Self-Doping of Gold Chains on Silicon: A New Structural Model for Si(111)5x2-Au

A new structural model for the Si(111)5x2-Au reconstruction is proposed and analyzed using first-principles calculations. The basic model consists of a "double honeycomb chain" decorated by Si adatoms. The 5x1 periodicity of the honeycomb chains is doubled by the presence of a half-occupied row of Si atoms that partially rebonds the chains. Additional adatoms supply electrons that dope the parent band structure and stabilize the period doubling; the optimal doping corresponds to one adatom per four 5x2 cells, in agreement with experiment. All the main features observed in scanning tunneling microscopy and photoemission are well reproduced.Comment: 4 pages, 4 figures, to appear in Phys. Rev. Lett. (preprint with high quality figures available at http://cst-www.nrl.navy.mil/~erwin/papers/ausi111

Assessment of post-operative pain in children: who knows best?

Pain assessment in children can be extremely challenging. Most professional bodies recommend that parents or carers should be involved with their child's pain assessment; but the evidence that parents can accurately report pain on behalf of their children is mixed. Our objective was to examine whether there were differences in post-operative pain score ratings between the child, nurse and parent or carer after surgery. Cognitively intact children aged four upwards, undergoing all surgical procedures, whose parents were present in the post-anaesthetic recovery unit (PACU), were studied. Thirty-three children were included in the study. The numerical rating scale was used to rate the child's pain by the child, nurse and parent on arrival to the PACU and prior to discharge. We found strong correlations between children's, nurses' and parent's pain scores on admission and discharge from PACU. The intraclass correlation coefficient of pain scores reported by children, nurses and parents was 0.94 (95% confidence intervals 0.91-0.96, P<0.0001). In cognitively intact children, it is adequate to manage pain based upon the assessment of children's and nurses' pain scores alone. The numerical rating scale appeared to be suitable for younger children. Whilst there are benefits of parents being present in recovery, it is not essential for optimizing the assessment of pain

Development of a bovine X chromosome linkage group and painting probes to assess cattle, sheep, and goat X chromosome segment homologies

The X chromosome linkage group is conserved in placental mammals. However, X chromosome morphological differences, due to internal chromosome rearrangements, exist among mammalian species. We have developed bovine chromosome painting probes for Xp and Xq to assess segment homologies between the submetacentric bovine X chromosome and the acrocentric sheep and goat X chromosomes. These painting probes and their corresponding DNA libraries were developed by chromosome micromanipulation, DNA micropurification, microcloning, and PCR amplification. The bovine Xp painting probe identified an interstitially located homologous segment in the sheep and goat Xq region, most probably resulting from chromosome inversion. Ten type II (microsatellite) markers obtained from the bovine Xq library and five other X chromosome assigned, but unlinked, markers were used to generate a linkage map for Xq spanning 89.4 centimorgans. The chromosome painting probes and molecular markers generated in this study would be useful for comparative mapping and tracing of internal X chromosome rearrangements in all ruminant species and would contribute to the understanding of mammalian sex chromosome evolution

Developing Metrics for Novel Value-Added Products: The Case of Hemp in Vermont

Vermont Farm to Plate 2020 identifies hemp as one of ten emergent agricultural products critical for Vermont’s future and has made recommendations for investments in hemp research, education, feasibility, and innovation programs. These investments are essential to develop niche food, feed, fiber, and industrial products, professionals, and markets that go “beyond CBD” (VFP, 2020). This project develops indicators for an important, value added budding crop in Vermont: hemp. For the purposes of this white paper, indicators are “a way to measure, indicate or point to with more or less exactness,” or “something used to show the condition of a system” (Feenstra et al., 2005). We focus on the example of hemp to illustrate how emerging value-added crops contribute to sustainable food systems. We use a set of design principles to ensure the applicability of developed indicators for decision making. This framework, its processes, and measures, are transferable to any nascent crop for evaluating economic, environmental, and social sustainability. Our objectives are to: Develop a set of indicators to measure the economic, social, and environmental inputs of hemp in Vermont. Identify techniques and data sources for mining hemp metrics. Evaluate the hierarchical levels of mined data and transecting indicators to inform growing discussions of metric integration and forecasting agricultural food sustainability. Our approach is grounded in the FAO food systems model, Doughnut Economics, which uses the UN Sustainable Development Goals as a foundation to describe “social floors” and planetary boundaries, and the concepts of seven community capitals: political, cultural, human, social, financial, built, and environmental. Our work plan included a two-day virtual workshop with required reading prior to the event, and involved both University researchers and stakeholders representing production, industry, finance, government, and NGOs. We describe 35 metrics to assess the sustainability of hemp in the Vermont economy, environment and community going forward (Figure 2 and Table 1). We also make several recommendations to move the collection of food system metrics forward. General recommendations include: Farmer surveys to specifically address challenges facing farmers growing a novel crop. In hemp this is particularly important, as the crop attracts many who are new to farming, and no one has been able to legally grow it at field scale in the US for the past several generations. Community/consumer surveys to collect data on community needs and impacts of novel value added crops (hemp) Collection and curation of spatial data tied to appropriate metrics Allocation of ARS funds for at least one data professional with skills across data types and methods, including individual, spatial, community level, etc. Funds to build out nutrient mass balance and soil carbon stock models for different soil types and production approaches The use of a grower-friendly tracking App with incentives (GoCrop) Development of a dashboard to easily visualize direction and degree of movement toward a desired state We make more specific recommendations in the Appendix where each metric is described in detail

