative tasks were held in four consecutive weeks. Learning was measured via pre-, post-, and delayed post- picture description test (PD), gap fill test (GF), and timed grammaticality judgment test (TGJT). An exit questionnaire, (e.g., Sheen [3]) to check awareness of the target feature and an attitudinal questionnaire to measure participants’ attitude towards error correction and grammatical accuracy were administered. The results demonstrate that metalinguistic information and recasts were beneficial for learning of English modals and learners’ preference for recast was more than that for metalinguistic information feedback.