Using Empirical Phase Diagrams to Understand the Role of Intramolecular Dynamics in Immunoglobulin G Stability

Understanding the relationship between protein dynamics and stability is of paramount importance to the fields of biology and pharmaceutics. Clarifying this relationship is complicated by the large amount of experimental data that must be generated and analyzed if motions that exist over the wide range of timescales are to be included. To address this issue, we propose an approach that utilizes a multidimensional vector-based empirical phase diagram (EPD) to analyze a set of dynamic results acquired across a temperature-pH perturbation plane. This approach is applied to a humanized immunoglobulin G1 (IgG1), a protein of major biological and pharmaceutical importance whose dynamic nature is linked to its multiple biological roles. Static and dynamic measurements are used to characterize the IgG and to construct both static and dynamic empirical phase diagrams. Between pH 5 and 8, a single, pH-dependent transition is observed that corresponds to thermal unfolding of the IgG. Under more acidic conditions, evidence exists for the formation of a more compact, aggregation resistant state of the immunoglobulin, known as A-form. The dynamics-based EPD presents a considerably more detailed pattern of apparent phase transitions over the temperature-pH plane. The utility and potential applications of this approach are discussed

Republication of “Open Repair of Acute Achilles Tendon Ruptures: Is the Incidence of Clinically Significant Wound Complications Overestimated?”

Background: Conflicting evidence exists regarding the optimal management of acute Achilles tendon ruptures. Operative repair is thought to afford patients a lower risk of rerupture, albeit at a higher overall risk of wound complications. Methods: A retrospective chart review of 369 consecutive patients undergoing open repair of acute Achilles tendon ruptures performed by a single foot and ankle fellowship-trained orthopedic surgeon was undertaken. Healing was classified as no complications, complications without prolonging treatment, complications requiring prolonged local treatment, and complications requiring operative intervention. A statistical analysis comparing the rates of complications in this cohort to that reported in the literature was conducted. Results: There were a total of 33 (8.94%) wound complications. Compared to the rates reported in the literature, no significant difference was detected (P = .3943; CI 6.24-12.33). However, when the complications not requiring additional treatment or prolonged care were excluded, only 9 wound complications (2.44%) were identified—a significantly lower complication rate than that reported in the literature (P \u3c .0001; CI 1.12-4.58). There were only 2 (0.54%) major complications requiring operative intervention, also a significantly lower rate than in the literature (P \u3c .0001; CI 0.067-1.94). Conclusion: In the past, wound-healing complications have been cited as a concern when treating patients operatively. We found that when solely looking at healing complications prolonging the patients’ overall recovery, a significantly lower rate of complications existed compared to that reported in the literature. Level of Evidence: Level IV

Galaxy Zoo: Reproducing Galaxy Morphologies Via Machine Learning

We present morphological classifications obtained using machine learning for objects in SDSS DR6 that have been classified by Galaxy Zoo into three classes, namely early types, spirals and point sources/artifacts. An artificial neural network is trained on a subset of objects classified by the human eye and we test whether the machine learning algorithm can reproduce the human classifications for the rest of the sample. We find that the success of the neural network in matching the human classifications depends crucially on the set of input parameters chosen for the machine-learning algorithm. The colours and parameters associated with profile-fitting are reasonable in separating the objects into three classes. However, these results are considerably improved when adding adaptive shape parameters as well as concentration and texture. The adaptive moments, concentration and texture parameters alone cannot distinguish between early type galaxies and the point sources/artifacts. Using a set of twelve parameters, the neural network is able to reproduce the human classifications to better than 90% for all three morphological classes. We find that using a training set that is incomplete in magnitude does not degrade our results given our particular choice of the input parameters to the network. We conclude that it is promising to use machine- learning algorithms to perform morphological classification for the next generation of wide-field imaging surveys and that the Galaxy Zoo catalogue provides an invaluable training set for such purposes.Comment: 13 Pages, 5 figures, 10 tables. Accepted for publication in MNRAS. Revised to match accepted version

Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22

A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated. © 2012 Cicek et al

Future vision for the quality assurance of oncology clinical trials

The National Cancer Institute clinical cooperative groups have been instrumental over the past 50 years in developing clinical trials and evidence-based process improvements for clinical oncology patient care. The cooperative groups are undergoing a transformation process as we further integrate molecular biology into personalized patient care and move to incorporate international partners in clinical trials. To support this vision, data acquisition and data management informatics tools must become both nimble and robust to support transformational research at an enterprise level. Information, including imaging, pathology, molecular biology, radiation oncology, surgery, systemic therapy, and patient outcome data needs to be integrated into the clinical trial charter using adaptive clinical trial mechanisms for design of the trial. This information needs to be made available to investigators using digital processes for real-time data analysis. Future clinical trials will need to be designed and completed in a timely manner facilitated by nimble informatics processes for data management. This paper discusses both past experience and future vision for clinical trials as we move to develop data management and quality assurance processes to meet the needs of the modern trial